diff --git a/docs/404.html b/docs/404.html
index 157b24a..0742b26 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -31,7 +31,7 @@
     
     <a class="navbar-brand me-2" href="https://garrettlab.github.io/HabitatConnectivity/index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index 919044a..b74720a 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/apple-touch-icon-120x120.png b/docs/apple-touch-icon-120x120.png
index 43642a2..c257d31 100644
Binary files a/docs/apple-touch-icon-120x120.png and b/docs/apple-touch-icon-120x120.png differ
diff --git a/docs/apple-touch-icon-152x152.png b/docs/apple-touch-icon-152x152.png
index 3eae1b4..967908c 100644
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diff --git a/docs/apple-touch-icon-180x180.png b/docs/apple-touch-icon-180x180.png
index b492d93..5ec0ecb 100644
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diff --git a/docs/apple-touch-icon-60x60.png b/docs/apple-touch-icon-60x60.png
index a1def23..980f98e 100644
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diff --git a/docs/apple-touch-icon-76x76.png b/docs/apple-touch-icon-76x76.png
index 874e61b..1119577 100644
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diff --git a/docs/apple-touch-icon.png b/docs/apple-touch-icon.png
index 7aba723..8756c36 100644
Binary files a/docs/apple-touch-icon.png and b/docs/apple-touch-icon.png differ
diff --git a/docs/articles/LinkWeightsAnalysis.html b/docs/articles/LinkWeightsAnalysis.html
index 96bc73b..f44125a 100644
--- a/docs/articles/LinkWeightsAnalysis.html
+++ b/docs/articles/LinkWeightsAnalysis.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,7 +86,7 @@
                         <h4 data-toc-skip class="author">Plex, Sula (<a href="mailto:plexaaron@ufl.edu" class="email">plexaaron@ufl.edu</a>),
 Krishna Keshav(<a href="mailto:kkeshav@ufl.edu" class="email">kkeshav@ufl.edu</a>)</h4>
             
-            <h4 data-toc-skip class="date">22 March, 2024</h4>
+            <h4 data-toc-skip class="date">05 April, 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/vignettes/LinkWeightsAnalysis.Rmd" class="external-link"><code>vignettes/LinkWeightsAnalysis.Rmd</code></a></small>
       <div class="d-none name"><code>LinkWeightsAnalysis.Rmd</code></div>
@@ -124,21 +124,21 @@ <h2 id="betweenness">Betweenness<a class="anchor" aria-label="anchor" href="#bet
 <span>                                                  weights <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, cutoff <span class="op">=</span> <span class="op">-</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code>## 
 |---------|---------|---------|---------|
-===
+=====
                                           </code></pre>
 <p><img src="LinkWeightsAnalysis_files/figure-html/run-1.png" width="700"></p>
 <pre><code>## 
 |---------|---------|---------|---------|
-=====
+=======
                                           
 
 |---------|---------|---------|---------|
-========
+==============
                                           </code></pre>
 <p><img src="LinkWeightsAnalysis_files/figure-html/run-2.png" width="700"></p>
 <pre><code>## 
 |---------|---------|---------|---------|
-===
+=====
                                           </code></pre>
 <p><img src="LinkWeightsAnalysis_files/figure-html/run-3.png" width="700"></p>
 <p>It is important to note that Betweenness centrality is a time
diff --git a/docs/articles/LinkWeightsAnalysis_files/figure-html/run-1.png b/docs/articles/LinkWeightsAnalysis_files/figure-html/run-1.png
index 425529a..a5e8543 100644
Binary files a/docs/articles/LinkWeightsAnalysis_files/figure-html/run-1.png and b/docs/articles/LinkWeightsAnalysis_files/figure-html/run-1.png differ
diff --git a/docs/articles/LinkWeightsAnalysis_files/figure-html/run-2.png b/docs/articles/LinkWeightsAnalysis_files/figure-html/run-2.png
index 6db2da7..e9b6d9d 100644
Binary files a/docs/articles/LinkWeightsAnalysis_files/figure-html/run-2.png and b/docs/articles/LinkWeightsAnalysis_files/figure-html/run-2.png differ
diff --git a/docs/articles/Using-raster-file.html b/docs/articles/Using-raster-file.html
index 4bba04f..4d74c8d 100644
--- a/docs/articles/Using-raster-file.html
+++ b/docs/articles/Using-raster-file.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html
index 974a958..9cf57f9 100644
--- a/docs/articles/analysis.html
+++ b/docs/articles/analysis.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,7 +86,7 @@
                         <h4 data-toc-skip class="author">Krishna
 Keshav(<a href="mailto:kkeshav@ufl.edu" class="email">kkeshav@ufl.edu</a>)</h4>
             
-            <h4 data-toc-skip class="date">22 March, 2024</h4>
+            <h4 data-toc-skip class="date">05 April, 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/vignettes/analysis.Rmd" class="external-link"><code>vignettes/analysis.Rmd</code></a></small>
       <div class="d-none name"><code>analysis.Rmd</code></div>
@@ -205,78 +205,84 @@ <h3 id="installation-and-loading">Installation and loading<a class="anchor" aria
 <span id="cb3-8"><a href="#cb3-8" tabindex="-1"></a><span class="co">#&gt; Warning in library(package, lib.loc = lib.loc, character.only = TRUE,</span></span>
 <span id="cb3-9"><a href="#cb3-9" tabindex="-1"></a><span class="co">#&gt; logical.return = TRUE, : there is no package called 'geohabnet'</span></span>
 <span id="cb3-10"><a href="#cb3-10" tabindex="-1"></a><span class="co">#&gt; Downloading GitHub repo GarrettLab/HabitatConnectivity@HEAD</span></span>
-<span id="cb3-11"><a href="#cb3-11" tabindex="-1"></a><span class="co">#&gt; parallelly (1.37.0  -&gt; 1.37.1) [CRAN]</span></span>
-<span id="cb3-12"><a href="#cb3-12" tabindex="-1"></a><span class="co">#&gt; globals    (0.16.2  -&gt; 0.16.3) [CRAN]</span></span>
-<span id="cb3-13"><a href="#cb3-13" tabindex="-1"></a><span class="co">#&gt; digest     (0.6.33  -&gt; 0.6.35) [CRAN]</span></span>
-<span id="cb3-14"><a href="#cb3-14" tabindex="-1"></a><span class="co">#&gt; Rcpp       (1.0.11  -&gt; 1.0.12) [CRAN]</span></span>
-<span id="cb3-15"><a href="#cb3-15" tabindex="-1"></a><span class="co">#&gt; curl       (5.2.0   -&gt; 5.2.1 ) [CRAN]</span></span>
-<span id="cb3-16"><a href="#cb3-16" tabindex="-1"></a><span class="co">#&gt; vctrs      (0.6.3   -&gt; 0.6.5 ) [CRAN]</span></span>
-<span id="cb3-17"><a href="#cb3-17" tabindex="-1"></a><span class="co">#&gt; stringi    (1.7.12  -&gt; 1.8.3 ) [CRAN]</span></span>
-<span id="cb3-18"><a href="#cb3-18" tabindex="-1"></a><span class="co">#&gt; rlang      (1.1.1   -&gt; 1.1.3 ) [CRAN]</span></span>
-<span id="cb3-19"><a href="#cb3-19" tabindex="-1"></a><span class="co">#&gt; glue       (1.6.2   -&gt; 1.7.0 ) [CRAN]</span></span>
-<span id="cb3-20"><a href="#cb3-20" tabindex="-1"></a><span class="co">#&gt; cli        (3.6.1   -&gt; 3.6.2 ) [CRAN]</span></span>
-<span id="cb3-21"><a href="#cb3-21" tabindex="-1"></a><span class="co">#&gt; terra      (1.7-39  -&gt; 1.7-71) [CRAN]</span></span>
-<span id="cb3-22"><a href="#cb3-22" tabindex="-1"></a><span class="co">#&gt; data.table (1.15.0  -&gt; 1.15.2) [CRAN]</span></span>
-<span id="cb3-23"><a href="#cb3-23" tabindex="-1"></a><span class="co">#&gt; igraph     (2.0.1.1 -&gt; 2.0.3 ) [CRAN]</span></span>
-<span id="cb3-24"><a href="#cb3-24" tabindex="-1"></a><span class="co">#&gt; Installing 13 packages: parallelly, globals, digest, Rcpp, curl, vctrs, stringi, rlang, glue, cli, terra, data.table, igraph</span></span>
-<span id="cb3-25"><a href="#cb3-25" tabindex="-1"></a><span class="co">#&gt; Installing packages into 'C:/Users/kkeshav/AppData/Local/Temp/Rtmp6Nnjmd/temp_libpath18786f31507e'</span></span>
-<span id="cb3-26"><a href="#cb3-26" tabindex="-1"></a><span class="co">#&gt; (as 'lib' is unspecified)</span></span>
-<span id="cb3-27"><a href="#cb3-27" tabindex="-1"></a><span class="co">#&gt; package 'parallelly' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-28"><a href="#cb3-28" tabindex="-1"></a><span class="co">#&gt; package 'globals' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-29"><a href="#cb3-29" tabindex="-1"></a><span class="co">#&gt; package 'digest' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-30"><a href="#cb3-30" tabindex="-1"></a><span class="co">#&gt; package 'Rcpp' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-31"><a href="#cb3-31" tabindex="-1"></a><span class="co">#&gt; package 'curl' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-32"><a href="#cb3-32" tabindex="-1"></a><span class="co">#&gt; package 'vctrs' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-33"><a href="#cb3-33" tabindex="-1"></a><span class="co">#&gt; package 'stringi' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-34"><a href="#cb3-34" tabindex="-1"></a><span class="co">#&gt; package 'rlang' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-35"><a href="#cb3-35" tabindex="-1"></a><span class="co">#&gt; package 'glue' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-36"><a href="#cb3-36" tabindex="-1"></a><span class="co">#&gt; package 'cli' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-37"><a href="#cb3-37" tabindex="-1"></a><span class="co">#&gt; package 'terra' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-38"><a href="#cb3-38" tabindex="-1"></a><span class="co">#&gt; package 'data.table' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-39"><a href="#cb3-39" tabindex="-1"></a><span class="co">#&gt; package 'igraph' successfully unpacked and MD5 sums checked</span></span>
-<span id="cb3-40"><a href="#cb3-40" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb3-41"><a href="#cb3-41" tabindex="-1"></a><span class="co">#&gt; The downloaded binary packages are in</span></span>
-<span id="cb3-42"><a href="#cb3-42" tabindex="-1"></a><span class="co">#&gt;  C:\Users\kkeshav\AppData\Local\Temp\RtmpyEq013\downloaded_packages</span></span>
-<span id="cb3-43"><a href="#cb3-43" tabindex="-1"></a><span class="co">#&gt; 
[36m--
[39m 
[36mR CMD build
[39m 
[36m-----------------------------------------------------------------
[39m</span></span>
-<span id="cb3-44"><a href="#cb3-44" tabindex="-1"></a><span class="co">#&gt;   </span></span>
-<span id="cb3-45"><a href="#cb3-45" tabindex="-1"></a>  </span>
-<span id="cb3-46"><a href="#cb3-46" tabindex="-1"></a>  </span>
-<span id="cb3-47"><a href="#cb3-47" tabindex="-1"></a>   checking <span class="cf">for</span> file <span class="st">'C:\Users\kkeshav\AppData\Local\Temp\RtmpyEq013</span><span class="sc">\r</span><span class="st">emotes49ac6a563953\GarrettLab-HabitatConnectivity-ea41a37\geohabnet/DESCRIPTION'</span> ...</span>
-<span id="cb3-48"><a href="#cb3-48" tabindex="-1"></a>  </span>
-<span id="cb3-49"><a href="#cb3-49" tabindex="-1"></a>   checking <span class="cf">for</span> file <span class="st">'C:\Users\kkeshav\AppData\Local\Temp\RtmpyEq013</span><span class="sc">\r</span><span class="st">emotes49ac6a563953\GarrettLab-HabitatConnectivity-ea41a37\geohabnet/DESCRIPTION'</span> ... </span>
-<span id="cb3-50"><a href="#cb3-50" tabindex="-1"></a>  </span>
-<span id="cb3-51"><a href="#cb3-51" tabindex="-1"></a>
[32mv
[39m  
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking <span class="cf">for</span> file <span class="st">'C:\Users\kkeshav\AppData\Local\Temp\RtmpyEq013</span><span class="sc">\r</span><span class="st">emotes49ac6a563953\GarrettLab-HabitatConnectivity-ea41a37\geohabnet/DESCRIPTION'</span>
[39m
[36m
[36m (346ms)
[36m
[39m</span>
-<span id="cb3-52"><a href="#cb3-52" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb3-53"><a href="#cb3-53" tabindex="-1"></a>  </span>
+<span id="cb3-11"><a href="#cb3-11" tabindex="-1"></a><span class="co">#&gt; parallelly   (1.37.0  -&gt; 1.37.1) [CRAN]</span></span>
+<span id="cb3-12"><a href="#cb3-12" tabindex="-1"></a><span class="co">#&gt; globals      (0.16.2  -&gt; 0.16.3) [CRAN]</span></span>
+<span id="cb3-13"><a href="#cb3-13" tabindex="-1"></a><span class="co">#&gt; digest       (0.6.33  -&gt; 0.6.35) [CRAN]</span></span>
+<span id="cb3-14"><a href="#cb3-14" tabindex="-1"></a><span class="co">#&gt; Rcpp         (1.0.11  -&gt; 1.0.12) [CRAN]</span></span>
+<span id="cb3-15"><a href="#cb3-15" tabindex="-1"></a><span class="co">#&gt; curl         (5.2.0   -&gt; 5.2.1 ) [CRAN]</span></span>
+<span id="cb3-16"><a href="#cb3-16" tabindex="-1"></a><span class="co">#&gt; vctrs        (0.6.3   -&gt; 0.6.5 ) [CRAN]</span></span>
+<span id="cb3-17"><a href="#cb3-17" tabindex="-1"></a><span class="co">#&gt; stringi      (1.7.12  -&gt; 1.8.3 ) [CRAN]</span></span>
+<span id="cb3-18"><a href="#cb3-18" tabindex="-1"></a><span class="co">#&gt; rlang        (1.1.1   -&gt; 1.1.3 ) [CRAN]</span></span>
+<span id="cb3-19"><a href="#cb3-19" tabindex="-1"></a><span class="co">#&gt; glue         (1.6.2   -&gt; 1.7.0 ) [CRAN]</span></span>
+<span id="cb3-20"><a href="#cb3-20" tabindex="-1"></a><span class="co">#&gt; cli          (3.6.1   -&gt; 3.6.2 ) [CRAN]</span></span>
+<span id="cb3-21"><a href="#cb3-21" tabindex="-1"></a><span class="co">#&gt; future       (1.33.1  -&gt; 1.33.2) [CRAN]</span></span>
+<span id="cb3-22"><a href="#cb3-22" tabindex="-1"></a><span class="co">#&gt; terra        (1.7-39  -&gt; 1.7-71) [CRAN]</span></span>
+<span id="cb3-23"><a href="#cb3-23" tabindex="-1"></a><span class="co">#&gt; sf           (1.0-15  -&gt; 1.0-16) [CRAN]</span></span>
+<span id="cb3-24"><a href="#cb3-24" tabindex="-1"></a><span class="co">#&gt; data.table   (1.15.0  -&gt; 1.15.4) [CRAN]</span></span>
+<span id="cb3-25"><a href="#cb3-25" tabindex="-1"></a><span class="co">#&gt; future.apply (1.11.1  -&gt; 1.11.2) [CRAN]</span></span>
+<span id="cb3-26"><a href="#cb3-26" tabindex="-1"></a><span class="co">#&gt; igraph       (2.0.1.1 -&gt; 2.0.3 ) [CRAN]</span></span>
+<span id="cb3-27"><a href="#cb3-27" tabindex="-1"></a><span class="co">#&gt; Installing 16 packages: parallelly, globals, digest, Rcpp, curl, vctrs, stringi, rlang, glue, cli, future, terra, sf, data.table, future.apply, igraph</span></span>
+<span id="cb3-28"><a href="#cb3-28" tabindex="-1"></a><span class="co">#&gt; Installing packages into 'C:/Users/kkeshav/AppData/Local/Temp/RtmpYLtssC/temp_libpath608453735b7e'</span></span>
+<span id="cb3-29"><a href="#cb3-29" tabindex="-1"></a><span class="co">#&gt; (as 'lib' is unspecified)</span></span>
+<span id="cb3-30"><a href="#cb3-30" tabindex="-1"></a><span class="co">#&gt; package 'parallelly' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-31"><a href="#cb3-31" tabindex="-1"></a><span class="co">#&gt; package 'globals' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-32"><a href="#cb3-32" tabindex="-1"></a><span class="co">#&gt; package 'digest' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-33"><a href="#cb3-33" tabindex="-1"></a><span class="co">#&gt; package 'Rcpp' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-34"><a href="#cb3-34" tabindex="-1"></a><span class="co">#&gt; package 'curl' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-35"><a href="#cb3-35" tabindex="-1"></a><span class="co">#&gt; package 'vctrs' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-36"><a href="#cb3-36" tabindex="-1"></a><span class="co">#&gt; package 'stringi' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-37"><a href="#cb3-37" tabindex="-1"></a><span class="co">#&gt; package 'rlang' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-38"><a href="#cb3-38" tabindex="-1"></a><span class="co">#&gt; package 'glue' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-39"><a href="#cb3-39" tabindex="-1"></a><span class="co">#&gt; package 'cli' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-40"><a href="#cb3-40" tabindex="-1"></a><span class="co">#&gt; package 'future' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-41"><a href="#cb3-41" tabindex="-1"></a><span class="co">#&gt; package 'terra' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-42"><a href="#cb3-42" tabindex="-1"></a><span class="co">#&gt; package 'sf' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-43"><a href="#cb3-43" tabindex="-1"></a><span class="co">#&gt; package 'data.table' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-44"><a href="#cb3-44" tabindex="-1"></a><span class="co">#&gt; package 'future.apply' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-45"><a href="#cb3-45" tabindex="-1"></a><span class="co">#&gt; package 'igraph' successfully unpacked and MD5 sums checked</span></span>
+<span id="cb3-46"><a href="#cb3-46" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb3-47"><a href="#cb3-47" tabindex="-1"></a><span class="co">#&gt; The downloaded binary packages are in</span></span>
+<span id="cb3-48"><a href="#cb3-48" tabindex="-1"></a><span class="co">#&gt;  C:\Users\kkeshav\AppData\Local\Temp\RtmpaU8FLa\downloaded_packages</span></span>
+<span id="cb3-49"><a href="#cb3-49" tabindex="-1"></a><span class="co">#&gt; 
[36m--
[39m 
[36mR CMD build
[39m 
[36m-----------------------------------------------------------------
[39m</span></span>
+<span id="cb3-50"><a href="#cb3-50" tabindex="-1"></a><span class="co">#&gt;   </span></span>
+<span id="cb3-51"><a href="#cb3-51" tabindex="-1"></a>  </span>
+<span id="cb3-52"><a href="#cb3-52" tabindex="-1"></a>  </span>
+<span id="cb3-53"><a href="#cb3-53" tabindex="-1"></a>   checking <span class="cf">for</span> file <span class="st">'C:\Users\kkeshav\AppData\Local\Temp\RtmpaU8FLa</span><span class="sc">\r</span><span class="st">emotes1fec34ae5e8a\GarrettLab-HabitatConnectivity-af9a6e8\geohabnet/DESCRIPTION'</span> ...</span>
 <span id="cb3-54"><a href="#cb3-54" tabindex="-1"></a>  </span>
-<span id="cb3-55"><a href="#cb3-55" tabindex="-1"></a>  </span>
-<span id="cb3-56"><a href="#cb3-56" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mpreparing <span class="st">'geohabnet'</span><span class="sc">:</span>
[39m
[36m
[36m (2s)
[36m
[39m</span>
-<span id="cb3-57"><a href="#cb3-57" tabindex="-1"></a><span class="co">#&gt;    checking DESCRIPTION meta-information ...</span></span>
-<span id="cb3-58"><a href="#cb3-58" tabindex="-1"></a>  </span>
-<span id="cb3-59"><a href="#cb3-59" tabindex="-1"></a>   checking DESCRIPTION meta<span class="sc">-</span>information ... </span>
+<span id="cb3-55"><a href="#cb3-55" tabindex="-1"></a>   checking <span class="cf">for</span> file <span class="st">'C:\Users\kkeshav\AppData\Local\Temp\RtmpaU8FLa</span><span class="sc">\r</span><span class="st">emotes1fec34ae5e8a\GarrettLab-HabitatConnectivity-af9a6e8\geohabnet/DESCRIPTION'</span> ... </span>
+<span id="cb3-56"><a href="#cb3-56" tabindex="-1"></a>  </span>
+<span id="cb3-57"><a href="#cb3-57" tabindex="-1"></a>
[32mv
[39m  
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking <span class="cf">for</span> file <span class="st">'C:\Users\kkeshav\AppData\Local\Temp\RtmpaU8FLa</span><span class="sc">\r</span><span class="st">emotes1fec34ae5e8a\GarrettLab-HabitatConnectivity-af9a6e8\geohabnet/DESCRIPTION'</span>
[39m
[36m
[39m</span>
+<span id="cb3-58"><a href="#cb3-58" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb3-59"><a href="#cb3-59" tabindex="-1"></a>  </span>
 <span id="cb3-60"><a href="#cb3-60" tabindex="-1"></a>  </span>
-<span id="cb3-61"><a href="#cb3-61" tabindex="-1"></a>
[32mv
[39m  
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking DESCRIPTION meta<span class="sc">-</span>information
[39m
[36m
[39m</span>
-<span id="cb3-62"><a href="#cb3-62" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb3-63"><a href="#cb3-63" tabindex="-1"></a>  </span>
+<span id="cb3-61"><a href="#cb3-61" tabindex="-1"></a>  </span>
+<span id="cb3-62"><a href="#cb3-62" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mpreparing <span class="st">'geohabnet'</span><span class="sc">:</span>
[39m
[36m
[36m (<span class="fl">2.4</span>s)
[36m
[39m</span>
+<span id="cb3-63"><a href="#cb3-63" tabindex="-1"></a><span class="co">#&gt;    checking DESCRIPTION meta-information ...</span></span>
 <span id="cb3-64"><a href="#cb3-64" tabindex="-1"></a>  </span>
-<span id="cb3-65"><a href="#cb3-65" tabindex="-1"></a>  </span>
-<span id="cb3-66"><a href="#cb3-66" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking <span class="cf">for</span> LF line<span class="sc">-</span>endings <span class="cf">in</span> source and make files and shell scripts
[39m
[36m
[39m</span>
-<span id="cb3-67"><a href="#cb3-67" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb3-68"><a href="#cb3-68" tabindex="-1"></a>  </span>
+<span id="cb3-65"><a href="#cb3-65" tabindex="-1"></a>   checking DESCRIPTION meta<span class="sc">-</span>information ... </span>
+<span id="cb3-66"><a href="#cb3-66" tabindex="-1"></a>  </span>
+<span id="cb3-67"><a href="#cb3-67" tabindex="-1"></a>
[32mv
[39m  
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking DESCRIPTION meta<span class="sc">-</span>information
[39m
[36m
[39m</span>
+<span id="cb3-68"><a href="#cb3-68" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb3-69"><a href="#cb3-69" tabindex="-1"></a>  </span>
 <span id="cb3-70"><a href="#cb3-70" tabindex="-1"></a>  </span>
-<span id="cb3-71"><a href="#cb3-71" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking <span class="cf">for</span> empty or unneeded directories
[39m
[36m
[39m</span>
-<span id="cb3-72"><a href="#cb3-72" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb3-73"><a href="#cb3-73" tabindex="-1"></a>  </span>
+<span id="cb3-71"><a href="#cb3-71" tabindex="-1"></a>  </span>
+<span id="cb3-72"><a href="#cb3-72" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking <span class="cf">for</span> LF line<span class="sc">-</span>endings <span class="cf">in</span> source and make files and shell scripts
[39m
[36m
[39m</span>
+<span id="cb3-73"><a href="#cb3-73" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb3-74"><a href="#cb3-74" tabindex="-1"></a>  </span>
 <span id="cb3-75"><a href="#cb3-75" tabindex="-1"></a>  </span>
-<span id="cb3-76"><a href="#cb3-76" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mbuilding <span class="st">'geohabnet_2.0.0.tar.gz'</span>
[39m
[36m
[39m</span>
-<span id="cb3-77"><a href="#cb3-77" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb3-78"><a href="#cb3-78" tabindex="-1"></a>  </span>
-<span id="cb3-79"><a href="#cb3-79" tabindex="-1"></a>   </span>
-<span id="cb3-80"><a href="#cb3-80" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb3-81"><a href="#cb3-81" tabindex="-1"></a><span class="co">#&gt; Installing package into 'C:/Users/kkeshav/AppData/Local/Temp/Rtmp6Nnjmd/temp_libpath18786f31507e'</span></span>
-<span id="cb3-82"><a href="#cb3-82" tabindex="-1"></a><span class="co">#&gt; (as 'lib' is unspecified)</span></span></code></pre></div>
+<span id="cb3-76"><a href="#cb3-76" tabindex="-1"></a>  </span>
+<span id="cb3-77"><a href="#cb3-77" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mchecking <span class="cf">for</span> empty or unneeded directories
[39m
[36m
[39m</span>
+<span id="cb3-78"><a href="#cb3-78" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb3-79"><a href="#cb3-79" tabindex="-1"></a>  </span>
+<span id="cb3-80"><a href="#cb3-80" tabindex="-1"></a>  </span>
+<span id="cb3-81"><a href="#cb3-81" tabindex="-1"></a>  </span>
+<span id="cb3-82"><a href="#cb3-82" tabindex="-1"></a>
[<span class="dv">38</span>;<span class="dv">5</span>;247m<span class="sc">-</span>
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247m  
[39m
[<span class="dv">38</span>;<span class="dv">5</span>;247mbuilding <span class="st">'geohabnet_2.0.0.tar.gz'</span>
[39m
[36m
[39m</span>
+<span id="cb3-83"><a href="#cb3-83" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb3-84"><a href="#cb3-84" tabindex="-1"></a>  </span>
+<span id="cb3-85"><a href="#cb3-85" tabindex="-1"></a>   </span>
+<span id="cb3-86"><a href="#cb3-86" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb3-87"><a href="#cb3-87" tabindex="-1"></a><span class="co">#&gt; Installing package into 'C:/Users/kkeshav/AppData/Local/Temp/RtmpYLtssC/temp_libpath608453735b7e'</span></span>
+<span id="cb3-88"><a href="#cb3-88" tabindex="-1"></a><span class="co">#&gt; (as 'lib' is unspecified)</span></span></code></pre></div>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://garrettlab.github.io/HabitatConnectivity/">geohabnet</a></span><span class="op">)</span></span></code></pre></div>
 <p>At any point, access the help page using following -</p>
@@ -296,22 +302,13 @@ <h3 id="run-analysis-on-default-configuration">Run analysis on default configura
 <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a>res <span class="ot">&lt;-</span> <span class="fu">sensitivity_analysis</span>()</span>
 <span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
 <span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
-<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="er">======</span></span>
+<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="er">==============</span></span>
 <span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>                                          </span></code></pre></div>
-<p><img src="analysis_files/figure-html/unnamed-chunk-5-1.png" width="700"></p>
+<p><img src="analysis_files/figure-html/unnamed-chunk-5-1.png" width="700"><img src="analysis_files/figure-html/unnamed-chunk-5-2.png" width="700"></p>
 <pre><code>#&gt; 
-|---------|---------|---------|---------|
-========
-                                          
-
 |---------|---------|---------|---------|
 ==============
                                           </code></pre>
-<p><img src="analysis_files/figure-html/unnamed-chunk-5-2.png" width="700"></p>
-<pre><code>#&gt; 
-|---------|---------|---------|---------|
-======
-                                          </code></pre>
 <p><img src="analysis_files/figure-html/unnamed-chunk-5-3.png" width="700"></p>
 <p>The results are the side effects and the similar information is
 captured in the object returned from it. Its based on the values set for
@@ -335,7 +332,7 @@ <h4 id="setting-values-in-a-function">Setting values in a function<a class="anch
 obtain raster and later we will understand the details.</p>
 <p>An effective way to look-up is search_crop(). It will return sources
 which contains the data-set for this crop.</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span></span>
 <span><span class="va">avocado</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/cropharvest_rast.html">cropharvest_rast</a></span><span class="op">(</span><span class="st">"avocado"</span>, <span class="st">"monfreda"</span><span class="op">)</span></span>
 <span></span>
@@ -354,24 +351,20 @@ <h4 id="setting-values-in-a-function">Setting values in a function<a class="anch
 workflow. We will only set the required parameter - <em>rast</em>. The
 value represents <em>Avocado</em> plantation in geographical area of
 North America.</p>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>geo_net <span class="ot">&lt;-</span> <span class="fu">msean</span>(avocado)</span>
-<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb10-3"><a href="#cb10-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
-<span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a><span class="er">======</span></span>
-<span id="cb10-5"><a href="#cb10-5" tabindex="-1"></a>                                          </span></code></pre></div>
+<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>geo_net <span class="ot">&lt;-</span> <span class="fu">msean</span>(avocado)</span>
+<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
+<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a><span class="er">==========</span></span>
+<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a>                                          </span></code></pre></div>
 <p><img src="analysis_files/figure-html/unnamed-chunk-7-1.png" width="700"></p>
 <pre><code>#&gt; 
-|---------|---------|---------|---------|
-==========
-                                          
-
 |---------|---------|---------|---------|
 ==============
                                           </code></pre>
 <p><img src="analysis_files/figure-html/unnamed-chunk-7-2.png" width="700"></p>
 <pre><code>#&gt; 
 |---------|---------|---------|---------|
-======
+==========
                                           </code></pre>
 <p><img src="analysis_files/figure-html/unnamed-chunk-7-3.png" width="700"></p>
 <p>The functions <code>msean</code> is same as <code>sean</code> except
@@ -393,7 +386,7 @@ <h4 id="setting-values-in-a-function">Setting values in a function<a class="anch
 <ul>
 <li>
 <p>Get geographical scales used in global analysis -</p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/global_scales.html">global_scales</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; $east</span></span>
 <span><span class="co">#&gt; [1] -24 180 -58  60</span></span>
@@ -405,7 +398,7 @@ <h4 id="setting-values-in-a-function">Setting values in a function<a class="anch
 <p>Although recommended not to change the global scales since it has
 been finalized after several tries. Still, for advance use, set the
 global geographic scales using -</p>
-<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co">#set_global_scales(list(east = c(-24, 180, -58, 60), west = c(-140, -34, -58, 60)))</span></span></code></pre></div>
 </li>
 </ul>
@@ -421,7 +414,7 @@ <h4 id="setting-values-in-a-function">Setting values in a function<a class="anch
 context of <em>SpatRaster</em>, it’s the number of pixels that are
 aggregated to produce a new finer/coarser version raster data. Default
 is</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/reso.html">reso</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] 12</span></span></code></pre></div>
 </li>
@@ -445,10 +438,10 @@ <h4 id="using-configuration">Using configuration<a class="anchor" aria-label="an
 recommend saving to path where program will have write permissions.
 Using <em>iwindow = TRUE</em> will prompt a selection window to save
 config file.</p>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">config_file</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/get_parameters.html">get_parameters</a></span><span class="op">(</span>out_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="va">config_file</span></span>
-<span><span class="co">#&gt; [1] "C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpyEq013/parameters.yaml"</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] "C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpaU8FLa/parameters.yaml"</span></span></code></pre></div>
 <p>The file should look something like this -</p>
 <div class="float">
 <img src="images/initconfig.png" width="700" alt="Initial parameters.yaml"><div class="figcaption">Initial parameters.yaml</div>
@@ -456,7 +449,7 @@ <h4 id="using-configuration">Using configuration<a class="anchor" aria-label="an
 <p>The values must be modified without modifying the structure. The
 order don’t matter for the program. The new values in the configuration
 must be fed to the workflow using -</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/set_parameters.html">set_parameters</a></span><span class="op">(</span>new_params <span class="op">=</span> <span class="va">config_file</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="co">#using iwindow = true will prompt a selction window to choose config file.</span></span></code></pre></div>
@@ -475,7 +468,7 @@ <h4 id="hosts">Hosts<a class="anchor" aria-label="anchor" href="#hosts"></a>
 </h4>
 <p>We have some helper functions to make the analysis easier. Available
 sources can be seen using -</p>
-<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">geohabnet</span><span class="fu">::</span><span class="fu"><a href="../reference/supported_sources.html">supported_sources</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "monfreda"          "mapspam2010"       "mapspam2017Africa"</span></span></code></pre></div>
 <p>More specifically, we support 2 data set sources - <a href="http://www.earthstat.org/harvested-area-yield-175-crops/" class="external-link">Monfreda</a>
@@ -484,7 +477,7 @@ <h4 id="hosts">Hosts<a class="anchor" aria-label="anchor" href="#hosts"></a>
 sources have crop presence in the geographical areas in the form of
 raster(tiff). To start with, we can check if a certain crop is available
 in the source -</p>
-<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/search_crop.html">search_crop</a></span><span class="op">(</span><span class="st">"avocado"</span><span class="op">)</span> <span class="co">#1</span></span>
 <span><span class="co">#&gt; [1] "monfreda"</span></span>
 <span><span class="fu"><a href="../reference/search_crop.html">search_crop</a></span><span class="op">(</span><span class="st">"bean"</span><span class="op">)</span> <span class="co">#2</span></span>
@@ -493,10 +486,10 @@ <h4 id="hosts">Hosts<a class="anchor" aria-label="anchor" href="#hosts"></a>
 <code>monfreda</code> . Now, #2 suggests that <em>banana</em> is present
 in 2 sources. We will use the results from here to obtain its raster
 data from the one of the specified sources.</p>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># get avocado data</span></span>
 <span><span class="va">rast_avocado</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/crops_rast.html">crops_rast</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>monfreda <span class="op">=</span> <span class="st">"avocado"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span></span>
 <span><span class="va">old_to</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span><span class="st">"timeout"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>timeout <span class="op">=</span> <span class="fl">6000</span><span class="op">)</span></span>
@@ -506,7 +499,7 @@ <h4 id="hosts">Hosts<a class="anchor" aria-label="anchor" href="#hosts"></a>
 <p>The returned is actually if type <code>SpatRaster</code>. In above,
 we will have separate raster information for each of the crop. Crops can
 be combined and be returned as one raster.</p>
-<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Back to back downloads causes connection to fail, this is a workaround</span></span>
 <span><span class="va">rast_avo_ban</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/crops_rast.html">crops_rast</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>monfreda <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"avocado"</span>, <span class="st">"banana"</span><span class="op">)</span>, mapspam2010 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"banana"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="va">old_to</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span><span class="va">old_to</span><span class="op">)</span></span></code></pre></div>
@@ -518,13 +511,13 @@ <h4 id="hosts">Hosts<a class="anchor" aria-label="anchor" href="#hosts"></a>
 <em>tiff -</em> <code><a href="../reference/tiff_torast.html">tiff_torast()</a></code> . Finally, we have
 <code><a href="../reference/get_rasters.html">get_rasters()</a></code> method, which is an abstraction of . To see
 the difference in data that was generated in last 3 methods -</p>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/gplot.html">gplot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">rast_avocado</span>, <span class="va">rast_ban</span>, <span class="va">rast_avo_ban</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p><img src="analysis_files/figure-html/combine_sps-1.png" width="700"></p>
 <p>The result obtained from one of these methods can be used as an
 argument to <code><a href="../reference/sean.html">sean()</a></code> . Value of <code>results</code> is list
 of risk indices.</p>
-<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">results</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">rast_avocado</span>, <span class="va">rast_avo_ban</span><span class="op">)</span>, <span class="va">msean</span><span class="op">)</span></span></code></pre></div>
 <p>Internally, <code><a href="../reference/cropharvest_rast.html">cropharvest_rast()</a></code> is used to fetch the crop
 data-set in it’s supported form.</p>
@@ -532,21 +525,16 @@ <h4 id="hosts">Hosts<a class="anchor" aria-label="anchor" href="#hosts"></a>
 and banana on global scale and default set of parameter values.
 Alternatively, we can just specify the crops under
 <code>parameters.yaml</code> and run the workflow -</p>
-<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a>results <span class="ot">&lt;-</span> <span class="fu">sensitivity_analysis</span>()</span>
-<span id="cb25-2"><a href="#cb25-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb25-3"><a href="#cb25-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
-<span id="cb25-4"><a href="#cb25-4" tabindex="-1"></a><span class="er">=======</span></span>
-<span id="cb25-5"><a href="#cb25-5" tabindex="-1"></a>                                          </span></code></pre></div>
-<p><img src="analysis_files/figure-html/unnamed-chunk-14-1.png" width="700"></p>
+<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a>results <span class="ot">&lt;-</span> <span class="fu">sensitivity_analysis</span>()</span>
+<span id="cb24-2"><a href="#cb24-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb24-3"><a href="#cb24-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
+<span id="cb24-4"><a href="#cb24-4" tabindex="-1"></a><span class="er">==========</span></span>
+<span id="cb24-5"><a href="#cb24-5" tabindex="-1"></a>                                          </span></code></pre></div>
+<p><img src="analysis_files/figure-html/unnamed-chunk-14-1.png" width="700"><img src="analysis_files/figure-html/unnamed-chunk-14-2.png" width="700"></p>
 <pre><code>#&gt; 
 |---------|---------|---------|---------|
 ==========
                                           </code></pre>
-<p><img src="analysis_files/figure-html/unnamed-chunk-14-2.png" width="700"></p>
-<pre><code>#&gt; 
-|---------|---------|---------|---------|
-=======
-                                          </code></pre>
 <p><img src="analysis_files/figure-html/unnamed-chunk-14-3.png" width="700"></p>
 </div>
 <div class="section level4">
@@ -558,20 +546,20 @@ <h4 id="thresholds">Thresholds<a class="anchor" aria-label="anchor" href="#thres
 network. The intermediate goal is to produce a adjacency graph which
 essentially determines the connectivity. Cells which doesn’t meet the
 threshold are removed from the consideration by dispersal models.</p>
-<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a>risk_indexes <span class="ot">&lt;-</span> <span class="fu">msean</span>(avocado, <span class="at">global =</span> <span class="cn">FALSE</span>, <span class="at">hd_threshold =</span> <span class="fl">0.00001</span>, <span class="at">link_threshold =</span> <span class="fl">0.00001</span>)</span>
-<span id="cb28-2"><a href="#cb28-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb28-3"><a href="#cb28-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
-<span id="cb28-4"><a href="#cb28-4" tabindex="-1"></a><span class="er">====</span></span>
-<span id="cb28-5"><a href="#cb28-5" tabindex="-1"></a>                                          </span></code></pre></div>
+<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1" tabindex="-1"></a>risk_indexes <span class="ot">&lt;-</span> <span class="fu">msean</span>(avocado, <span class="at">global =</span> <span class="cn">FALSE</span>, <span class="at">hd_threshold =</span> <span class="fl">0.00001</span>, <span class="at">link_threshold =</span> <span class="fl">0.00001</span>)</span>
+<span id="cb26-2"><a href="#cb26-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb26-3"><a href="#cb26-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
+<span id="cb26-4"><a href="#cb26-4" tabindex="-1"></a><span class="er">=======</span></span>
+<span id="cb26-5"><a href="#cb26-5" tabindex="-1"></a>                                          </span></code></pre></div>
 <p><img src="analysis_files/figure-html/unnamed-chunk-15-1.png" width="700"></p>
 <pre><code>#&gt; 
 |---------|---------|---------|---------|
-=====
+=======
                                           </code></pre>
 <p><img src="analysis_files/figure-html/unnamed-chunk-15-2.png" width="700"></p>
 <pre><code>#&gt; 
 |---------|---------|---------|---------|
-====
+======
                                           </code></pre>
 <p><img src="analysis_files/figure-html/unnamed-chunk-15-3.png" width="700"></p>
 <div class="section level5">
@@ -646,7 +634,7 @@ <h4 id="distance-methods">Distance methods<a class="anchor" aria-label="anchor"
 of these options should be used as input to run the analysis. Check for
 supported methods in analysis by running <code><a href="../reference/dist_methods.html">dist_methods()</a></code> in
 the console.</p>
-<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/dist_methods.html">dist_methods</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "geodesic"          "vincentyellipsoid"</span></span></code></pre></div>
 </div>
@@ -667,7 +655,7 @@ <h4 id="resolution">Resolution<a class="anchor" aria-label="anchor" href="#resol
 <h4 id="metrics">Metrics<a class="anchor" aria-label="anchor" href="#metrics"></a>
 </h4>
 <p>See available metrics using</p>
-<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/supported_metrics.html">supported_metrics</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "betweeness"               "node_strength"           </span></span>
 <span><span class="co">#&gt; [3] "sum_of_nearest_neighbors" "eigenvector_centrality"  </span></span>
@@ -711,7 +699,7 @@ <h4 id="geographical-extent">Geographical Extent<a class="anchor" aria-label="an
 <ol style="list-style-type: decimal">
 <li>
 <p>Using function</p>
-<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">results</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/sean.html">msean</a></span><span class="op">(</span><span class="va">avocado</span>, global <span class="op">=</span> <span class="cn">FALSE</span>, geoscale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">115</span>, <span class="op">-</span><span class="fl">75</span>, <span class="fl">5</span>, <span class="fl">32</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p><img src="analysis_files/figure-html/non-global-1.png" width="700"><img src="analysis_files/figure-html/non-global-2.png" width="700"><img src="analysis_files/figure-html/non-global-3.png" width="700"></p>
 </li>
@@ -745,23 +733,23 @@ <h2 id="outputs">Outputs<a class="anchor" aria-label="anchor" href="#outputs"></
 <code><a href="../reference/sean.html">msean()</a></code> which produces maps as side effect. The user
 function equivalent is connectivity() which accepts primitives types
 instead of S4 class.</p>
-<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb34-1"><a href="#cb34-1" tabindex="-1"></a>final <span class="ot">&lt;-</span> <span class="fu">msean</span>(avocado, <span class="at">link_threshold =</span> <span class="fl">0.000001</span>, <span class="at">hd_threshold =</span> <span class="fl">0.000025</span>)</span>
-<span id="cb34-2"><a href="#cb34-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb34-3"><a href="#cb34-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
-<span id="cb34-4"><a href="#cb34-4" tabindex="-1"></a><span class="er">=======</span></span>
-<span id="cb34-5"><a href="#cb34-5" tabindex="-1"></a>                                          </span></code></pre></div>
+<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb32-1"><a href="#cb32-1" tabindex="-1"></a>final <span class="ot">&lt;-</span> <span class="fu">msean</span>(avocado, <span class="at">link_threshold =</span> <span class="fl">0.000001</span>, <span class="at">hd_threshold =</span> <span class="fl">0.000025</span>)</span>
+<span id="cb32-2"><a href="#cb32-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb32-3"><a href="#cb32-3" tabindex="-1"></a><span class="sc">|---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span><span class="sc">---------</span><span class="er">|</span></span>
+<span id="cb32-4"><a href="#cb32-4" tabindex="-1"></a><span class="er">==========</span></span>
+<span id="cb32-5"><a href="#cb32-5" tabindex="-1"></a>                                          </span></code></pre></div>
 <p><img src="analysis_files/figure-html/final-1.png" width="700"></p>
 <pre><code>#&gt; 
 |---------|---------|---------|---------|
-==========
+==============
                                           </code></pre>
 <p><img src="analysis_files/figure-html/final-2.png" width="700"></p>
 <pre><code>#&gt; 
 |---------|---------|---------|---------|
-=======
+==========
                                           </code></pre>
 <p><img src="analysis_files/figure-html/final-3.png" width="700"></p>
-<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span></span>
 <span><span class="co"># checkout the type of an object</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">final</span><span class="op">)</span></span>
@@ -773,15 +761,15 @@ <h2 id="outputs">Outputs<a class="anchor" aria-label="anchor" href="#outputs"></
 and that’s really the whole point. See the result summary by simply
 calling the <code>final</code> object and navigate using the standard S4
 classes approach.</p>
-<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">final</span></span>
 <span><span class="co">#&gt; class            :  GeoNetwork </span></span>
 <span><span class="co">#&gt; host density     :  118 , 320  (nrow, ncol) SpatRaster </span></span>
-<span><span class="co">#&gt; mean             :  C:\Users\kkeshav\AppData\Local\Temp\RtmpyEq013/plots/mean_20240322135029696171.tif </span></span>
+<span><span class="co">#&gt; mean             :  C:\Users\kkeshav\AppData\Local\Temp\RtmpaU8FLa/plots/mean_20240405165709138196.tif </span></span>
 <span><span class="co">#&gt; mean raster      :  1416 , 3840  (nrow, ncol) </span></span>
-<span><span class="co">#&gt; variance          :  C:\Users\kkeshav\AppData\Local\Temp\RtmpyEq013/plots/variance_20240322135043271863.tif </span></span>
+<span><span class="co">#&gt; variance          :  C:\Users\kkeshav\AppData\Local\Temp\RtmpaU8FLa/plots/variance_20240405165722357352.tif </span></span>
 <span><span class="co">#&gt; variance raster   :  1416 , 3840  (nrow, ncol) </span></span>
-<span><span class="co">#&gt; difference        :  C:\Users\kkeshav\AppData\Local\Temp\RtmpyEq013/plots/difference_20240322135055407492.tif </span></span>
+<span><span class="co">#&gt; difference        :  C:\Users\kkeshav\AppData\Local\Temp\RtmpaU8FLa/plots/difference_20240405165734248025.tif </span></span>
 <span><span class="co">#&gt; difference raster :  1416 , 3840  (nrow, ncol)</span></span></code></pre></div>
 <p>The final operations are performed risk indices and on the 3 results
 that are produced -</p>
@@ -793,7 +781,7 @@ <h2 id="outputs">Outputs<a class="anchor" aria-label="anchor" href="#outputs"></
 indices and divided by number of indices. It represents the connectivity
 based on host density in the given area.</p>
 <p>Navigating the resulting object -</p>
-<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/gplot.html">gplot</a></span><span class="op">(</span><span class="va">final</span><span class="op">@</span><span class="va">me_rast</span><span class="op">)</span></span></code></pre></div>
 <p><img src="analysis_files/figure-html/mean-1.png" width="700"></p>
 </li>
@@ -802,7 +790,7 @@ <h2 id="outputs">Outputs<a class="anchor" aria-label="anchor" href="#outputs"></
 <p>Uses <code><a href="https://rdrr.io/r/stats/cor.html" class="external-link">stats::var</a></code> on risk indices, subset is extracted for
 provided scale and finally pixels are dis-aggregated using <em>factor =
 resolution value in original parameter</em> to from previous step.</p>
-<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/gplot.html">gplot</a></span><span class="op">(</span><span class="va">final</span><span class="op">@</span><span class="va">var_rast</span><span class="op">)</span></span></code></pre></div>
 <p><img src="analysis_files/figure-html/var-1.png" width="700"></p>
 </li>
@@ -812,7 +800,7 @@ <h2 id="outputs">Outputs<a class="anchor" aria-label="anchor" href="#outputs"></
 then difference is calculated between the rank of matrices which are
 essentially numeric cells of risk indices of type <em>SpatRaster</em>.
 The result is dis-aggregated in the same way as previous step.</p>
-<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/gplot.html">gplot</a></span><span class="op">(</span><span class="va">final</span><span class="op">@</span><span class="va">diff_rast</span><span class="op">)</span></span></code></pre></div>
 <p><img src="analysis_files/figure-html/diff-1.png" width="700"></p>
 </li>
@@ -821,7 +809,7 @@ <h2 id="outputs">Outputs<a class="anchor" aria-label="anchor" href="#outputs"></
 Additionally, access the risk indices and it’s corresponding adjacency
 are further accessible within slots in the <code>GeoNetwork</code>
 class.</p>
-<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span></span>
 <span><span class="co"># checkout the results</span></span>
 <span><span class="va">final</span><span class="op">@</span><span class="va">rasters</span></span>
@@ -845,7 +833,7 @@ <h2 id="outputs">Outputs<a class="anchor" aria-label="anchor" href="#outputs"></
 <span><span class="co">#&gt; adjacency matrix :  839 ,  839  (nrow, ncol) </span></span>
 <span><span class="co">#&gt; risk index       :  ,   (nrow, ncol)</span></span></code></pre></div>
 <p>Checkout the adjacency matrices by running the code below -</p>
-<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span></span>
 <span><span class="co"># replace the indexing with any arbitary index,</span></span>
 <span><span class="co"># uncomment line below to see the results.</span></span>
@@ -897,7 +885,7 @@ <h2 id="computing">Computing<a class="anchor" aria-label="anchor" href="#computi
 SpatRaster is an external pointer in C++ rather than an R object and
 thus adds overhead of conversion, neutralizing the performance
 gains.</p>
-<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">avocado</span> <span class="op">&lt;-</span> <span class="fu">geohabnet</span><span class="fu">::</span><span class="fu"><a href="../reference/cropharvest_rast.html">cropharvest_rast</a></span><span class="op">(</span><span class="st">"avocado"</span>, <span class="st">"monfreda"</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># see ?future::plan for details</span></span>
diff --git a/docs/articles/analysis_files/figure-html/diff-1.png b/docs/articles/analysis_files/figure-html/diff-1.png
index 5933020..d4f08eb 100644
Binary files a/docs/articles/analysis_files/figure-html/diff-1.png and b/docs/articles/analysis_files/figure-html/diff-1.png differ
diff --git a/docs/articles/analysis_files/figure-html/final-1.png b/docs/articles/analysis_files/figure-html/final-1.png
index 78aafa3..9d933a5 100644
Binary files a/docs/articles/analysis_files/figure-html/final-1.png and b/docs/articles/analysis_files/figure-html/final-1.png differ
diff --git a/docs/articles/analysis_files/figure-html/final-2.png b/docs/articles/analysis_files/figure-html/final-2.png
index 43a6541..fc69668 100644
Binary files a/docs/articles/analysis_files/figure-html/final-2.png and b/docs/articles/analysis_files/figure-html/final-2.png differ
diff --git a/docs/articles/analysis_files/figure-html/final-3.png b/docs/articles/analysis_files/figure-html/final-3.png
index 5891ec0..b7f3239 100644
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index f97e25a..b3e17bd 100644
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index 526af4c..0dd569a 100644
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index 437552b..3f522f9 100644
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diff --git a/docs/authors.html b/docs/authors.html
index 86678d7..f81d2b9 100644
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@@ -84,7 +84,7 @@ <h2 id="citation">Citation</h2>
 
       <p>Keshav K, Plex A, Garrett K (2024).
 <em>geohabnet: Geographical Risk Analysis Based on Habitat Connectivity</em>.
-R package version 2.0.0, 
+R package version 2.1.1, 
 https://CRAN.R-project.org/package=geohabnet/,
 https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/,
 https://www.garrettlab.com/, <a href="https://garrettlab.github.io/HabitatConnectivity/">https://garrettlab.github.io/HabitatConnectivity/</a>. 
@@ -93,7 +93,7 @@ <h2 id="citation">Citation</h2>
   title = {geohabnet: Geographical Risk Analysis Based on Habitat Connectivity},
   author = {Krishna Keshav and Aaron Plex and Karen Garrett},
   year = {2024},
-  note = {R package version 2.0.0, 
+  note = {R package version 2.1.1, 
 https://CRAN.R-project.org/package=geohabnet/,
 https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/,
 https://www.garrettlab.com/},
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index 14f8005..1b76075 100644
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+++ b/docs/index.html
@@ -63,7 +63,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
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diff --git a/docs/news/index.html b/docs/news/index.html
index aded223..ebea214 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -10,7 +10,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
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@@ -54,6 +54,15 @@
       <small>Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="2.1.1" id="geohabnet-211">geohabnet 2.1.1<a class="anchor" aria-label="anchor" href="#geohabnet-211"></a></h2>
+<ul><li>Removed dependency with Amazon S3</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="2.1.0" id="geohabnet-210">geohabnet 2.1.0<a class="anchor" aria-label="anchor" href="#geohabnet-210"></a></h2><p class="text-muted">CRAN release: 2024-03-28</p>
+<ul><li>Dispersal kernels can now either be Inverse Power Law or Exponential or both</li>
+<li>Renamed CCRI to HCI</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="2.0.0" id="geohabnet-200">geohabnet 2.0.0<a class="anchor" aria-label="anchor" href="#geohabnet-200"></a></h2><p class="text-muted">CRAN release: 2024-02-27</p>
 <ul><li>Adoption of habitat connectivity</li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 925115e..79bfd25 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   global_analysis: global_analysis.html
   Using-raster-file: Using-raster-file.html
   LinkWeightsAnalysis: LinkWeightsAnalysis.html
-last_built: 2024-03-22T17:41Z
+last_built: 2024-04-05T20:47Z
 urls:
   reference: https://garrettlab.github.io/HabitatConnectivity/reference
   article: https://garrettlab.github.io/HabitatConnectivity/articles
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index 7850914..e034445 100644
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index 03299f3..34fc693 100644
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index db80572..29b0528 100644
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index 621b41c..b0ad2ff 100644
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index 12825fb..781e99b 100644
--- a/docs/reference/Gmap-class.html
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index 4098fcd..b97ea16 100644
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diff --git a/docs/reference/STR_DEGREE.html b/docs/reference/STR_DEGREE.html
index 7bc32f7..df4bfd9 100644
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/STR_DISTANCE_MATRIX.html b/docs/reference/STR_DISTANCE_MATRIX.html
index 7c2e2b0..b413ed7 100644
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diff --git a/docs/reference/STR_EAST.html b/docs/reference/STR_EAST.html
index 299b882..78260b1 100644
--- a/docs/reference/STR_EAST.html
+++ b/docs/reference/STR_EAST.html
@@ -10,7 +10,7 @@
     
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index 20caa48..36dce14 100644
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diff --git a/docs/reference/STR_NEAREST_NEIGHBORS_SUM.html b/docs/reference/STR_NEAREST_NEIGHBORS_SUM.html
index bb7feca..871db3d 100644
--- a/docs/reference/STR_NEAREST_NEIGHBORS_SUM.html
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@@ -10,7 +10,7 @@
     
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diff --git a/docs/reference/STR_NODE_STRENGTH.html b/docs/reference/STR_NODE_STRENGTH.html
index 5bdb2ab..c1c1644 100644
--- a/docs/reference/STR_NODE_STRENGTH.html
+++ b/docs/reference/STR_NODE_STRENGTH.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/STR_PAGE_RANK.html b/docs/reference/STR_PAGE_RANK.html
index b2d4469..bc64fe0 100644
--- a/docs/reference/STR_PAGE_RANK.html
+++ b/docs/reference/STR_PAGE_RANK.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/STR_WEST.html b/docs/reference/STR_WEST.html
index aaf4d94..321369e 100644
--- a/docs/reference/STR_WEST.html
+++ b/docs/reference/STR_WEST.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/connectivity.html b/docs/reference/connectivity.html
index 19b9b16..45ed8e0 100644
--- a/docs/reference/connectivity.html
+++ b/docs/reference/connectivity.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/cropharvest_rast.html b/docs/reference/cropharvest_rast.html
index 6328055..7c3a1a6 100644
--- a/docs/reference/cropharvest_rast.html
+++ b/docs/reference/cropharvest_rast.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/crops_rast.html b/docs/reference/crops_rast.html
index e09543e..4d15a68 100644
--- a/docs/reference/crops_rast.html
+++ b/docs/reference/crops_rast.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dist_methods.html b/docs/reference/dist_methods.html
index be27664..b5ff534 100644
--- a/docs/reference/dist_methods.html
+++ b/docs/reference/dist_methods.html
@@ -1,10 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains supported strategies to calculate distance between two points.
-Use of one the methods in sean() or sensitivity_analysis().
-Contains supported strategies to calculate distance between two points.
 Use of one the methods in sean() or sensitivity_analysis()."><title>Distance methods supported — dist_methods • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Distance methods supported — dist_methods"><meta property="og:description" content="Contains supported strategies to calculate distance between two points.
-Use of one the methods in sean() or sensitivity_analysis().
-Contains supported strategies to calculate distance between two points.
 Use of one the methods in sean() or sensitivity_analysis()."><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -16,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -57,39 +53,30 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Distance methods supported</h1>
-      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/ccri_helper.R" class="external-link"><code>R/ccri_helper.R</code></a>, <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
       <div class="d-none name"><code>dist_methods.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Contains supported strategies to calculate distance between two points.
-Use of one the methods in <code><a href="sean.html">sean()</a></code> or <code><a href="sensitivity_analysis.html">sensitivity_analysis()</a></code>.</p>
-<p>Contains supported strategies to calculate distance between two points.
 Use of one the methods in <code><a href="sean.html">sean()</a></code> or <code><a href="sensitivity_analysis.html">sensitivity_analysis()</a></code>.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">dist_methods</span><span class="op">(</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">dist_methods</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">dist_methods</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>vector</p>
-
-
 <p>vector</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">dist_methods</span><span class="op">(</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">dist_methods</span><span class="op">(</span><span class="op">)</span></span>
 <span></span></code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/docs/reference/dot-indices.html b/docs/reference/dot-indices.html
index 7a324a2..f52ff44 100644
--- a/docs/reference/dot-indices.html
+++ b/docs/reference/dot-indices.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/geohabnet-package.html b/docs/reference/geohabnet-package.html
index 2a86fe1..afcddbf 100644
--- a/docs/reference/geohabnet-package.html
+++ b/docs/reference/geohabnet-package.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/geoscale_param.html b/docs/reference/geoscale_param.html
index 4a47164..e682448 100644
--- a/docs/reference/geoscale_param.html
+++ b/docs/reference/geoscale_param.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_parameters.html b/docs/reference/get_parameters.html
index 6efe3ff..5099c38 100644
--- a/docs/reference/get_parameters.html
+++ b/docs/reference/get_parameters.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_rasters.html b/docs/reference/get_rasters.html
index 6ce23a2..a568868 100644
--- a/docs/reference/get_rasters.html
+++ b/docs/reference/get_rasters.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/global_scales.html b/docs/reference/global_scales.html
index 247cdbf..b864e04 100644
--- a/docs/reference/global_scales.html
+++ b/docs/reference/global_scales.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/gplot.html b/docs/reference/gplot.html
index 9c0cea1..4d2e9f0 100644
--- a/docs/reference/gplot.html
+++ b/docs/reference/gplot.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/hci_diff.html b/docs/reference/hci_diff.html
index 468e316..fc297d9 100644
--- a/docs/reference/hci_diff.html
+++ b/docs/reference/hci_diff.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/hci_mean.html b/docs/reference/hci_mean.html
index 7f3e72b..0dd6f09 100644
--- a/docs/reference/hci_mean.html
+++ b/docs/reference/hci_mean.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/hci_variance.html b/docs/reference/hci_variance.html
index 7526dda..38a87ff 100644
--- a/docs/reference/hci_variance.html
+++ b/docs/reference/hci_variance.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/host_density-set.html b/docs/reference/host_density-set.html
index feaba60..1af3c68 100644
--- a/docs/reference/host_density-set.html
+++ b/docs/reference/host_density-set.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6d0b1a0..5d47791 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,7 +86,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Dispersal kernels</dd>
       </dl><dl><dt>
           
-          <code><a href="dist_methods.html">dist_methods()</a></code> <code><a href="dist_methods.html">dist_methods()</a></code> 
+          <code><a href="dist_methods.html">dist_methods()</a></code> 
         </dt>
         <dd>Distance methods supported</dd>
       </dl><dl><dt>
@@ -171,12 +171,12 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Load Parameters from YAML File</dd>
       </dl><dl><dt>
           
-          <code><a href="mapspam.html">mapspam()</a></code> <code><a href="mapspam.html">mapspam()</a></code> 
+          <code><a href="mapspam.html">mapspam()</a></code> 
         </dt>
         <dd>Supported sources for Mapspam</dd>
       </dl><dl><dt>
           
-          <code><a href="monfreda.html">monfreda()</a></code> <code><a href="monfreda.html">monfreda()</a></code> 
+          <code><a href="monfreda.html">monfreda()</a></code> 
         </dt>
         <dd>Supported sources for monfreda</dd>
       </dl><dl><dt>
@@ -201,7 +201,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>RiskMap class</dd>
       </dl><dl><dt>
           
-          <code><a href="risk_indices.html">risk_indices()</a></code> <code><a href="risk_indices.html">risk_indices()</a></code> 
+          <code><a href="risk_indices.html">risk_indices()</a></code> 
         </dt>
         <dd>Get risk indices</dd>
       </dl><dl><dt>
@@ -216,7 +216,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Sensitivity analysis across maps of habitat connectivity</dd>
       </dl><dl><dt>
           
-          <code><a href="search_crop.html">search_crop()</a></code> <code><a href="search_crop.html">search_crop()</a></code> 
+          <code><a href="search_crop.html">search_crop()</a></code> 
         </dt>
         <dd>Search for crop</dd>
       </dl><dl><dt>
@@ -251,7 +251,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Returns metrics currently supported in the analysis.</dd>
       </dl><dl><dt>
           
-          <code><a href="supported_sources.html">supported_sources()</a></code> <code><a href="supported_sources.html">supported_sources()</a></code> 
+          <code><a href="supported_sources.html">supported_sources()</a></code> 
         </dt>
         <dd>Get supported sources of crops</dd>
       </dl><dl><dt>
diff --git a/docs/reference/load_parameters.html b/docs/reference/load_parameters.html
index 90d9bd3..0bb395f 100644
--- a/docs/reference/load_parameters.html
+++ b/docs/reference/load_parameters.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/mapspam.html b/docs/reference/mapspam.html
index 8f5e7d1..50d8ed3 100644
--- a/docs/reference/mapspam.html
+++ b/docs/reference/mapspam.html
@@ -1,7 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Supported sources for Mapspam
-Supported sources for Mapspam"><title>Supported sources for Mapspam — mapspam • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Supported sources for Mapspam — mapspam"><meta property="og:description" content="Supported sources for Mapspam
-Supported sources for Mapspam"><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Supported sources for Mapspam"><title>Supported sources for Mapspam — mapspam • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Supported sources for Mapspam — mapspam"><meta property="og:description" content="Supported sources for Mapspam"><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -12,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -53,20 +51,17 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Supported sources for Mapspam</h1>
-      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/ccri_helper.R" class="external-link"><code>R/ccri_helper.R</code></a>, <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
       <div class="d-none name"><code>mapspam.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Supported sources for Mapspam</p>
-<p>Supported sources for Mapspam</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mapspam</span><span class="op">(</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">mapspam</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mapspam</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
     </div>
 
 
diff --git a/docs/reference/monfreda.html b/docs/reference/monfreda.html
index 42cf9cc..c7dffef 100644
--- a/docs/reference/monfreda.html
+++ b/docs/reference/monfreda.html
@@ -1,7 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Supported sources for monfreda
-Supported sources for monfreda"><title>Supported sources for monfreda — monfreda • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Supported sources for monfreda — monfreda"><meta property="og:description" content="Supported sources for monfreda
-Supported sources for monfreda"><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Supported sources for monfreda"><title>Supported sources for monfreda — monfreda • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Supported sources for monfreda — monfreda"><meta property="og:description" content="Supported sources for monfreda"><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -12,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -53,20 +51,17 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Supported sources for monfreda</h1>
-      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/ccri_helper.R" class="external-link"><code>R/ccri_helper.R</code></a>, <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
       <div class="d-none name"><code>monfreda.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Supported sources for monfreda</p>
-<p>Supported sources for monfreda</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">monfreda</span><span class="op">(</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">monfreda</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">monfreda</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
     </div>
 
 
diff --git a/docs/reference/nn_sum.html b/docs/reference/nn_sum.html
index 67b33e1..77ac43e 100644
--- a/docs/reference/nn_sum.html
+++ b/docs/reference/nn_sum.html
@@ -48,7 +48,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html
index ec1a78d..edde540 100644
--- a/docs/reference/pipe.html
+++ b/docs/reference/pipe.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/reset_params.html b/docs/reference/reset_params.html
index 7dec4ad..a69a0e2 100644
--- a/docs/reference/reset_params.html
+++ b/docs/reference/reset_params.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/reso.html b/docs/reference/reso.html
index 629b42f..1611ea4 100644
--- a/docs/reference/reso.html
+++ b/docs/reference/reso.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/risk_indices.html b/docs/reference/risk_indices.html
index c092caf..90a8f35 100644
--- a/docs/reference/risk_indices.html
+++ b/docs/reference/risk_indices.html
@@ -1,7 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Get risk indices from GeoRasters object.
-Get risk indices from GeoRasters object."><title>Get risk indices — risk_indices • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get risk indices — risk_indices"><meta property="og:description" content="Get risk indices from GeoRasters object.
-Get risk indices from GeoRasters object."><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Get risk indices from GeoRasters object."><title>Get risk indices — risk_indices • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get risk indices — risk_indices"><meta property="og:description" content="Get risk indices from GeoRasters object."><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -12,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -53,20 +51,17 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Get risk indices</h1>
-      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/ccri_helper.R" class="external-link"><code>R/ccri_helper.R</code></a>, <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
       <div class="d-none name"><code>risk_indices.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Get risk indices from GeoRasters object.</p>
-<p>Get risk indices from GeoRasters object.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">risk_indices</span><span class="op">(</span><span class="va">ri</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">risk_indices</span><span class="op">(</span><span class="va">ri</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">risk_indices</span><span class="op">(</span><span class="va">ri</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -79,11 +74,6 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>List of risk indices. If the <code>ri</code> is global, the list will contain two elements,
-one for each hemisphere. e.g. <code>list(east = list(), west = list())</code>. If the <code>ri</code> is not global,
-the list will contain a single element, e.g. <code><a href="https://rdrr.io/r/base/list.html" class="external-link">list()</a></code>.</p>
-
-
 <p>List of risk indices. If the <code>ri</code> is global, the list will contain two elements,
 one for each hemisphere. e.g. <code>list(east = list(), west = list())</code>. If the <code>ri</code> is not global,
 the list will contain a single element, e.g. <code><a href="https://rdrr.io/r/base/list.html" class="external-link">list()</a></code>.</p>
@@ -91,7 +81,6 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
     <p>This function will unpack SpatRasters from GeoMadel and thus is <code><a href="https://future.futureverse.org/reference/future.html" class="external-link">future::future()</a></code> safe.</p>
-<p>This function will unpack SpatRasters from GeoMadel and thus is <code><a href="https://future.futureverse.org/reference/future.html" class="external-link">future::future()</a></code> safe.</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/docs/reference/sa_onrasters.html b/docs/reference/sa_onrasters.html
index cffc7de..2b9fc79 100644
--- a/docs/reference/sa_onrasters.html
+++ b/docs/reference/sa_onrasters.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/scales.html b/docs/reference/scales.html
index 512babe..b893dbc 100644
--- a/docs/reference/scales.html
+++ b/docs/reference/scales.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/sean.html b/docs/reference/sean.html
index e08164d..b2c10cb 100644
--- a/docs/reference/sean.html
+++ b/docs/reference/sean.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/search_crop.html b/docs/reference/search_crop.html
index b7218c1..bf0dfb9 100644
--- a/docs/reference/search_crop.html
+++ b/docs/reference/search_crop.html
@@ -1,11 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="It returns the dataset sources in which crop data is available.
-It's a wrapper around geodata::spamCrops() and geodata::monfredaCrops()
-It returns the dataset sources in which crop data is available.
-It's a wrapper around geodata::spamCrops() and geodata::monfredaCrops()"><title>Search for crop — search_crop • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Search for crop — search_crop"><meta property="og:description" content="It returns the dataset sources in which crop data is available.
-It's a wrapper around geodata::spamCrops() and geodata::monfredaCrops()
-It returns the dataset sources in which crop data is available.
-It's a wrapper around geodata::spamCrops() and geodata::monfredaCrops()"><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+Essentially, a wrapper around geodata::spamCrops() and geodata::monfredaCrops()"><title>Search for crop — search_crop • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Search for crop — search_crop"><meta property="og:description" content="It returns the dataset sources in which crop data is available.
+Essentially, a wrapper around geodata::spamCrops() and geodata::monfredaCrops()"><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -16,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -57,22 +53,18 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Search for crop</h1>
-      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/ccri_helper.R" class="external-link"><code>R/ccri_helper.R</code></a>, <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
       <div class="d-none name"><code>search_crop.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>It returns the dataset sources in which crop data is available.
-It's a wrapper around <code><a href="https://rdrr.io/pkg/geodata/man/crop_spam.html" class="external-link">geodata::spamCrops()</a></code> and <code><a href="https://rdrr.io/pkg/geodata/man/crop_monfreda.html" class="external-link">geodata::monfredaCrops()</a></code></p>
-<p>It returns the dataset sources in which crop data is available.
-It's a wrapper around <code><a href="https://rdrr.io/pkg/geodata/man/crop_spam.html" class="external-link">geodata::spamCrops()</a></code> and <code><a href="https://rdrr.io/pkg/geodata/man/crop_monfreda.html" class="external-link">geodata::monfredaCrops()</a></code></p>
+Essentially, a wrapper around <code><a href="https://rdrr.io/pkg/geodata/man/crop_spam.html" class="external-link">geodata::spamCrops()</a></code> and <code><a href="https://rdrr.io/pkg/geodata/man/crop_monfreda.html" class="external-link">geodata::monfredaCrops()</a></code></p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">search_crop</span><span class="op">(</span><span class="va">name</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">search_crop</span><span class="op">(</span><span class="va">name</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">search_crop</span><span class="op">(</span><span class="va">name</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -85,15 +77,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>Logical. Sources iin crop data is available.</p>
-
-
 <p>Logical. Sources iin crop data is available.</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="supported_sources.html">supported_sources()</a></code></p>
-<p><code><a href="supported_sources.html">supported_sources()</a></code></p></div>
+    <div class="dont-index"><p><code><a href="supported_sources.html">supported_sources()</a></code></p></div>
     </div>
 
     <div class="section level2">
@@ -103,12 +91,6 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span><span class="co"># \donttest{</span></span>
 <span><span class="fu">search_crop</span><span class="op">(</span><span class="st">"jackfruit"</span><span class="op">)</span></span>
 <span><span class="co"># }</span></span>
-<span></span>
-<span><span class="fu">search_crop</span><span class="op">(</span><span class="st">"coffee"</span><span class="op">)</span></span>
-<span><span class="fu">search_crop</span><span class="op">(</span><span class="st">"wheat"</span><span class="op">)</span></span>
-<span><span class="co"># \donttest{</span></span>
-<span><span class="fu">search_crop</span><span class="op">(</span><span class="st">"jackfruit"</span><span class="op">)</span></span>
-<span><span class="co"># }</span></span>
 <span></span></code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/docs/reference/sensitivity_analysis.html b/docs/reference/sensitivity_analysis.html
index eb58393..0b8a21b 100644
--- a/docs/reference/sensitivity_analysis.html
+++ b/docs/reference/sensitivity_analysis.html
@@ -30,7 +30,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
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diff --git a/docs/reference/set_global_scales.html b/docs/reference/set_global_scales.html
index 65f39c3..44ed6dd 100644
--- a/docs/reference/set_global_scales.html
+++ b/docs/reference/set_global_scales.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
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diff --git a/docs/reference/set_parameters.html b/docs/reference/set_parameters.html
index 865d319..a8a74d5 100644
--- a/docs/reference/set_parameters.html
+++ b/docs/reference/set_parameters.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
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diff --git a/docs/reference/setmaps-Gmap-method.html b/docs/reference/setmaps-Gmap-method.html
index 24ee943..22b11b8 100644
--- a/docs/reference/setmaps-Gmap-method.html
+++ b/docs/reference/setmaps-Gmap-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/sp_rast.html b/docs/reference/sp_rast.html
index 93f06f2..8c798fd 100644
--- a/docs/reference/sp_rast.html
+++ b/docs/reference/sp_rast.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/supported_metrics.html b/docs/reference/supported_metrics.html
index d5744d8..c9d40c9 100644
--- a/docs/reference/supported_metrics.html
+++ b/docs/reference/supported_metrics.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/supported_sources.html b/docs/reference/supported_sources.html
index 95d6426..b6c7c91 100644
--- a/docs/reference/supported_sources.html
+++ b/docs/reference/supported_sources.html
@@ -1,10 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="When provided, cropharvest_rast() will
-look for cropland data in this specific source.
-When provided, cropharvest_rast() will
 look for cropland data in this specific source."><title>Get supported sources of crops — supported_sources • geohabnet</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get supported sources of crops — supported_sources"><meta property="og:description" content="When provided, cropharvest_rast() will
-look for cropland data in this specific source.
-When provided, cropharvest_rast() will
 look for cropland data in this specific source."><meta property="og:image" content="https://garrettlab.github.io/HabitatConnectivity/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -16,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -57,32 +53,24 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Get supported sources of crops</h1>
-      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/ccri_helper.R" class="external-link"><code>R/ccri_helper.R</code></a>, <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/GarrettLab/HabitatConnectivity/blob/HEAD/R/hci_helper.R" class="external-link"><code>R/hci_helper.R</code></a></small>
       <div class="d-none name"><code>supported_sources.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>When provided, <code><a href="cropharvest_rast.html">cropharvest_rast()</a></code> will
-look for cropland data in this specific source.</p>
-<p>When provided, <code><a href="cropharvest_rast.html">cropharvest_rast()</a></code> will
 look for cropland data in this specific source.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">supported_sources</span><span class="op">(</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">supported_sources</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">supported_sources</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>Vector of supported sources.
-Also used as a lookup to find get raster object.</p>
-
-
 <p>Vector of supported sources.
 Also used as a lookup to find get raster object.</p>
     </div>
@@ -90,8 +78,6 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># Get currently supported sources</span></span>
-<span><span class="fu">supported_sources</span><span class="op">(</span><span class="op">)</span></span>
-<span><span class="co"># Get currently supported sources</span></span>
 <span><span class="fu">supported_sources</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/docs/reference/tiff_torast.html b/docs/reference/tiff_torast.html
index a1a1d0c..b85a0e1 100644
--- a/docs/reference/tiff_torast.html
+++ b/docs/reference/tiff_torast.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">geohabnet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/search.json b/docs/search.json
index f66f81d..67a2f28 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"abstract","dir":"Articles","previous_headings":"","what":"Abstract","title":"Analyzing risk index using habitat connectivity","text":"network connectivity cropland can used analyse potential spread plant pathogen. network plays crucial role, several factors affects spread thus connectivity. Although croplands may geographically connected, risk generalized pathogen may spread ’s exclusive specific crop. (Keshav et al. 2023) supports 10 parameters potential impact risk connectivity among croplands. implementation expanded upon (Xing et al. 2020), discusses global cropland connectivity. framework uses default values paper time making parameters eventually turning framework analysis crops. Although article focused usage, useful know interested developers package design inspired widely used Configuration-based design software development (Majors 2022), (Nash DeMore 2009), (Allaire 2023) provides text based interface control parameters values risk analysis context. Primary objective vignette help user getting started, list capabilities intuition behind . also describes underlying implementation high level support intuition behind functions. Throughout article, citing external sites resources relevant usage package.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"definitions","dir":"Articles","previous_headings":"Pre-requisites","what":"Definitions","title":"Analyzing risk index using habitat connectivity","text":"Raster - Raster digital encoding 2D digital image underlying pixels underlying. also encapsulates details like resolution, dimensions etc useful identification processing. , use raster represent maps. TIFF(Tag Image File Format) file stores raster information.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"external-materials","dir":"Articles","previous_headings":"Pre-requisites","what":"External materials","title":"Analyzing risk index using habitat connectivity","text":"Download install R, R Studio - https://rstudio-education.github.io/hopr/starting.html/ Raster - https://www.adobe.com/creativecloud/file-types/image/raster.html TIFF - https://www.adobe.com/creativecloud/file-types/image/raster/tiff-file.html/","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"data-sets","dir":"Articles","previous_headings":"Pre-requisites","what":"Data sets","title":"Analyzing risk index using habitat connectivity","text":"use publicly available sources obtain crop information - Monfreda (Monfreda, Ramankutty, Foley 2008) MapSpam (2010, 2017) (International Food Policy Research Institute 2019) Geodata provides set APIs access data-sets. visualization plots, use rnaturalearth.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"meta-information","dir":"Articles","previous_headings":"Quick Start","what":"Meta information","title":"Analyzing risk index using habitat connectivity","text":"Package information - https://garrettlab.github.io/HabitatConnectivity/ CRAN site - https://CRAN.R-project.org/package=geohabnet Source code - https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/ Report issues - https://github.com/GarrettLab/CroplandConnectivity/issues/ Lab website - https://www.garrettlab.com/","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"installation-and-loading","dir":"Articles","previous_headings":"Quick Start","what":"Installation and loading","title":"Analyzing risk index using habitat connectivity","text":"Installing geohabnet also install dependencies. Please see list dependencies using desc::desc(package = \"geohabnet\") Alternatively, install github source. point, access help page using following -","code":"if (!require(\"devtools\")) {   install.packages(\"devtools\") } if (!require(\"geohabnet\")) {   utils::install.packages(\"geohabnet\") } library(\"devtools\") #> Loading required package: usethis  if (!require(\"geohabnet\")) {   install_github(\"GarrettLab/HabitatConnectivity\", subdir = \"geohabnet\") } #> Loading required package: geohabnet #> Warning in library(package, lib.loc = lib.loc, character.only = TRUE, #> logical.return = TRUE, : there is no package called 'geohabnet' #> Downloading GitHub repo GarrettLab/HabitatConnectivity@HEAD #> parallelly (1.37.0  -> 1.37.1) [CRAN] #> globals    (0.16.2  -> 0.16.3) [CRAN] #> digest     (0.6.33  -> 0.6.35) [CRAN] #> Rcpp       (1.0.11  -> 1.0.12) [CRAN] #> curl       (5.2.0   -> 5.2.1 ) [CRAN] #> vctrs      (0.6.3   -> 0.6.5 ) [CRAN] #> stringi    (1.7.12  -> 1.8.3 ) [CRAN] #> rlang      (1.1.1   -> 1.1.3 ) [CRAN] #> glue       (1.6.2   -> 1.7.0 ) [CRAN] #> cli        (3.6.1   -> 3.6.2 ) [CRAN] #> terra      (1.7-39  -> 1.7-71) [CRAN] #> data.table (1.15.0  -> 1.15.2) [CRAN] #> igraph     (2.0.1.1 -> 2.0.3 ) [CRAN] #> Installing 13 packages: parallelly, globals, digest, Rcpp, curl, vctrs, stringi, rlang, glue, cli, terra, data.table, igraph #> Installing packages into 'C:/Users/kkeshav/AppData/Local/Temp/Rtmp6Nnjmd/temp_libpath18786f31507e' #> (as 'lib' is unspecified) #> package 'parallelly' successfully unpacked and MD5 sums checked #> package 'globals' successfully unpacked and MD5 sums checked #> package 'digest' successfully unpacked and MD5 sums checked #> package 'Rcpp' successfully unpacked and MD5 sums checked #> package 'curl' successfully unpacked and MD5 sums checked #> package 'vctrs' successfully unpacked and MD5 sums checked #> package 'stringi' successfully unpacked and MD5 sums checked #> package 'rlang' successfully unpacked and MD5 sums checked #> package 'glue' successfully unpacked and MD5 sums checked #> package 'cli' successfully unpacked and MD5 sums checked #> package 'terra' successfully unpacked and MD5 sums checked #> package 'data.table' successfully unpacked and MD5 sums checked #> package 'igraph' successfully unpacked and MD5 sums checked #>  #> The downloaded binary packages are in #>  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpyEq013\\downloaded_packages #> 
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[39m #>         #>  #> Installing package into 'C:/Users/kkeshav/AppData/Local/Temp/Rtmp6Nnjmd/temp_libpath18786f31507e' #> (as 'lib' is unspecified) library(geohabnet) ?geohabnet # and ?geohabnet::msean # any function"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"run-analysis-on-default-configuration","dir":"Articles","previous_headings":"Quick Start","what":"Run analysis on default configuration","title":"Analyzing risk index using habitat connectivity","text":"run analysis default set values supported parameters. Initially, values set based Xing et al(2021) (Xing et al. 2020) crop Avocado. run workflow global geographical extent quickly since crop presence relatively low.    results side effects similar information captured object returned . based values set parameters see details sections.","code":"res <- sensitivity_analysis() #>  |---------|---------|---------|---------| ====== #>  |---------|---------|---------|---------| ========                                             |---------|---------|---------|---------| ============== #>  |---------|---------|---------|---------| ======"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"running-new-analysis","dir":"Articles","previous_headings":"Quick Start","what":"Running new analysis","title":"Analyzing risk index using habitat connectivity","text":"provide 2 methods entry points run analysis setting new values supported parameters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"setting-values-in-a-function","dir":"Articles","previous_headings":"Quick Start > Running new analysis","what":"Setting values in a function","title":"Analyzing risk index using habitat connectivity","text":"goal function provide simple invasive factors parameters. internal implementation program deals object terra (Hijmans 2023) igraph(Csardi Nepusz 2006) . primary object type SpatRaster terra . get started, use quick way obtain raster later understand details. effective way look-search_crop(). return sources contains data-set crop.  Now raster object, can fed directly workflow. set required parameter - rast. value represents Avocado plantation geographical area North America.    functions msean sean except msean side effects return different S4 objects, GeoNetwork GeoRasters respectively. use interchangeably article. results interpreted accordance values parameters factored arguments sean. Run ?sean see supported parameters. later see usage parameters well. rast - spatRaster. Represents map crop presence geographical area. geoscale - Vector. Geographical coordinates form c(Xmin, Xmax, Ymin, Ymax) global - Logical. set TRUE, geoscale ignored. Get geographical scales used global analysis - Although recommended change global scales since finalized several tries. Still, advance use, set global geographic scales using - thresholds - Numeric. 2 types thresholds: host density link weights represented hd_threshold link_threshold respectively. former threshold filters aggregation input data-set/raster latter filter cells adjacency matrix used calculate network connectivity. resolution - Numeric. resolution value. context SpatRaster, ’s number pixels aggregated produce new finer/coarser version raster data. Default Side effect - Calculates, produces plots maps sensitivity_analysis() [sensitivity_analysis()]. alternative sean() can called obtain results function call side effects.","code":"avocado <- cropharvest_rast(\"avocado\", \"monfreda\")  # verify the raster object avocado #> class       : SpatRaster  #> dimensions  : 2160, 4320, 1  (nrow, ncol, nlyr) #> resolution  : 0.08333333, 0.08333333  (x, y) #> extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326)  #> source      : avocado_HarvestedAreaFraction.tif  #> name        : avocado_HarvestedAreaFraction gplot(avocado) geo_net <- msean(avocado) #>  |---------|---------|---------|---------| ====== #>  |---------|---------|---------|---------| ==========                                             |---------|---------|---------|---------| ============== #>  |---------|---------|---------|---------| ====== global_scales() #> $east #> [1] -24 180 -58  60 #>  #> $west #> [1] -140  -34  -58   60 #set_global_scales(list(east = c(-24, 180, -58, 60), west = c(-140, -34, -58, 60))) reso() #> [1] 12"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"using-configuration","dir":"Articles","previous_headings":"Quick Start > Running new analysis","what":"Using configuration","title":"Analyzing risk index using habitat connectivity","text":"parameters available configuration thus control analysis. configuration file name parameters.yaml, currently supporting 10 parameters. intuition behind methodology provide basic interface setting new values. snippet describes basic usage configuration. Get initial configuration file. default function save file temporary directory tempdir(), however recommend saving path program write permissions. Using iwindow = TRUE prompt selection window save config file. file look something like - values must modified without modifying structure. order don’t matter program. new values configuration must fed workflow using - get_parameters() fetch initial parameters. can, required re-fetch parameters modified configuration. Modify value feed workflow using set_parameters().","code":"config_file <- get_parameters(out_path = tempdir()) config_file #> [1] \"C:\\\\Users\\\\kkeshav\\\\AppData\\\\Local\\\\Temp\\\\RtmpyEq013/parameters.yaml\" set_parameters(new_params = config_file) #> [1] TRUE #using iwindow = true will prompt a selction window to choose config file."},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"hosts","dir":"Articles","previous_headings":"Parameters","what":"Hosts","title":"Analyzing risk index using habitat connectivity","text":"helper functions make analysis easier. Available sources can seen using - specifically, support 2 data set sources - Monfreda Mapspam using APIs provided Geodata. sources crop presence geographical areas form raster(tiff). start , can check certain crop available source - #1 result suggests crop information available monfreda . Now, #2 suggests banana present 2 sources. use results obtain raster data one specified sources. returned actually type SpatRaster. , separate raster information crop. Crops can combined returned one raster. case banana, information sources first combined using mean crop information .e. banana avocado combined one raster. done produce single map contains information requested crops. one method obtain raster, using tiff - tiff_torast() . Finally, get_rasters() method, abstraction . see difference data generated last 3 methods -  result obtained one methods can used argument sean() . Value results list risk indices. Internally, cropharvest_rast() used fetch crop data-set ’s supported form. far, now run sensitivity analysis workflow avocado banana global scale default set parameter values. Alternatively, can just specify crops parameters.yaml run workflow -","code":"geohabnet::supported_sources() #> [1] \"monfreda\"          \"mapspam2010\"       \"mapspam2017Africa\" search_crop(\"avocado\") #1 #> [1] \"monfreda\" search_crop(\"bean\") #2 #> [1] \"monfreda\" \"spam\" # get avocado data rast_avocado <- crops_rast(list(monfreda = \"avocado\")) old_to <- options(\"timeout\") options(timeout = 6000)  #get data of banana crop rast_ban <- crops_rast(list(mapspam2010 = \"banana\")) # Back to back downloads causes connection to fail, this is a workaround rast_avo_ban <- crops_rast(list(monfreda = c(\"avocado\", \"banana\"), mapspam2010 = c(\"banana\"))) old_to <- options(old_to) gplot(c(rast_avocado, rast_ban, rast_avo_ban)) results <- lapply(list(rast_avocado, rast_avo_ban), msean) results <- sensitivity_analysis() #>  |---------|---------|---------|---------| ======= #>  |---------|---------|---------|---------| ========== #>  |---------|---------|---------|---------| ======="},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"thresholds","dir":"Articles","previous_headings":"Parameters","what":"Thresholds","title":"Analyzing risk index using habitat connectivity","text":"Thresholds used select subset values SpatRaster operations applied. directly effects connectivity gives sense sensitivity network. intermediate goal produce adjacency graph essentially determines connectivity. Cells doesn’t meet threshold removed consideration dispersal models.","code":"risk_indexes <- msean(avocado, global = FALSE, hd_threshold = 0.00001, link_threshold = 0.00001) #>  |---------|---------|---------|---------| ==== #>  |---------|---------|---------|---------| ===== #>  |---------|---------|---------|---------| ===="},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"density-thresholds","dir":"Articles","previous_headings":"Parameters > Thresholds","what":"Density Thresholds","title":"Analyzing risk index using habitat connectivity","text":"host density threshold. host density threshold minimum cropland proportion grid cells (locations) included analysis. parameter called HostDensityThreshold supports list values 0 1. running sensitivity_analysis() function, check values host density threshold smaller maximum host density map prevent errors. values rounded 5 decimal points.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"link-thresholds","dir":"Articles","previous_headings":"Parameters > Thresholds","what":"Link Thresholds","title":"Analyzing risk index using habitat connectivity","text":"Based information host distribution dispersal kernels, adjacency matrices created, entries likelihood pathogen movement locations. , adjacency matrices converted graph objects perform network analysis, entries adjacency matrices now weight links network. Choosing link weight thresholds helps focus analysis likely pathogen dispersal landscape. Like host density threshold, can provide list positive values LinkThreshold. running sensitivity_analysis() function, check values link weight threshold smaller maximum link weight network prevent errors.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"aggregation","dir":"Articles","previous_headings":"Parameters","what":"Aggregation","title":"Analyzing risk index using habitat connectivity","text":"Aggregation strategy refers function used create new map host density lower resolution (larger cells). Reducing spatial resolution helps reduce computational power needed run analysis. AggregationStrategy: [sum], sum cropland proportion initially small grids within large grid divided total number initially small grids within large grid. AggregationStrategy: [mean], sum cropland proportion initially small grids within large grid divided total number initially small grids containing land (small grids water excluded) within large grid. default, analysis run can opted one. one method used, difference map skipped outcome.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"distance-methods","dir":"Articles","previous_headings":"Parameters","what":"Distance methods","title":"Analyzing risk index using habitat connectivity","text":"pair locations host map values greater host density threshold, sensitivity_analysis() function calculate physical distances use calculate relative likelihood pathogen movement locations based pairwise geographical proximity. two different options calculate distance locations. · Vincenty ellipsoid distance option highly accurate computationally expensive. · Geodesic distance option less computationally expensive less accurate option . can set distance option either DistanceStrategy: “vincentyEllipsoid” DistanceStrategy: “geodesic”. One options used input run analysis. Check supported methods analysis running dist_methods() console.","code":"dist_methods() #> [1] \"geodesic\"          \"vincentyellipsoid\""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"resolution","dir":"Articles","previous_headings":"Parameters","what":"Resolution","title":"Analyzing risk index using habitat connectivity","text":"aggregation factor granularity number small grid cells aggregated larger grid cells direction (horizontally vertically). finest value 1 can require analysis run hours large number cells SpatRaster . resolution also used calculation variance dis-aggregating risk indices coarser resolution producing maps. provided, defaulted value selected reso()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"metrics","dir":"Articles","previous_headings":"Parameters","what":"Metrics","title":"Analyzing risk index using habitat connectivity","text":"See available metrics using Metrics corresponding dispersal models applied distance matrix specified weights. weights must specified % sum weights equal 100. use functions (Csardi Nepusz 2006) calculate metrics dispersal model. 2 dispersal models applied parameters inverse power law negative exponential. formally, metrics way determine connectivity among nodes network. graph functions (Csardi Nepusz 2006), links interpreted distances. However, context habitat connectivity, network adapted interpret links weights means likelihood pathogen spread lower distance larger.\\[ L = \\frac{1}{W}, \\\\ W' = \\sum_{=1}^{N} \\max(W - W_i) \\] L link weights W original weights undirected graph. W’ transformed weight vector calculating network centrality.","code":"supported_metrics() #> [1] \"betweeness\"               \"node_strength\"            #> [3] \"sum_of_nearest_neighbors\" \"eigenvector_centrality\"   #> [5] \"closeness\"                \"degree\"                   #> [7] \"page_rank\""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"geographical-extent","dir":"Articles","previous_headings":"Parameters","what":"Geographical Extent","title":"Analyzing risk index using habitat connectivity","text":"Geographical extent subset world map defined coordinate reference system. corresponding parameter set area sean() sensitivity_analyis() geoscale GeoExtent respectively. Default setting global = TRUE ignore value geoscale. consider taking world map account using values global_scales() . non-global analysis, either set global = FALSE without setting geoscale. default, geoscale extracted extents input SpatRaster. recommend using EPSG:4326 coordinate reference system functions tested . Using function  Using config Set Global = FALSE CustomExt = [-115, -75, 5, 32] . initial parameters.yaml already contains value run combination parameters. provided geoscale, program take subset provided raster (data-set crop). workflow apply graph operations network connectivity subset.","code":"results <- msean(avocado, global = FALSE, geoscale = c(-115, -75, 5, 32))"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"outputs","dir":"Articles","previous_headings":"","what":"Outputs","title":"Analyzing risk index using habitat connectivity","text":"default, 3 maps produced analysis. sean() also returns risk indices without maps can, fed connectivity() . flexibility supposed allow users use risk indices purposes use function produce maps different parameters. code , obtaining results, maps produced. order calculate variance, cells SpatRaster extended coarser value using res parameter. Setting maps = FALSE suppress calculation outputs. sean(avocado) + .connectivity(georast) equivalent sensitivity_analysis() msean() produces maps side effect. user function equivalent connectivity() accepts primitives types instead S4 class.    Based result obtained last cell, let’s navigate object final object. noticed maps side effect ’s really whole point. See result summary simply calling final object navigate using standard S4 classes approach. final operations performed risk indices 3 results produced - Mean mean SpatRasters resulting combination parameter values. values cells added across indices divided number indices. represents connectivity based host density given area. Navigating resulting object -  Variance Uses stats::var risk indices, subset extracted provided scale finally pixels dis-aggregated using factor = resolution value original parameter previous step.  Difference aggregation methods (sum mean) selected, difference calculated rank matrices essentially numeric cells risk indices type SpatRaster. result dis-aggregated way previous step.  path saved raster can accessed using ‘type_out’ slot. Additionally, access risk indices ’s corresponding adjacency accessible within slots GeoNetwork class. Checkout adjacency matrices running code - Set pmean, pvar, pdiff FALSE skip calculation connectivity() skip calculation. sean() sensitivity_analysis(), set map = FALSE skip generation maps outcome. case global analysis, result eastern western geographic extents merged using terra::merge() . outcome operation saved new directory plots specified path OutDir name opt_datetime.tif, opt one suffixed datetime file created. outdir empty, value defaulted tempdir() . applies corresponding parameter outdir functions.","code":"final <- msean(avocado, link_threshold = 0.000001, hd_threshold = 0.000025) #>  |---------|---------|---------|---------| ======= #>  |---------|---------|---------|---------| ========== #>  |---------|---------|---------|---------| ======= # checkout the type of an object class(final) #> [1] \"GeoNetwork\" #> attr(,\"package\") #> [1] \"geohabnet\" final #> class            :  GeoNetwork  #> host density     :  118 , 320  (nrow, ncol) SpatRaster  #> mean             :  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpyEq013/plots/mean_20240322135029696171.tif  #> mean raster      :  1416 , 3840  (nrow, ncol)  #> variance          :  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpyEq013/plots/variance_20240322135043271863.tif  #> variance raster   :  1416 , 3840  (nrow, ncol)  #> difference        :  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpyEq013/plots/difference_20240322135055407492.tif  #> difference raster :  1416 , 3840  (nrow, ncol) gplot(final@me_rast) gplot(final@var_rast) gplot(final@diff_rast) # checkout the results final@rasters #> class   :  GeoRasters  #> global  :  TRUE  #> globals :  1  # global is TRUE because we original set the global analysis # thus, we will have set of 2 risk indices, eastern and wetern hemisphere final@rasters$global_rast #> [[1]] #> class :  GlobalRast  #> east  :  14  #> west  :  14  # Number of elements from above determines the the number of parameter values provided  # To access the adjacency matrix, final@rasters$global_rast[[1]]$east[[1]] # this is also s4 class 'GeoModel' #> class            :  Model  #> adjacency matrix :  839 ,  839  (nrow, ncol)  #> risk index       :  ,   (nrow, ncol) # replace the indexing with any arbitary index, # uncomment line below to see the results.  #final@rasters$global_rast[[1]]$east[[1]]$amatrix"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"computing","dir":"Articles","previous_headings":"","what":"Computing","title":"Analyzing risk index using habitat connectivity","text":"understand motivation behind implementation, let’s analyze complexity. Since link host density threshold list, let size N. kernel models, let’s represent metrics dispersal coefficients x 4 reprectively. overall complexity turns \\(N \\cdot N \\cdot (7X + 7Y)\\) . , assumed availability host density. Although, crop data fetched parallel minimize download time. Considering \\(X = max(X, Y)\\) , complexity now \\(T = 7N^2 X^2 \\approx 7N^4\\). discount complexity graph operations like centrality scores haven’t attempted optimize operations. try optimize performance scaling fixed problem size, increasing parallelism. operations compute intensive. run_msean snippet Hosts used 8.3GB memory 81% memory allotted RStudio. part, implementation focused performance efficient memory usage. Package applies mechanisms vectorization foreach improve performance efficiency. workflow several parts running independently. independent functions performs operations adjacency matrix aggregation. created opportunity task level parallelism running functions within geohabnet. combination parameters can run independently parallel parts using future mechanism. implementation supports workflow acceleration using (Bengtsson 2021a, 2021b) . also important note use SpatRaster object throughout computation. SpatRaster external pointer C++ rather R object thus adds overhead conversion, neutralizing performance gains.","code":"avocado <- geohabnet::cropharvest_rast(\"avocado\", \"monfreda\")  # see ?future::plan for details future::plan(future::multicore()) msean(avocado)  future::plan(future::multisession()) msean(avocado)"},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/LinkWeightsAnalysis.html","id":"betweenness","dir":"Articles","previous_headings":"","what":"Betweenness","title":"Network centralities in GeoHabnet","text":"Getting host density Running Sensitivity Analysis    important note Betweenness centrality time intensive operation. Geohabnet uses wrapper around igraph::betweenness(). Refer (Csardi Nepusz 2006) details reading. cutoff parameter can used set threshold include link weights based threshold. Setting parameter also reflected closeness. configuration based run follows - get_parameters() -> modify values parameters.yaml -> set_parameters() -> run sensitivity_analysis()","code":"avocado_mon <- geohabnet::cropharvest_rast(\"potato\", \"monfreda\") avocado_result <- geohabnet::msean(avocado_mon, global = TRUE, link_threshold  = 0.000001,                                    inv_pl = list(beta = c(0.5),                                                  metrics = c(\"betweeness\"),                                                  weights = c(100),                                                  cutoff = -1), res = 24,                                    neg_exp = list(gamma = c(0.1),                                                   metrics = c(\"betweeness\"),                                                   weights = c(100), cutoff = -1)) ##  |---------|---------|---------|---------| === ##  |---------|---------|---------|---------| =====                                             |---------|---------|---------|---------| ======== ##  |---------|---------|---------|---------| ==="},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Krishna Keshav. Author, maintainer. Aaron Plex. Author. Garrett Lab. Contributor.            https://garrettlab.com Karen Garrett. Author. University Florida. Copyright holder, funder.            https://www.ufl.edu","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Keshav K, Plex , Garrett K (2024). geohabnet: Geographical Risk Analysis Based Habitat Connectivity. R package version 2.0.0,  https://CRAN.R-project.org/package=geohabnet/, https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/, https://www.garrettlab.com/, https://garrettlab.github.io/HabitatConnectivity/.","code":"@Manual{,   title = {geohabnet: Geographical Risk Analysis Based on Habitat Connectivity},   author = {Krishna Keshav and Aaron Plex and Karen Garrett},   year = {2024},   note = {R package version 2.0.0,  https://CRAN.R-project.org/package=geohabnet/, https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/, https://www.garrettlab.com/},   url = {https://garrettlab.github.io/HabitatConnectivity/}, }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/index.html","id":"geohabnet","dir":"","previous_headings":"","what":"Geographical Risk Analysis Based on Habitat Connectivity","title":"Geographical Risk Analysis Based on Habitat Connectivity","text":"package expands Xing et al (2021). adds capabilities customize parameter values using functions shows results habitat connectivity risk index form plots. goal geohabnet enable users visualize habitat connectivity risk index using parameter values. risk analysis outputs 3 maps - Mean habitat connectivity (based habitat connectivity index defined user) Difference habitat connectivity Variance habitat connectivity package currently supports crop maps sourced geodata::monfredaCrops() geodata::spamCrops(). analysis produces 3 maps listed . multiple ways functions can used - generate final outcome intermediate outcomes sophisticated use cases. vignettes provide several examples. output values propagated functions performing operations distance matrix calculation. values set parameters.yaml can accessed using get_parameters(). See usage .","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Geographical Risk Analysis Based on Habitat Connectivity","text":"Package can either installed CRAN: source version package can installed GitHub :","code":"install.packages(\"geohabnet\") #> Installing package into 'C:/Users/kkeshav/AppData/Local/Temp/Rtmp6Nnjmd/temp_libpath1878707c7a53' #> (as 'lib' is unspecified) #> package 'geohabnet' successfully unpacked and MD5 sums checked #>  #> The downloaded binary packages are in #>  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpSm8hLm\\downloaded_packages if (!require(\"devtools\")) {   install.packages(\"devtools\") }  devtools::install_github(\"GarrettLab/HabitatConnectivity\", subdir = \"geohabnet\")"},{"path":"https://garrettlab.github.io/HabitatConnectivity/index.html","id":"geohabnet-example","dir":"","previous_headings":"","what":"geohabnet Example","title":"Geographical Risk Analysis Based on Habitat Connectivity","text":"Run analysis using - parameters.yaml stores parameter values. can accessed set using get_parameters() set_parameters() respectively. default risk analysis run global index, scales present global_scales() . Refer help using ?geohabnet::fun help(geohabnet::fun) Refer article Analyzing risk index using cropland connectivity elaborate description usages functions package.","code":"library(geohabnet)  param_file <- geohabnet::get_parameters() # now edit the file geohabnet::set_parameters(new_params = param_file) geohabnet::senstivity_analysis()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate difference map — ccri_diff","title":"Calculate difference map — ccri_diff","text":"function produces map difference b/w mean sum indexes rank cropland harvested area fraction.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate difference map — ccri_diff","text":"","code":"ccri_diff(x, y, global, geoscale, res = reso(), outdir = tempdir())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate difference map — ccri_diff","text":"x SpatRaster. y SpatRaster. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. geoscale Numeric vector. x cropped extent. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate difference map — ccri_diff","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate difference map — ccri_diff","text":"Ideally, function tested yield desired results length((y[] > 0)) > length((x[] > 0)).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate mean of raster objects — ccri_mean","title":"Calculate mean of raster objects — ccri_mean","text":"Wrapper terra::mean(). Calculates mean list rasters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate mean of raster objects — ccri_mean","text":"","code":"ccri_mean(   indices,   global = FALSE,   east = NULL,   west = NULL,   geoscale = NULL,   res = reso(),   plt = TRUE,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate mean of raster objects — ccri_mean","text":"indices List SpatRasters. input represents spatial raster collection mean calculated. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). plt TRUE need plot mean map, FALSE otherwise. outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate mean of raster objects — ccri_mean","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate variance of CCRI — ccri_variance","title":"Calculate variance of CCRI — ccri_variance","text":"function produces map variance CCRI based input parameters","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate variance of CCRI — ccri_variance","text":"","code":"ccri_variance(   indices,   rast,   global,   east = NULL,   west = NULL,   geoscale,   res = reso(),   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate variance of CCRI — ccri_variance","text":"indices SpatRaster. Collection risk indices. rast SpatRaster. Template variance output global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate variance of CCRI — ccri_variance","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate and plot maps — connectivity","title":"Calculate and plot maps — connectivity","text":"Calculate mean, variance difference. result produced form maps plotted predefined settings. Currently, settings plot customized. Default value TRUE logical arguments","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate and plot maps — connectivity","text":"","code":"connectivity(   host,   indices,   global = FALSE,   east = NULL,   west = NULL,   geoscale = NULL,   res = reso(),   pmean = TRUE,   pvar = TRUE,   pdiff = TRUE,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate and plot maps — connectivity","text":"host SpatRaster. Host density map aka SpatRaster object indices SpatRaster. Collection risk indices. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). pmean Logical. TRUE map mean plotted, FALSE otherwise. pvar Logical. TRUE variance map plotted, FALSE otherwise. pdiff Logical. TRUE difference map plotted, FALSE otherwise. outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate and plot maps — connectivity","text":"Gmap. See details.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate and plot maps — connectivity","text":"indexes actually risk indices .e. lis spatRaster objects resulting operations crop's raster parameters provided either parameters.yaml sean(). save opted plots using - pmean, pvar pdiff. File saved provided value outdir  tempdir().interactive() TRUE, plots can seen active plot window. E.g. Rstudio. maps plotted using SpatRaster object. objects available return value function.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate and plot maps — connectivity","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Get raster object for crop — cropharvest_rast","title":"Get raster object for crop — cropharvest_rast","text":"Get cropland information form raster object data source crop","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get raster object for crop — cropharvest_rast","text":"","code":"cropharvest_rast(crop_name, data_source)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get raster object for crop — cropharvest_rast","text":"crop_name Name crop data_source Data source cropland information","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get raster object for crop — cropharvest_rast","text":"Raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get raster object for crop — cropharvest_rast","text":"","code":"# \\donttest{ cropharvest_rast(\"avocado\", \"monfreda\") # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Get sum of rasters for individual crops — crops_rast","title":"Get sum of rasters for individual crops — crops_rast","text":"Takes crop names returns raster object sum raster individual crops. Currently, supports crops listed geodata::monfredaCrops(), geodata::spamCrops() crop present multiple sources, mean calculated.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get sum of rasters for individual crops — crops_rast","text":"","code":"crops_rast(crop_names)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get sum of rasters for individual crops — crops_rast","text":"crop_names named list source along crop names","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get sum of rasters for individual crops — crops_rast","text":"SpatRaster. Raster object sum individual crop raster","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get sum of rasters for individual crops — crops_rast","text":"","code":"# \\donttest{ crops_rast(list(monfreda = c(\"wheat\", \"barley\"), mapspam2010 = c(\"wheat\", \"potato\"))) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":null,"dir":"Reference","previous_headings":"","what":"Dispersal kernels — inv_powerlaw","title":"Dispersal kernels — inv_powerlaw","text":"-[inv_powerlaw()] Get parameters values pertaining inverse power law model. -[neg_exp()] Get parameters values pertaining negative exponential model.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dispersal kernels — inv_powerlaw","text":"","code":"inv_powerlaw(   params = load_parameters(),   betas = NULL,   mets = NULL,   we = NULL,   linkcutoff = NULL )  neg_expo(   params = load_parameters(),   gammas = NULL,   mets = NULL,   we = NULL,   linkcutoff = NULL )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dispersal kernels — inv_powerlaw","text":"params Object.load_parameters() default. provided, function require parameters. takes precedence parameters. betas Numeric. Parameter calculating inverse power law. mets Character. metrics applied adjacency matrix produced intermediate step. Numeric link weights used network analysis. linkcutoff Numeric. Currently used parameter calculate centrality network. gammas Numeric. Parameter calculating negative exponential.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dispersal kernels — inv_powerlaw","text":"List parameters values. See details.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Dispersal kernels — inv_powerlaw","text":"list object following values used running analysis -beta Parameter calculating inverse power law. -gamma Parameter calculating negative exponential. -metrics metrics applied adjacency matrix produced intermediate step. -weights link weights used network analysis. -cutoff Currently used parameter calculate centrality network - betweeness() closeness(). defined igraph::betweenness(), maximum length consider calculating centrality. zero negative, limit.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Dispersal kernels — inv_powerlaw","text":"Csardi G, Nepusz T (2006). “igraph software package complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org. Csárdi G, Nepusz T, Traag V, Horvát Sz, Zanini F, Noom D, Müller K (2024). igraph: Network Analysis Visualization R. doi:10.5281/zenodo.7682609 , R package version 1.5.1, https://CRAN.R-project.org/package=igraph.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Distance methods supported — dist_methods","title":"Distance methods supported — dist_methods","text":"Contains supported strategies calculate distance two points. Use one methods sean() sensitivity_analysis(). Contains supported strategies calculate distance two points. Use one methods sean() sensitivity_analysis().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distance methods supported — dist_methods","text":"","code":"dist_methods()  dist_methods()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distance methods supported — dist_methods","text":"vector vector","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Distance methods supported — dist_methods","text":"","code":"dist_methods()  dist_methods()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function to extract risk indices from a list of crop rasters. — .indices","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"Internal function extract risk indices list crop rasters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"","code":".indices(crop_rasters)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"crop_rasters List raster objects.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"list risk indices.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geohabnet-package.html","id":null,"dir":"Reference","previous_headings":"","what":"geohabnet: Geographical Risk Analysis Based on Habitat Connectivity — geohabnet-package","title":"geohabnet: Geographical Risk Analysis Based on Habitat Connectivity — geohabnet-package","text":"geohabnet package designed perform geographically spatially explicit risk analysis habitat connectivity. Xing et al (2021) doi:10.1093/biosci/biaa067  proposed concept cropland connectivity risk factor plant pathogen pest invasions. functions geohabnet initially developed thinking cropland connectivity, users recommended first familiar concept looking Xing et al paper. nutshell, habitat connectivity analysis combines information maps host density, estimates relative likelihood pathogen movement habitat locations area interest, applies network analysis calculate connectivity habitat locations. functions geohabnet built conduct habitat connectivity analysis relying geographic parameters (spatial resolution spatial extent), dispersal parameters (two commonly used dispersal kernels: inverse power law negative exponential models), network parameters (link weight thresholds network metrics). functionality main extensions provided functions geohabnet habitat connectivity analysis ) Capability easily calculate connectivity locations landscape using single function, sensitivity_analysis() msean(). b) backbone datasets, geohabnet package supports use two publicly available global datasets calculate cropland density. backbone datasets geohabnet package include crop distribution maps Monfreda, C., N. Ramankutty, J. . Foley (2008) doi:10.1029/2007gb002947  \"Farming planet: 2. Geographic distribution crop areas, yields, physiological types, net primary production year 2000, Global Biogeochem. Cycles, 22, GB1022\" International Food Policy Research Institute (2019) doi:10.7910/DVN/PRFF8V  \"Global Spatially-Disaggregated Crop Production Statistics Data 2010 Version 2.0, Harvard Dataverse, V4\". Users can also provide geographic dataset represents host density. c) geohabnet package allows R users provide maps host density (originally Xing et al (2021)), host landscape density (representing geographic distribution either crops wild species), habitat distribution (host landscape density adjusted climate suitability) inputs, propose term habitat connectivity. d) geohabnet package allows R users customize parameter values habitat connectivity analysis, facilitating context-specific (pathogen- pest-specific) analyses. e) geohabnet package allows users automatically visualize maps habitat connectivity locations resulting sensitivity analysis across customized parameter combinations. primary function sean() sensitivity analysis(). functions geohabnet provide three main outcomes: ) map mean habitat connectivity across parameters selected user, ii) map variance habitat connectivity across selected parameters, iii) map difference ranks habitat connectivity habitat density. function can used generate maps 'final' outcomes. function can also provide intermediate outcomes, adjacency matrices built perform analysis, can used network analysis. Refer article https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html see examples function access outcome types. change parameter values, file called parameters.yaml stores parameters values, can accessed using get_parameters() set new parameter values set_parameters(). Users can modify ten parameters.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geohabnet-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"geohabnet: Geographical Risk Analysis Based on Habitat Connectivity — geohabnet-package","text":"Maintainer: Krishna Keshav kkeshav@ufl.edu Authors: Aaron Plex plexaaron@ufl.edu (ORCID) Karen Garrett karengarrett@ufl.edu (ORCID) contributors: Garrett Lab karengarrett@ufl.edu (https://garrettlab.com) [contributor] University Florida (https://www.ufl.edu) [copyright holder, funder]","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoModel-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GeoModel class — GeoModel-class","title":"GeoModel class — GeoModel-class","text":"ref class represent results dispersal models.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoModel-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"GeoModel class — GeoModel-class","text":"matrix adjacency matrix represent network.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GeoNetwork — GeoNetwork-class","title":"GeoNetwork — GeoNetwork-class","text":"S4 class representing network geographical data. wrap results risk analysis using sean() sensitivity_analysis(). class contains field Gmap class results form SpatRaster TIFF file.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GeoNetwork — GeoNetwork-class","text":"","code":"# S4 method for GeoNetwork host_density(x) <- value"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GeoNetwork — GeoNetwork-class","text":"x GeoNetwork. value SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GeoNetwork — GeoNetwork-class","text":"GeoNetwork.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"GeoNetwork — GeoNetwork-class","text":"rasters list GeoRasters objects. host_density SpatRaster representing host density. me_rast raster representing mean risk index. me_out Character. file path mean risk index raster. diff_rast raster representing difference. diff_out Character. file path difference raster. var_rast raster representing variance. var_out Character. file path variance raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoRasters-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GeoRaster class — GeoRasters-class","title":"GeoRaster class — GeoRasters-class","text":"class represent raster vis--vis risk indices. class encapsulates results apply dispersal models metrics.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoRasters-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"GeoRaster class — GeoRasters-class","text":"host_density SpatRaster. spatial raster representing host density. rasters List. List raster representing risk indices. type GeoModels. global Boolean. True contains GlobalRast object, False otherwise.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":null,"dir":"Reference","previous_headings":"","what":"Get geographical scales from the parameters — geoscale_param","title":"Get geographical scales from the parameters — geoscale_param","text":"function returns list geographical scales set global custom extent parameters.yaml. global TRUE, CustomExt ignored.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get geographical scales from the parameters — geoscale_param","text":"","code":"geoscale_param(gparams = load_parameters())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get geographical scales from the parameters — geoscale_param","text":"gparams Optional. load_parameters() null","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get geographical scales from the parameters — geoscale_param","text":"Vector. set geographical scales","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Parameters — get_parameters","title":"Get Parameters — get_parameters","text":"Retrieves parameters copies parameter file specified output path.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Parameters — get_parameters","text":"","code":"get_parameters(out_path = tempdir(), iwindow = FALSE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Parameters — get_parameters","text":"out_path character. output path parameter file copied. Default temporary directory tempdir() iwindow logical. TRUE, prompts user select output directory using file chooser window. Default FALSE","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Parameters — get_parameters","text":"character. path copied parameter file.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Parameters — get_parameters","text":"Using configuration file alternative sean()","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Parameters — get_parameters","text":"","code":"get_parameters() get_parameters(out = tempdir())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":null,"dir":"Reference","previous_headings":"","what":"Get rasters object from parameters — get_rasters","title":"Get rasters object from parameters — get_rasters","text":"Takes named list hosts input. See host object get_parameters() load_parameters(). also wrapper crops_rast(). Function creates 2 raster object - one sum crops specified sources using provided raster file. See tiff_torast()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get rasters object from parameters — get_rasters","text":"","code":"get_rasters(hosts)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get rasters object from parameters — get_rasters","text":"hosts List hosts values. synonym Hosts object parameters","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get rasters object from parameters — get_rasters","text":"List SpatRaster.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get rasters object from parameters — get_rasters","text":"","code":"# Get default rasters if (FALSE) { get_rasters(list(mapspam2010 = c(\"wheat\"), monfreda = c(\"avocado\"), file = \"some_raster.tif\")) }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GlobalRast-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GlobalRast class — GlobalRast-class","title":"GlobalRast class — GlobalRast-class","text":"class represent raster global scales. Global scales accessible using global_scales(). However, class encapsulates results apply dispersal models metrics.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GlobalRast-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"GlobalRast class — GlobalRast-class","text":"east list raster eastern hemisphere. west list raster western hemisphere.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":null,"dir":"Reference","previous_headings":"","what":"Global geographical extent — global_scales","title":"Global geographical extent — global_scales","text":"See geographical extents used global analysis. Returns eastern western hemisphere extents. extent form c(Xmin, Xmax, Ymin, Ymax).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Global geographical extent — global_scales","text":"","code":"global_scales()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Global geographical extent — global_scales","text":"List. Named list scales eastern western hemisphere","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Global geographical extent — global_scales","text":"Seperate analysis geographical scales eastern western hemisphere combined run global analysis.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Gmap class — Gmap-class","title":"Gmap class — Gmap-class","text":"S4 class represent various maps form SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gmap class — Gmap-class","text":"","code":"setmaps(x, me, vari, dif)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gmap class — Gmap-class","text":"x Gmap object. SpatRaster. raster representing mean risk index. vari SpatRaster. raster representing variance. dif SpatRaster. raster representing difference.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gmap class — Gmap-class","text":"Gmap object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Gmap class — Gmap-class","text":"me_rast raster representing mean risk index. me_out Character. file path mean risk index raster. diff_rast raster representing difference. diff_out Character. file path difference raster. var_rast raster representing variance. var_out Character. file path variance raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot a Raster* object — gplot","title":"Plot a Raster* object — gplot","text":"wrapper terra::plot()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot a Raster* object — gplot","text":"","code":"gplot(x, ...)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot a Raster* object — gplot","text":"x Raster* object ... additional arguments passed terra::plot()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot a Raster* object — gplot","text":"plot","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot a Raster* object — gplot","text":"","code":"r <- terra::rast(nrows=108, ncols=21, xmin=0, xmax=10) gplot(r) gplot(r, col = \"red\") gplot(r, col = \"red\", breaks = 10)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate difference map — hci_diff","title":"Calculate difference map — hci_diff","text":"function produces map difference b/w mean sum indexes rank cropland harvested area fraction.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate difference map — hci_diff","text":"","code":"hci_diff(x, y, global, geoscale, res = reso(), outdir = tempdir())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate difference map — hci_diff","text":"x SpatRaster. y SpatRaster. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. geoscale Numeric vector. x cropped extent. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate difference map — hci_diff","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate difference map — hci_diff","text":"Ideally, function tested yield desired results length((y[] > 0)) > length((x[] > 0)).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate mean of raster objects — hci_mean","title":"Calculate mean of raster objects — hci_mean","text":"Wrapper terra::mean(). Calculates mean list rasters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate mean of raster objects — hci_mean","text":"","code":"hci_mean(   indices,   global = FALSE,   east = NULL,   west = NULL,   geoscale = NULL,   res = reso(),   plt = TRUE,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate mean of raster objects — hci_mean","text":"indices List SpatRasters. input represents spatial raster collection mean calculated. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). plt TRUE need plot mean map, FALSE otherwise. outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate mean of raster objects — hci_mean","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate variance of CCRI — hci_variance","title":"Calculate variance of CCRI — hci_variance","text":"function produces map variance CCRI based input parameters","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate variance of CCRI — hci_variance","text":"","code":"hci_variance(   indices,   rast,   global,   east = NULL,   west = NULL,   geoscale,   res = reso(),   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate variance of CCRI — hci_variance","text":"indices SpatRaster. Collection risk indices. rast SpatRaster. Template variance output global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate variance of CCRI — hci_variance","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/host_density-set.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the host density. — host_density<-","title":"Set the host density. — host_density<-","text":"Sets host density slot GeoNetwork object","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/host_density-set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the host density. — host_density<-","text":"","code":"host_density(x) <- value"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/host_density-set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the host density. — host_density<-","text":"x GeoNetwork object. value SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Load Parameters from YAML File — load_parameters","title":"Load Parameters from YAML File — load_parameters","text":"function loads parameters YAML file stores object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load Parameters from YAML File — load_parameters","text":"","code":"load_parameters(filepath = .param_fp())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load Parameters from YAML File — load_parameters","text":"filepath Path YAML file containing parameters. default, takes value parameters.yaml R user's directory.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load Parameters from YAML File — load_parameters","text":"object parameters values","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load Parameters from YAML File — load_parameters","text":"","code":"# Load parameters from default file load_parameters()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/mapspam.html","id":null,"dir":"Reference","previous_headings":"","what":"Supported sources for Mapspam — mapspam","title":"Supported sources for Mapspam — mapspam","text":"Supported sources Mapspam Supported sources Mapspam","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/mapspam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supported sources for Mapspam — mapspam","text":"","code":"mapspam()  mapspam()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/monfreda.html","id":null,"dir":"Reference","previous_headings":"","what":"Supported sources for monfreda — monfreda","title":"Supported sources for monfreda — monfreda","text":"Supported sources monfreda Supported sources monfreda","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/monfreda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supported sources for monfreda — monfreda","text":"","code":"monfreda()  monfreda()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculation on network metrics a.k.a centralities. — nn_sum","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"functions igraph package adapted calculate habitat connectivity. context habitat connectivity, functions can interpreted follows: [nn_sum()]: Calculates sum nearest neighbors igraph::graph.knn(). [node_strength()]: Calculates sum edge weights adjacent nodes igraph::graph.strength(). [betweeness()]: Calculates node betweenness based number shortest paths. igraph::betweenness() function igraph interprets link weights distances calculate shortest paths, betweenness() function geohabnet transforms link weights (relative likelihood pathogen pest movement) adjacency matrix higher link weight values shortest (likely) paths pathogen pest movement. [ev()]: Calculates eigenvector centrality positions within network igraph::evcent(). [closeness()]: measures many steps required access every vertex given vertex igraph::closeness(). igraph::closeness() function igraph interprets link weights distances calculate shortest paths, closeness() function geohabnet transforms link weights (relative likelihood pathogen pest movement) adjacency matrix higher link weight values shortest (likely) paths pathogen pest movement. [degree()]: number adjacent edges igraph::degree(). [pagerank()]: page rank score vertices igraph::page_rank().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"","code":"nn_sum(crop_dm, ...)  node_strength(crop_dm, ...)  betweeness(crop_dm, ...)  ev(crop_dm, ...)  degree(crop_dm, ...)  closeness(crop_dm, ...)  pagerank(crop_dm, ...)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"crop_dm square adjacency matrix, rows columns names represent nodes (locations) entry indicate relative likelihood pathogen pest movement pair nodes. internal workflow, adjacency matrix comes result operations within sean() function. weight represents importance network metric habitat connectivity analysis. ... arguments corresponding igraph fun","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"SpatRaster. Representing connectivity node location.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset parameters.yaml — reset_params","title":"Reset parameters.yaml — reset_params","text":"Resets values parameters.yaml file default initial values.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset parameters.yaml — reset_params","text":"","code":"reset_params()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset parameters.yaml — reset_params","text":"Logical. TRUE function successfully executed","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reset parameters.yaml — reset_params","text":"","code":"reset_params()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reso.html","id":null,"dir":"Reference","previous_headings":"","what":"Get resolution value — reso","title":"Get resolution value — reso","text":"Resolution stored parameter.yaml. present result default value.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reso.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get resolution value — reso","text":"","code":"reso()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reso.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get resolution value — reso","text":"Numeric. Resolution parameters.yaml. Default 24.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/RiskMap-class.html","id":null,"dir":"Reference","previous_headings":"","what":"RiskMap class — RiskMap-class","title":"RiskMap class — RiskMap-class","text":"S4 class representing resulting maps specific operation type.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/RiskMap-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"RiskMap class — RiskMap-class","text":"map Character. file path map. riid SpatRaster. one risk maps. spr SpatRaster. spatial raster representing risk index. fp Character. file path risk index raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get risk indices — risk_indices","title":"Get risk indices — risk_indices","text":"Get risk indices GeoRasters object. Get risk indices GeoRasters object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get risk indices — risk_indices","text":"","code":"risk_indices(ri)  risk_indices(ri)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get risk indices — risk_indices","text":"ri GeoRasters object","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get risk indices — risk_indices","text":"List risk indices. ri global, list contain two elements, one hemisphere. e.g. list(east = list(), west = list()). ri global, list contain single element, e.g. list(). List risk indices. ri global, list contain two elements, one hemisphere. e.g. list(east = list(), west = list()). ri global, list contain single element, e.g. list().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get risk indices — risk_indices","text":"function unpack SpatRasters GeoMadel thus future::future() safe. function unpack SpatRasters GeoMadel thus future::future() safe.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":null,"dir":"Reference","previous_headings":"","what":"Run sensitivity analysis — sa_onrasters","title":"Run sensitivity analysis — sa_onrasters","text":"sensitivity_analysis() takes raster object parameters input. sa_onrasters() wrapper around sean() function. Takes raster object parameters input. msean_onrast() sa_onrasters(). Use side effects + results. Produces plots maps outcomes results returned object. produces plots maps outcomes results returned object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run sensitivity analysis — sa_onrasters","text":"","code":"sa_onrasters(rast, link_thresholds = c(0), hd_thresholds = c(0), ...)  msean_onrast(   global = TRUE,   geoscale = NULL,   res = reso(),   outdir = tempdir(),   ... )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run sensitivity analysis — sa_onrasters","text":"rast Raster object used analysis. link_thresholds Numeric vector. link threshold values hd_thresholds Numeric vector. host density threshold values ... Additional parameters passed sean(). global Logical. TRUE global analysis, FALSE otherwise. Default TRUE geoscale Numeric vector. Geographical coordinates form c(Xmin, Xmax, Ymin, Ymax) EPSG:4326 coordinate reference system. geoscale NuLL, extent extracted rast(SpatRaster) using terra::ext(). res Numeric. Resolution raster. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run sensitivity analysis — sa_onrasters","text":"list calculated CCRI indices operations. index generated combination paramters. One combination equivalent sean() function.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Run sensitivity analysis — sa_onrasters","text":"Error handled non-overlapping extents.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Run sensitivity analysis — sa_onrasters","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run sensitivity analysis — sa_onrasters","text":"","code":"# \\donttest{ rr <- get_rasters(list(monfreda = c(\"avocado\"))) res1 <- sa_onrasters(rr[[1]],             global = FALSE,             geoscale = c(-115, -75, 5, 32),             c(0.0001, 0.00004),             c(0.0001, 0.00005),             c(\"sum\", \"mean\"),             res = 12) res2 <- sa_onrasters(rr[[1]],             global = TRUE,             link_thresholds = c(0.000001),             hd_thresholds = c(0.00015),             agg_methods = c(\"sum\"),             res = 12) res3 <- msean_onrast(rast = rr[[1]],           link_thresholds = c(0.000001),           hd_thresholds = c(0.00015)) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/scales.html","id":null,"dir":"Reference","previous_headings":"","what":"Only meant to global variables — scales","title":"Only meant to global variables — scales","text":"meant global variables","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/scales.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Only meant to global variables — scales","text":"","code":"scales"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/scales.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Only meant to global variables — scales","text":"object class environment length 2.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":null,"dir":"Reference","previous_headings":"","what":"Sensitivity analysis across maps of habitat connectivity — sean","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"function performs sensitivity analysis across different values habitat connectivity location map. combination selected parameters, index habitat connectivity calculated. sensitivity_analysis() wrapper around sean() function. msean() wrapper around sean() function. additional argument specify maps calculated using connectivity() function. maps essentially risk network.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"","code":"sean(   rast,   global = TRUE,   geoscale = NULL,   agg_methods = c(\"sum\", \"mean\"),   dist_method = \"geodesic\",   link_threshold = 0,   hd_threshold = 0,   res = reso(),   inv_pl = inv_powerlaw(NULL, betas = c(0.5, 1, 1.5), mets = c(\"betweeness\",     \"NODE_STRENGTH\", \"Sum_of_nearest_neighbors\", \"eigenVector_centrAlitY\"), we = c(50,     15, 15, 20), linkcutoff = -1),   neg_exp = neg_expo(NULL, gammas = c(0.05, 1, 0.2, 0.3), mets = c(\"betweeness\",     \"NODE_STRENGTH\", \"Sum_of_nearest_neighbors\", \"eigenVector_centrAlitY\"), we = c(50,     15, 15, 20), linkcutoff = -1) )  msean(   rast,   global = TRUE,   geoscale = NULL,   res = reso(),   ...,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"rast Raster object used analysis. global Logical. TRUE global analysis, FALSE otherwise. Default TRUE geoscale Numeric vector. Geographical coordinates form c(Xmin, Xmax, Ymin, Ymax) EPSG:4326 coordinate reference system. geoscale NuLL, extent extracted rast(SpatRaster) using terra::ext(). agg_methods Character. One values - SUM, MEAN. Aggregation strategy scaling input raster desired resolution. dist_method Character. method calculate distance matrix. link_threshold Numeric. threshold value link weight. link weights threshold replaced zero connectivity analysis. Link weights represent relative likelihood pathogen, pest, invasive species movement pair host locations, calculated using gravity models based host density (availability) dispersal kernels. hd_threshold Numeric. threshold value host density. locations host density selected threshold excluded connectivity analysis, focuses analysis important locations. values host density threshold can range 0 1; value 1, locations excluded analysis 0 include locations analysis. Selecting threshold host density requires least knowing maximum value host density map avoid excluding locations analysis. value 1, locations excluded analysis 0 include locations analysis. Selecting threshold host density requires least knowing maximum value host density map avoid excluding locations analysis. res Numeric. Resolution raster. Default reso(). inv_pl List. named list parameters inverse power law. See details. neg_exp List. named list parameters inverse negative exponential. See details. locations host density selected threshold excluded connectivity analysis, focuses analysis important locations. values host density threshold can range 0 1; ... arguments passed sean() outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"GeoRasters. GeoNetwork.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"global = TRUE, geoscale ignored global_scales() used default. functions sean() msean() perform sensitivity analysis, differ return value. return value msean() GeoNetwork, contains result applying connectivity() function habitat connectivity indexes. Essentially, risk maps. neither inverse power law negative exponential dispersal kernel specified, function return error. msean(), three spatRasters produced following values. location area interest, mean habitat connectivity across selected parameters calculated. location area interest, variance habitat connectivity across selected parameters calculated. location area interest, difference rank habitat connectivity rank host density calculated. default, spatRasters plotted visualization.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"","code":"# \\donttest{ avocado <- cropharvest_rast(\"avocado\", \"monfreda\")  # global ri <- sean(avocado) # returns a list of GeoRasters mri <- msean(rast = avocado) # returns GeoNetwork object  # non-global # geoscale is a vector of xmin, xmax, ymin, ymax  # returns GeoRasters object ri <- sean(avocado, global = FALSE, geoscale = c(-115, -75, 5, 32)) ri  # returns GeoNetwork object mri <- msean(rast = avocado, global = FALSE, geoscale = c(-115, -75, 5, 32)) mri # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":null,"dir":"Reference","previous_headings":"","what":"Search for crop — search_crop","title":"Search for crop — search_crop","text":"returns dataset sources crop data available. wrapper around geodata::spamCrops() geodata::monfredaCrops() returns dataset sources crop data available. wrapper around geodata::spamCrops() geodata::monfredaCrops()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search for crop — search_crop","text":"","code":"search_crop(name)  search_crop(name)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search for crop — search_crop","text":"name name crop","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search for crop — search_crop","text":"Logical. Sources iin crop data available. Logical. Sources iin crop data available.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search for crop — search_crop","text":"","code":"search_crop(\"coffee\") search_crop(\"wheat\") # \\donttest{ search_crop(\"jackfruit\") # }  search_crop(\"coffee\") search_crop(\"wheat\") # \\donttest{ search_crop(\"jackfruit\") # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"function runs sensitivity analysis habitat connectivity calculated based every combination selected parameters. Parameter values sensitivity_analysis() provided using function set_parameters(). parameters provided, sensitivity_analysis() function run sensitivity analysis using default set parameter values, accessible function get_parameters(). customize parameter values, open parameters.yaml automatically downloaded geohabnet installed, change, remove, add parameter values directly parameters.yaml save . values changed manually, run set_parameters() set new parameter values, return TRUE parameters set successfully.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"","code":"sensitivity_analysis(maps = TRUE, alert = TRUE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"maps logical. TRUE maps outcomes plotted, FALSE otherwise. TRUE, three maps possible: map mean habitat connectivity, map variance habitat connectivity, map difference ranks habitat connectivity habitat density. alert logical. TRUE beep sound played analysis completed, FALSE otherwise","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"GeoNetwork. Errors handled.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"location region, sensitivity_analysis() calculates habitat connectivity risk index (CCRI) proposed Xing et al. (2021). default, sensitivity_analysis() runs sensitivity analysis global extent, see global_scales() details. function also plots maps outcomes automatically, suppress maps outcomes maps = FALSE interactive() FALSE. returned object class GeoNetwork, contains two types outcomes. One outcome type corresponds spatRasters representing maps habitat connectivity. second type corresponds adjacency matrices used calculate habitat connectivity, columns rows represent locations maps entries relative likelihood pathogen pest movement pair nodes.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"","code":"# \\donttest{ # Run analysis on specified parameters.yaml ss1 <- sensitivity_analysis() ss2 <- sensitivity_analysis(FALSE, FALSE) ss3 <- sensitivity_analysis(TRUE, FALSE) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"wraps results(SpatRasters) risk analysis.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"","code":"# S4 method for Gmap setmaps(x, me, vari, dif)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"x Gmap object. GeoRaster object representing mean risk index. vari GeoRaster object representing variance. dif GeoRaster object representing difference.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"Gmap object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":null,"dir":"Reference","previous_headings":"","what":"Set global geographical extent — set_global_scales","title":"Set global geographical extent — set_global_scales","text":"Set geographical extents used global analysis. extent form c(Xmin, Xmax, Ymin, Ymax)","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set global geographical extent — set_global_scales","text":"","code":"set_global_scales(value)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set global geographical extent — set_global_scales","text":"value list. Named list eastern western hemisphere extents. See usage.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set global geographical extent — set_global_scales","text":"List. Named list scales eastern western hemisphere","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set global geographical extent — set_global_scales","text":"","code":"set_global_scales(list(east = c(-24, 180, -58, 60), west = c(-140, -34, -58, 60)))"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Parameters — set_parameters","title":"Set Parameters — set_parameters","text":"function allows set parameters replacing existing parameters file new one. Use get_parameters() modify parameter values.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Parameters — set_parameters","text":"","code":"set_parameters(new_params, iwindow = FALSE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Parameters — set_parameters","text":"new_params path new parameters file. iwindow Logical indicating whether prompt user select new parameters file using file selection window. Defaults FALSE.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Parameters — set_parameters","text":"None","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Parameters — set_parameters","text":"","code":"param_fp <- get_parameters() set_parameters(param_fp)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Raster for mapspam crop. — sp_rast","title":"Raster for mapspam crop. — sp_rast","text":"get raster crop mapspam dataset","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raster for mapspam crop. — sp_rast","text":"","code":"sp_rast(crp, africa = FALSE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raster for mapspam crop. — sp_rast","text":"crp character. name crop. Case-insensitive. africa Fetch 2017 Mpaspam crop data Africa. Default FALSE.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Raster for mapspam crop. — sp_rast","text":"SpatRaster","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Raster for mapspam crop. — sp_rast","text":"See geodata::spamCrops() supported crops.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Raster for mapspam crop. — sp_rast","text":"International Food Policy Research Institute, 2020. Spatially-Disaggregated Crop Production Statistics Data Africa South Sahara 2017. <doi: 10.7910/DVN/FSSKBW>, Harvard Dataverse, V2","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Raster for mapspam crop. — sp_rast","text":"","code":"# \\donttest{ sp_rast(\"potato\") sp_rast(\"potato\", TRUE) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_BETWEENNESS.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","title":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_BETWEENNESS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","text":"","code":"STR_BETWEENNESS"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_BETWEENNESS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_CLOSENESS_CENTRALITY.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","title":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_CLOSENESS_CENTRALITY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","text":"","code":"STR_CLOSENESS_CENTRALITY"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_CLOSENESS_CENTRALITY.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DEGREE.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_DEGREE","title":"global variable containing string. Not intended to modify. — STR_DEGREE","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DEGREE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_DEGREE","text":"","code":"STR_DEGREE"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DEGREE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_DEGREE","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DISTANCE_MATRIX.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","title":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DISTANCE_MATRIX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","text":"","code":"STR_DISTANCE_MATRIX"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DISTANCE_MATRIX.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EAST.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_EAST","title":"global variable containing string. Not intended to modify. — STR_EAST","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EAST.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_EAST","text":"","code":"STR_EAST"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EAST.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_EAST","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EIGEN_VECTOR_CENTRALITY.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","title":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EIGEN_VECTOR_CENTRALITY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","text":"","code":"STR_EIGEN_VECTOR_CENTRALITY"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EIGEN_VECTOR_CENTRALITY.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NEAREST_NEIGHBORS_SUM.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","title":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NEAREST_NEIGHBORS_SUM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","text":"","code":"STR_NEAREST_NEIGHBORS_SUM"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NEAREST_NEIGHBORS_SUM.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NODE_STRENGTH.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","title":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NODE_STRENGTH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","text":"","code":"STR_NODE_STRENGTH"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NODE_STRENGTH.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_PAGE_RANK.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","title":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_PAGE_RANK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","text":"","code":"STR_PAGE_RANK"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_PAGE_RANK.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_WEST.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_WEST","title":"global variable containing string. Not intended to modify. — STR_WEST","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_WEST.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_WEST","text":"","code":"STR_WEST"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_WEST.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_WEST","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns metrics currently supported in the analysis. — supported_metrics","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"Returns metrics currently supported analysis.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"","code":"supported_metrics()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"vector supported metrics.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"","code":"supported_metrics()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":null,"dir":"Reference","previous_headings":"","what":"Get supported sources of crops — supported_sources","title":"Get supported sources of crops — supported_sources","text":"provided, cropharvest_rast() look cropland data specific source. provided, cropharvest_rast() look cropland data specific source.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get supported sources of crops — supported_sources","text":"","code":"supported_sources()  supported_sources()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get supported sources of crops — supported_sources","text":"Vector supported sources. Also used lookup find get raster object. Vector supported sources. Also used lookup find get raster object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get supported sources of crops — supported_sources","text":"","code":"# Get currently supported sources supported_sources() # Get currently supported sources supported_sources()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":null,"dir":"Reference","previous_headings":"","what":"Get raster object from tif file — tiff_torast","title":"Get raster object from tif file — tiff_torast","text":"wrapper terra::rast() generates raster object provided TIF file.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get raster object from tif file — tiff_torast","text":"","code":"tiff_torast(path_to_tif)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get raster object from tif file — tiff_torast","text":"path_to_tif TIFF file. encoding map raster format.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get raster object from tif file — tiff_torast","text":"SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get raster object from tif file — tiff_torast","text":"","code":"# \\donttest{ # Generate raster for usage fp <- paste(tempfile(), \".tif\", sep = \"\") ret <- utils::download.file( \"https://geohabnet.s3.us-east-2.amazonaws.com/util-rasters/avocado_HarvestedAreaFraction.tif\", destfile = fp, method = \"auto\", mode = \"wb\") tiff_torast(fp) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-200","dir":"Changelog","previous_headings":"","what":"geohabnet 2.0.0","title":"geohabnet 2.0.0","text":"CRAN release: 2024-02-27 Adoption habitat connectivity Corrected difference map Added support mapspam 2010 2017 Africa data Corrected weight transformation closeness betweenness Removed global variables Fixed bugs New functions - msean() New parameters Returning objects S4 classes sensitivity_analysis() include Adjacency matrix Supports parallel processing future package functions support risk parameters New/updated vignette New/updated examples New tests New/updated documentation","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-101","dir":"Changelog","previous_headings":"","what":"geohabnet 1.0.1","title":"geohabnet 1.0.1","text":"CRAN release: 2023-10-31","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-100","dir":"Changelog","previous_headings":"","what":"geohabnet 1.0.0","title":"geohabnet 1.0.0","text":"CRAN release: 2023-10-20","code":""},{"path":[]},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-0009000","dir":"Changelog","previous_headings":"","what":"geohabnet 0.0.0.9000","title":"geohabnet 0.0.0.9000","text":"Added NEWS.md file track changes package.","code":""}]
+[{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"abstract","dir":"Articles","previous_headings":"","what":"Abstract","title":"Analyzing risk index using habitat connectivity","text":"network connectivity cropland can used analyse potential spread plant pathogen. network plays crucial role, several factors affects spread thus connectivity. Although croplands may geographically connected, risk generalized pathogen may spread ’s exclusive specific crop. (Keshav et al. 2023) supports 10 parameters potential impact risk connectivity among croplands. implementation expanded upon (Xing et al. 2020), discusses global cropland connectivity. framework uses default values paper time making parameters eventually turning framework analysis crops. Although article focused usage, useful know interested developers package design inspired widely used Configuration-based design software development (Majors 2022), (Nash DeMore 2009), (Allaire 2023) provides text based interface control parameters values risk analysis context. Primary objective vignette help user getting started, list capabilities intuition behind . also describes underlying implementation high level support intuition behind functions. Throughout article, citing external sites resources relevant usage package.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"definitions","dir":"Articles","previous_headings":"Pre-requisites","what":"Definitions","title":"Analyzing risk index using habitat connectivity","text":"Raster - Raster digital encoding 2D digital image underlying pixels underlying. also encapsulates details like resolution, dimensions etc useful identification processing. , use raster represent maps. TIFF(Tag Image File Format) file stores raster information.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"external-materials","dir":"Articles","previous_headings":"Pre-requisites","what":"External materials","title":"Analyzing risk index using habitat connectivity","text":"Download install R, R Studio - https://rstudio-education.github.io/hopr/starting.html/ Raster - https://www.adobe.com/creativecloud/file-types/image/raster.html TIFF - https://www.adobe.com/creativecloud/file-types/image/raster/tiff-file.html/","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"data-sets","dir":"Articles","previous_headings":"Pre-requisites","what":"Data sets","title":"Analyzing risk index using habitat connectivity","text":"use publicly available sources obtain crop information - Monfreda (Monfreda, Ramankutty, Foley 2008) MapSpam (2010, 2017) (International Food Policy Research Institute 2019) Geodata provides set APIs access data-sets. visualization plots, use rnaturalearth.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"meta-information","dir":"Articles","previous_headings":"Quick Start","what":"Meta information","title":"Analyzing risk index using habitat connectivity","text":"Package information - https://garrettlab.github.io/HabitatConnectivity/ CRAN site - https://CRAN.R-project.org/package=geohabnet Source code - https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/ Report issues - https://github.com/GarrettLab/CroplandConnectivity/issues/ Lab website - https://www.garrettlab.com/","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"installation-and-loading","dir":"Articles","previous_headings":"Quick Start","what":"Installation and loading","title":"Analyzing risk index using habitat connectivity","text":"Installing geohabnet also install dependencies. Please see list dependencies using desc::desc(package = \"geohabnet\") Alternatively, install github source. point, access help page using following -","code":"if (!require(\"devtools\")) {   install.packages(\"devtools\") } if (!require(\"geohabnet\")) {   utils::install.packages(\"geohabnet\") } library(\"devtools\") #> Loading required package: usethis  if (!require(\"geohabnet\")) {   install_github(\"GarrettLab/HabitatConnectivity\", subdir = \"geohabnet\") } #> Loading required package: geohabnet #> Warning in library(package, lib.loc = lib.loc, character.only = TRUE, #> logical.return = TRUE, : there is no package called 'geohabnet' #> Downloading GitHub repo GarrettLab/HabitatConnectivity@HEAD #> parallelly   (1.37.0  -> 1.37.1) [CRAN] #> globals      (0.16.2  -> 0.16.3) [CRAN] #> digest       (0.6.33  -> 0.6.35) [CRAN] #> Rcpp         (1.0.11  -> 1.0.12) [CRAN] #> curl         (5.2.0   -> 5.2.1 ) [CRAN] #> vctrs        (0.6.3   -> 0.6.5 ) [CRAN] #> stringi      (1.7.12  -> 1.8.3 ) [CRAN] #> rlang        (1.1.1   -> 1.1.3 ) [CRAN] #> glue         (1.6.2   -> 1.7.0 ) [CRAN] #> cli          (3.6.1   -> 3.6.2 ) [CRAN] #> future       (1.33.1  -> 1.33.2) [CRAN] #> terra        (1.7-39  -> 1.7-71) [CRAN] #> sf           (1.0-15  -> 1.0-16) [CRAN] #> data.table   (1.15.0  -> 1.15.4) [CRAN] #> future.apply (1.11.1  -> 1.11.2) [CRAN] #> igraph       (2.0.1.1 -> 2.0.3 ) [CRAN] #> Installing 16 packages: parallelly, globals, digest, Rcpp, curl, vctrs, stringi, rlang, glue, cli, future, terra, sf, data.table, future.apply, igraph #> Installing packages into 'C:/Users/kkeshav/AppData/Local/Temp/RtmpYLtssC/temp_libpath608453735b7e' #> (as 'lib' is unspecified) #> package 'parallelly' successfully unpacked and MD5 sums checked #> package 'globals' successfully unpacked and MD5 sums checked #> package 'digest' successfully unpacked and MD5 sums checked #> package 'Rcpp' successfully unpacked and MD5 sums checked #> package 'curl' successfully unpacked and MD5 sums checked #> package 'vctrs' successfully unpacked and MD5 sums checked #> package 'stringi' successfully unpacked and MD5 sums checked #> package 'rlang' successfully unpacked and MD5 sums checked #> package 'glue' successfully unpacked and MD5 sums checked #> package 'cli' successfully unpacked and MD5 sums checked #> package 'future' successfully unpacked and MD5 sums checked #> package 'terra' successfully unpacked and MD5 sums checked #> package 'sf' successfully unpacked and MD5 sums checked #> package 'data.table' successfully unpacked and MD5 sums checked #> package 'future.apply' successfully unpacked and MD5 sums checked #> package 'igraph' successfully unpacked and MD5 sums checked #>  #> The downloaded binary packages are in #>  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpaU8FLa\\downloaded_packages #> 
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[39m #>         #>  #> Installing package into 'C:/Users/kkeshav/AppData/Local/Temp/RtmpYLtssC/temp_libpath608453735b7e' #> (as 'lib' is unspecified) library(geohabnet) ?geohabnet # and ?geohabnet::msean # any function"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"run-analysis-on-default-configuration","dir":"Articles","previous_headings":"Quick Start","what":"Run analysis on default configuration","title":"Analyzing risk index using habitat connectivity","text":"run analysis default set values supported parameters. Initially, values set based Xing et al(2021) (Xing et al. 2020) crop Avocado. run workflow global geographical extent quickly since crop presence relatively low.   results side effects similar information captured object returned . based values set parameters see details sections.","code":"res <- sensitivity_analysis() #>  |---------|---------|---------|---------| ============== #>  |---------|---------|---------|---------| =============="},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"running-new-analysis","dir":"Articles","previous_headings":"Quick Start","what":"Running new analysis","title":"Analyzing risk index using habitat connectivity","text":"provide 2 methods entry points run analysis setting new values supported parameters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"setting-values-in-a-function","dir":"Articles","previous_headings":"Quick Start > Running new analysis","what":"Setting values in a function","title":"Analyzing risk index using habitat connectivity","text":"goal function provide simple invasive factors parameters. internal implementation program deals object terra (Hijmans 2023) igraph(Csardi Nepusz 2006) . primary object type SpatRaster terra . get started, use quick way obtain raster later understand details. effective way look-search_crop(). return sources contains data-set crop.  Now raster object, can fed directly workflow. set required parameter - rast. value represents Avocado plantation geographical area North America.    functions msean sean except msean side effects return different S4 objects, GeoNetwork GeoRasters respectively. use interchangeably article. results interpreted accordance values parameters factored arguments sean. Run ?sean see supported parameters. later see usage parameters well. rast - spatRaster. Represents map crop presence geographical area. geoscale - Vector. Geographical coordinates form c(Xmin, Xmax, Ymin, Ymax) global - Logical. set TRUE, geoscale ignored. Get geographical scales used global analysis - Although recommended change global scales since finalized several tries. Still, advance use, set global geographic scales using - thresholds - Numeric. 2 types thresholds: host density link weights represented hd_threshold link_threshold respectively. former threshold filters aggregation input data-set/raster latter filter cells adjacency matrix used calculate network connectivity. resolution - Numeric. resolution value. context SpatRaster, ’s number pixels aggregated produce new finer/coarser version raster data. Default Side effect - Calculates, produces plots maps sensitivity_analysis() [sensitivity_analysis()]. alternative sean() can called obtain results function call side effects.","code":"avocado <- cropharvest_rast(\"avocado\", \"monfreda\")  # verify the raster object avocado #> class       : SpatRaster  #> dimensions  : 2160, 4320, 1  (nrow, ncol, nlyr) #> resolution  : 0.08333333, 0.08333333  (x, y) #> extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326)  #> source      : avocado_HarvestedAreaFraction.tif  #> name        : avocado_HarvestedAreaFraction gplot(avocado) geo_net <- msean(avocado) #>  |---------|---------|---------|---------| ========== #>  |---------|---------|---------|---------| ============== #>  |---------|---------|---------|---------| ========== global_scales() #> $east #> [1] -24 180 -58  60 #>  #> $west #> [1] -140  -34  -58   60 #set_global_scales(list(east = c(-24, 180, -58, 60), west = c(-140, -34, -58, 60))) reso() #> [1] 12"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"using-configuration","dir":"Articles","previous_headings":"Quick Start > Running new analysis","what":"Using configuration","title":"Analyzing risk index using habitat connectivity","text":"parameters available configuration thus control analysis. configuration file name parameters.yaml, currently supporting 10 parameters. intuition behind methodology provide basic interface setting new values. snippet describes basic usage configuration. Get initial configuration file. default function save file temporary directory tempdir(), however recommend saving path program write permissions. Using iwindow = TRUE prompt selection window save config file. file look something like - values must modified without modifying structure. order don’t matter program. new values configuration must fed workflow using - get_parameters() fetch initial parameters. can, required re-fetch parameters modified configuration. Modify value feed workflow using set_parameters().","code":"config_file <- get_parameters(out_path = tempdir()) config_file #> [1] \"C:\\\\Users\\\\kkeshav\\\\AppData\\\\Local\\\\Temp\\\\RtmpaU8FLa/parameters.yaml\" set_parameters(new_params = config_file) #> [1] TRUE #using iwindow = true will prompt a selction window to choose config file."},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"hosts","dir":"Articles","previous_headings":"Parameters","what":"Hosts","title":"Analyzing risk index using habitat connectivity","text":"helper functions make analysis easier. Available sources can seen using - specifically, support 2 data set sources - Monfreda Mapspam using APIs provided Geodata. sources crop presence geographical areas form raster(tiff). start , can check certain crop available source - #1 result suggests crop information available monfreda . Now, #2 suggests banana present 2 sources. use results obtain raster data one specified sources. returned actually type SpatRaster. , separate raster information crop. Crops can combined returned one raster. case banana, information sources first combined using mean crop information .e. banana avocado combined one raster. done produce single map contains information requested crops. one method obtain raster, using tiff - tiff_torast() . Finally, get_rasters() method, abstraction . see difference data generated last 3 methods -  result obtained one methods can used argument sean() . Value results list risk indices. Internally, cropharvest_rast() used fetch crop data-set ’s supported form. far, now run sensitivity analysis workflow avocado banana global scale default set parameter values. Alternatively, can just specify crops parameters.yaml run workflow -","code":"geohabnet::supported_sources() #> [1] \"monfreda\"          \"mapspam2010\"       \"mapspam2017Africa\" search_crop(\"avocado\") #1 #> [1] \"monfreda\" search_crop(\"bean\") #2 #> [1] \"monfreda\" \"spam\" # get avocado data rast_avocado <- crops_rast(list(monfreda = \"avocado\")) old_to <- options(\"timeout\") options(timeout = 6000)  #get data of banana crop rast_ban <- crops_rast(list(mapspam2010 = \"banana\")) # Back to back downloads causes connection to fail, this is a workaround rast_avo_ban <- crops_rast(list(monfreda = c(\"avocado\", \"banana\"), mapspam2010 = c(\"banana\"))) old_to <- options(old_to) gplot(c(rast_avocado, rast_ban, rast_avo_ban)) results <- lapply(list(rast_avocado, rast_avo_ban), msean) results <- sensitivity_analysis() #>  |---------|---------|---------|---------| ========== #>  |---------|---------|---------|---------| =========="},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"thresholds","dir":"Articles","previous_headings":"Parameters","what":"Thresholds","title":"Analyzing risk index using habitat connectivity","text":"Thresholds used select subset values SpatRaster operations applied. directly effects connectivity gives sense sensitivity network. intermediate goal produce adjacency graph essentially determines connectivity. Cells doesn’t meet threshold removed consideration dispersal models.","code":"risk_indexes <- msean(avocado, global = FALSE, hd_threshold = 0.00001, link_threshold = 0.00001) #>  |---------|---------|---------|---------| ======= #>  |---------|---------|---------|---------| ======= #>  |---------|---------|---------|---------| ======"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"density-thresholds","dir":"Articles","previous_headings":"Parameters > Thresholds","what":"Density Thresholds","title":"Analyzing risk index using habitat connectivity","text":"host density threshold. host density threshold minimum cropland proportion grid cells (locations) included analysis. parameter called HostDensityThreshold supports list values 0 1. running sensitivity_analysis() function, check values host density threshold smaller maximum host density map prevent errors. values rounded 5 decimal points.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"link-thresholds","dir":"Articles","previous_headings":"Parameters > Thresholds","what":"Link Thresholds","title":"Analyzing risk index using habitat connectivity","text":"Based information host distribution dispersal kernels, adjacency matrices created, entries likelihood pathogen movement locations. , adjacency matrices converted graph objects perform network analysis, entries adjacency matrices now weight links network. Choosing link weight thresholds helps focus analysis likely pathogen dispersal landscape. Like host density threshold, can provide list positive values LinkThreshold. running sensitivity_analysis() function, check values link weight threshold smaller maximum link weight network prevent errors.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"aggregation","dir":"Articles","previous_headings":"Parameters","what":"Aggregation","title":"Analyzing risk index using habitat connectivity","text":"Aggregation strategy refers function used create new map host density lower resolution (larger cells). Reducing spatial resolution helps reduce computational power needed run analysis. AggregationStrategy: [sum], sum cropland proportion initially small grids within large grid divided total number initially small grids within large grid. AggregationStrategy: [mean], sum cropland proportion initially small grids within large grid divided total number initially small grids containing land (small grids water excluded) within large grid. default, analysis run can opted one. one method used, difference map skipped outcome.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"distance-methods","dir":"Articles","previous_headings":"Parameters","what":"Distance methods","title":"Analyzing risk index using habitat connectivity","text":"pair locations host map values greater host density threshold, sensitivity_analysis() function calculate physical distances use calculate relative likelihood pathogen movement locations based pairwise geographical proximity. two different options calculate distance locations. · Vincenty ellipsoid distance option highly accurate computationally expensive. · Geodesic distance option less computationally expensive less accurate option . can set distance option either DistanceStrategy: “vincentyEllipsoid” DistanceStrategy: “geodesic”. One options used input run analysis. Check supported methods analysis running dist_methods() console.","code":"dist_methods() #> [1] \"geodesic\"          \"vincentyellipsoid\""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"resolution","dir":"Articles","previous_headings":"Parameters","what":"Resolution","title":"Analyzing risk index using habitat connectivity","text":"aggregation factor granularity number small grid cells aggregated larger grid cells direction (horizontally vertically). finest value 1 can require analysis run hours large number cells SpatRaster . resolution also used calculation variance dis-aggregating risk indices coarser resolution producing maps. provided, defaulted value selected reso()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"metrics","dir":"Articles","previous_headings":"Parameters","what":"Metrics","title":"Analyzing risk index using habitat connectivity","text":"See available metrics using Metrics corresponding dispersal models applied distance matrix specified weights. weights must specified % sum weights equal 100. use functions (Csardi Nepusz 2006) calculate metrics dispersal model. 2 dispersal models applied parameters inverse power law negative exponential. formally, metrics way determine connectivity among nodes network. graph functions (Csardi Nepusz 2006), links interpreted distances. However, context habitat connectivity, network adapted interpret links weights means likelihood pathogen spread lower distance larger.\\[ L = \\frac{1}{W}, \\\\ W' = \\sum_{=1}^{N} \\max(W - W_i) \\] L link weights W original weights undirected graph. W’ transformed weight vector calculating network centrality.","code":"supported_metrics() #> [1] \"betweeness\"               \"node_strength\"            #> [3] \"sum_of_nearest_neighbors\" \"eigenvector_centrality\"   #> [5] \"closeness\"                \"degree\"                   #> [7] \"page_rank\""},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"geographical-extent","dir":"Articles","previous_headings":"Parameters","what":"Geographical Extent","title":"Analyzing risk index using habitat connectivity","text":"Geographical extent subset world map defined coordinate reference system. corresponding parameter set area sean() sensitivity_analyis() geoscale GeoExtent respectively. Default setting global = TRUE ignore value geoscale. consider taking world map account using values global_scales() . non-global analysis, either set global = FALSE without setting geoscale. default, geoscale extracted extents input SpatRaster. recommend using EPSG:4326 coordinate reference system functions tested . Using function  Using config Set Global = FALSE CustomExt = [-115, -75, 5, 32] . initial parameters.yaml already contains value run combination parameters. provided geoscale, program take subset provided raster (data-set crop). workflow apply graph operations network connectivity subset.","code":"results <- msean(avocado, global = FALSE, geoscale = c(-115, -75, 5, 32))"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"outputs","dir":"Articles","previous_headings":"","what":"Outputs","title":"Analyzing risk index using habitat connectivity","text":"default, 3 maps produced analysis. sean() also returns risk indices without maps can, fed connectivity() . flexibility supposed allow users use risk indices purposes use function produce maps different parameters. code , obtaining results, maps produced. order calculate variance, cells SpatRaster extended coarser value using res parameter. Setting maps = FALSE suppress calculation outputs. sean(avocado) + .connectivity(georast) equivalent sensitivity_analysis() msean() produces maps side effect. user function equivalent connectivity() accepts primitives types instead S4 class.    Based result obtained last cell, let’s navigate object final object. noticed maps side effect ’s really whole point. See result summary simply calling final object navigate using standard S4 classes approach. final operations performed risk indices 3 results produced - Mean mean SpatRasters resulting combination parameter values. values cells added across indices divided number indices. represents connectivity based host density given area. Navigating resulting object -  Variance Uses stats::var risk indices, subset extracted provided scale finally pixels dis-aggregated using factor = resolution value original parameter previous step.  Difference aggregation methods (sum mean) selected, difference calculated rank matrices essentially numeric cells risk indices type SpatRaster. result dis-aggregated way previous step.  path saved raster can accessed using ‘type_out’ slot. Additionally, access risk indices ’s corresponding adjacency accessible within slots GeoNetwork class. Checkout adjacency matrices running code - Set pmean, pvar, pdiff FALSE skip calculation connectivity() skip calculation. sean() sensitivity_analysis(), set map = FALSE skip generation maps outcome. case global analysis, result eastern western geographic extents merged using terra::merge() . outcome operation saved new directory plots specified path OutDir name opt_datetime.tif, opt one suffixed datetime file created. outdir empty, value defaulted tempdir() . applies corresponding parameter outdir functions.","code":"final <- msean(avocado, link_threshold = 0.000001, hd_threshold = 0.000025) #>  |---------|---------|---------|---------| ========== #>  |---------|---------|---------|---------| ============== #>  |---------|---------|---------|---------| ========== # checkout the type of an object class(final) #> [1] \"GeoNetwork\" #> attr(,\"package\") #> [1] \"geohabnet\" final #> class            :  GeoNetwork  #> host density     :  118 , 320  (nrow, ncol) SpatRaster  #> mean             :  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpaU8FLa/plots/mean_20240405165709138196.tif  #> mean raster      :  1416 , 3840  (nrow, ncol)  #> variance          :  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpaU8FLa/plots/variance_20240405165722357352.tif  #> variance raster   :  1416 , 3840  (nrow, ncol)  #> difference        :  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpaU8FLa/plots/difference_20240405165734248025.tif  #> difference raster :  1416 , 3840  (nrow, ncol) gplot(final@me_rast) gplot(final@var_rast) gplot(final@diff_rast) # checkout the results final@rasters #> class   :  GeoRasters  #> global  :  TRUE  #> globals :  1  # global is TRUE because we original set the global analysis # thus, we will have set of 2 risk indices, eastern and wetern hemisphere final@rasters$global_rast #> [[1]] #> class :  GlobalRast  #> east  :  14  #> west  :  14  # Number of elements from above determines the the number of parameter values provided  # To access the adjacency matrix, final@rasters$global_rast[[1]]$east[[1]] # this is also s4 class 'GeoModel' #> class            :  Model  #> adjacency matrix :  839 ,  839  (nrow, ncol)  #> risk index       :  ,   (nrow, ncol) # replace the indexing with any arbitary index, # uncomment line below to see the results.  #final@rasters$global_rast[[1]]$east[[1]]$amatrix"},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html","id":"computing","dir":"Articles","previous_headings":"","what":"Computing","title":"Analyzing risk index using habitat connectivity","text":"understand motivation behind implementation, let’s analyze complexity. Since link host density threshold list, let size N. kernel models, let’s represent metrics dispersal coefficients x 4 reprectively. overall complexity turns \\(N \\cdot N \\cdot (7X + 7Y)\\) . , assumed availability host density. Although, crop data fetched parallel minimize download time. Considering \\(X = max(X, Y)\\) , complexity now \\(T = 7N^2 X^2 \\approx 7N^4\\). discount complexity graph operations like centrality scores haven’t attempted optimize operations. try optimize performance scaling fixed problem size, increasing parallelism. operations compute intensive. run_msean snippet Hosts used 8.3GB memory 81% memory allotted RStudio. part, implementation focused performance efficient memory usage. Package applies mechanisms vectorization foreach improve performance efficiency. workflow several parts running independently. independent functions performs operations adjacency matrix aggregation. created opportunity task level parallelism running functions within geohabnet. combination parameters can run independently parallel parts using future mechanism. implementation supports workflow acceleration using (Bengtsson 2021a, 2021b) . also important note use SpatRaster object throughout computation. SpatRaster external pointer C++ rather R object thus adds overhead conversion, neutralizing performance gains.","code":"avocado <- geohabnet::cropharvest_rast(\"avocado\", \"monfreda\")  # see ?future::plan for details future::plan(future::multicore()) msean(avocado)  future::plan(future::multisession()) msean(avocado)"},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/articles/LinkWeightsAnalysis.html","id":"betweenness","dir":"Articles","previous_headings":"","what":"Betweenness","title":"Network centralities in GeoHabnet","text":"Getting host density Running Sensitivity Analysis    important note Betweenness centrality time intensive operation. Geohabnet uses wrapper around igraph::betweenness(). Refer (Csardi Nepusz 2006) details reading. cutoff parameter can used set threshold include link weights based threshold. Setting parameter also reflected closeness. configuration based run follows - get_parameters() -> modify values parameters.yaml -> set_parameters() -> run sensitivity_analysis()","code":"avocado_mon <- geohabnet::cropharvest_rast(\"potato\", \"monfreda\") avocado_result <- geohabnet::msean(avocado_mon, global = TRUE, link_threshold  = 0.000001,                                    inv_pl = list(beta = c(0.5),                                                  metrics = c(\"betweeness\"),                                                  weights = c(100),                                                  cutoff = -1), res = 24,                                    neg_exp = list(gamma = c(0.1),                                                   metrics = c(\"betweeness\"),                                                   weights = c(100), cutoff = -1)) ##  |---------|---------|---------|---------| ===== ##  |---------|---------|---------|---------| =======                                             |---------|---------|---------|---------| ============== ##  |---------|---------|---------|---------| ====="},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Krishna Keshav. Author, maintainer. Aaron Plex. Author. Garrett Lab. Contributor.            https://garrettlab.com Karen Garrett. Author. University Florida. Copyright holder, funder.            https://www.ufl.edu","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Keshav K, Plex , Garrett K (2024). geohabnet: Geographical Risk Analysis Based Habitat Connectivity. R package version 2.1.1,  https://CRAN.R-project.org/package=geohabnet/, https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/, https://www.garrettlab.com/, https://garrettlab.github.io/HabitatConnectivity/.","code":"@Manual{,   title = {geohabnet: Geographical Risk Analysis Based on Habitat Connectivity},   author = {Krishna Keshav and Aaron Plex and Karen Garrett},   year = {2024},   note = {R package version 2.1.1,  https://CRAN.R-project.org/package=geohabnet/, https://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/, https://www.garrettlab.com/},   url = {https://garrettlab.github.io/HabitatConnectivity/}, }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/index.html","id":"geohabnet","dir":"","previous_headings":"","what":"Geographical Risk Analysis Based on Habitat Connectivity","title":"Geographical Risk Analysis Based on Habitat Connectivity","text":"package expands Xing et al (2021). adds capabilities customize parameter values using functions shows results habitat connectivity risk index form plots. goal geohabnet enable users visualize habitat connectivity risk index using parameter values. risk analysis outputs 3 maps - Mean habitat connectivity (based habitat connectivity index defined user) Difference habitat connectivity Variance habitat connectivity package currently supports crop maps sourced geodata::monfredaCrops() geodata::spamCrops(). analysis produces 3 maps listed . multiple ways functions can used - generate final outcome intermediate outcomes sophisticated use cases. vignettes provide several examples. output values propagated functions performing operations distance matrix calculation. values set parameters.yaml can accessed using get_parameters(). See usage .","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Geographical Risk Analysis Based on Habitat Connectivity","text":"Package can either installed CRAN: source version package can installed GitHub :","code":"install.packages(\"geohabnet\") #> Installing package into 'C:/Users/kkeshav/AppData/Local/Temp/Rtmp6Nnjmd/temp_libpath1878707c7a53' #> (as 'lib' is unspecified) #> package 'geohabnet' successfully unpacked and MD5 sums checked #>  #> The downloaded binary packages are in #>  C:\\Users\\kkeshav\\AppData\\Local\\Temp\\RtmpSm8hLm\\downloaded_packages if (!require(\"devtools\")) {   install.packages(\"devtools\") }  devtools::install_github(\"GarrettLab/HabitatConnectivity\", subdir = \"geohabnet\")"},{"path":"https://garrettlab.github.io/HabitatConnectivity/index.html","id":"geohabnet-example","dir":"","previous_headings":"","what":"geohabnet Example","title":"Geographical Risk Analysis Based on Habitat Connectivity","text":"Run analysis using - parameters.yaml stores parameter values. can accessed set using get_parameters() set_parameters() respectively. default risk analysis run global index, scales present global_scales() . Refer help using ?geohabnet::fun help(geohabnet::fun) Refer article Analyzing risk index using cropland connectivity elaborate description usages functions package.","code":"library(geohabnet)  param_file <- geohabnet::get_parameters() # now edit the file geohabnet::set_parameters(new_params = param_file) geohabnet::senstivity_analysis()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate difference map — ccri_diff","title":"Calculate difference map — ccri_diff","text":"function produces map difference b/w mean sum indexes rank cropland harvested area fraction.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate difference map — ccri_diff","text":"","code":"ccri_diff(x, y, global, geoscale, res = reso(), outdir = tempdir())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate difference map — ccri_diff","text":"x SpatRaster. y SpatRaster. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. geoscale Numeric vector. x cropped extent. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate difference map — ccri_diff","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_diff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate difference map — ccri_diff","text":"Ideally, function tested yield desired results length((y[] > 0)) > length((x[] > 0)).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate mean of raster objects — ccri_mean","title":"Calculate mean of raster objects — ccri_mean","text":"Wrapper terra::mean(). Calculates mean list rasters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate mean of raster objects — ccri_mean","text":"","code":"ccri_mean(   indices,   global = FALSE,   east = NULL,   west = NULL,   geoscale = NULL,   res = reso(),   plt = TRUE,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate mean of raster objects — ccri_mean","text":"indices List SpatRasters. input represents spatial raster collection mean calculated. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). plt TRUE need plot mean map, FALSE otherwise. outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_mean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate mean of raster objects — ccri_mean","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate variance of CCRI — ccri_variance","title":"Calculate variance of CCRI — ccri_variance","text":"function produces map variance CCRI based input parameters","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate variance of CCRI — ccri_variance","text":"","code":"ccri_variance(   indices,   rast,   global,   east = NULL,   west = NULL,   geoscale,   res = reso(),   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate variance of CCRI — ccri_variance","text":"indices SpatRaster. Collection risk indices. rast SpatRaster. Template variance output global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/ccri_variance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate variance of CCRI — ccri_variance","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate and plot maps — connectivity","title":"Calculate and plot maps — connectivity","text":"Calculate mean, variance difference. result produced form maps plotted predefined settings. Currently, settings plot customized. Default value TRUE logical arguments","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate and plot maps — connectivity","text":"","code":"connectivity(   host,   indices,   global = FALSE,   east = NULL,   west = NULL,   geoscale = NULL,   res = reso(),   pmean = TRUE,   pvar = TRUE,   pdiff = TRUE,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate and plot maps — connectivity","text":"host SpatRaster. Host density map aka SpatRaster object indices SpatRaster. Collection risk indices. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). pmean Logical. TRUE map mean plotted, FALSE otherwise. pvar Logical. TRUE variance map plotted, FALSE otherwise. pdiff Logical. TRUE difference map plotted, FALSE otherwise. outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate and plot maps — connectivity","text":"Gmap. See details.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate and plot maps — connectivity","text":"indexes actually risk indices .e. lis spatRaster objects resulting operations crop's raster parameters provided either parameters.yaml sean(). save opted plots using - pmean, pvar pdiff. File saved provided value outdir  tempdir().interactive() TRUE, plots can seen active plot window. E.g. Rstudio. maps plotted using SpatRaster object. objects available return value function.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/connectivity.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate and plot maps — connectivity","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Get raster object for crop — cropharvest_rast","title":"Get raster object for crop — cropharvest_rast","text":"Get cropland information form raster object data source crop","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get raster object for crop — cropharvest_rast","text":"","code":"cropharvest_rast(crop_name, data_source)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get raster object for crop — cropharvest_rast","text":"crop_name Name crop data_source Data source cropland information","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get raster object for crop — cropharvest_rast","text":"Raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/cropharvest_rast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get raster object for crop — cropharvest_rast","text":"","code":"# \\donttest{ cropharvest_rast(\"avocado\", \"monfreda\") # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Get sum of rasters for individual crops — crops_rast","title":"Get sum of rasters for individual crops — crops_rast","text":"Takes crop names returns raster object sum raster individual crops. Currently, supports crops listed geodata::monfredaCrops(), geodata::spamCrops() crop present multiple sources, mean calculated.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get sum of rasters for individual crops — crops_rast","text":"","code":"crops_rast(crop_names)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get sum of rasters for individual crops — crops_rast","text":"crop_names named list source along crop names","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get sum of rasters for individual crops — crops_rast","text":"SpatRaster. Raster object sum individual crop raster","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/crops_rast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get sum of rasters for individual crops — crops_rast","text":"","code":"# \\donttest{ crops_rast(list(monfreda = c(\"wheat\", \"barley\"), mapspam2010 = c(\"wheat\", \"potato\"))) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":null,"dir":"Reference","previous_headings":"","what":"Dispersal kernels — inv_powerlaw","title":"Dispersal kernels — inv_powerlaw","text":"-[inv_powerlaw()] Get parameters values pertaining inverse power law model. -[neg_exp()] Get parameters values pertaining negative exponential model.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dispersal kernels — inv_powerlaw","text":"","code":"inv_powerlaw(   params = load_parameters(),   betas = NULL,   mets = NULL,   we = NULL,   linkcutoff = NULL )  neg_expo(   params = load_parameters(),   gammas = NULL,   mets = NULL,   we = NULL,   linkcutoff = NULL )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dispersal kernels — inv_powerlaw","text":"params Object.load_parameters() default. provided, function require parameters. takes precedence parameters. betas Numeric. Parameter calculating inverse power law. mets Character. metrics applied adjacency matrix produced intermediate step. Numeric link weights used network analysis. linkcutoff Numeric. Currently used parameter calculate centrality network. gammas Numeric. Parameter calculating negative exponential.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dispersal kernels — inv_powerlaw","text":"List parameters values. See details.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Dispersal kernels — inv_powerlaw","text":"list object following values used running analysis -beta Parameter calculating inverse power law. -gamma Parameter calculating negative exponential. -metrics metrics applied adjacency matrix produced intermediate step. -weights link weights used network analysis. -cutoff Currently used parameter calculate centrality network - betweeness() closeness(). defined igraph::betweenness(), maximum length consider calculating centrality. zero negative, limit.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Dispersal-kernels.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Dispersal kernels — inv_powerlaw","text":"Csardi G, Nepusz T (2006). “igraph software package complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org. Csárdi G, Nepusz T, Traag V, Horvát Sz, Zanini F, Noom D, Müller K (2024). igraph: Network Analysis Visualization R. doi:10.5281/zenodo.7682609 , R package version 1.5.1, https://CRAN.R-project.org/package=igraph.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Distance methods supported — dist_methods","title":"Distance methods supported — dist_methods","text":"Contains supported strategies calculate distance two points. Use one methods sean() sensitivity_analysis().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distance methods supported — dist_methods","text":"","code":"dist_methods()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distance methods supported — dist_methods","text":"vector","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dist_methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Distance methods supported — dist_methods","text":"","code":"dist_methods()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function to extract risk indices from a list of crop rasters. — .indices","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"Internal function extract risk indices list crop rasters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"","code":".indices(crop_rasters)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"crop_rasters List raster objects.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/dot-indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Internal function to extract risk indices from a list of crop rasters. — .indices","text":"list risk indices.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geohabnet-package.html","id":null,"dir":"Reference","previous_headings":"","what":"geohabnet: Geographical Risk Analysis Based on Habitat Connectivity — geohabnet-package","title":"geohabnet: Geographical Risk Analysis Based on Habitat Connectivity — geohabnet-package","text":"geohabnet package designed perform geographically spatially explicit risk analysis habitat connectivity. Xing et al (2021) doi:10.1093/biosci/biaa067  proposed concept cropland connectivity risk factor plant pathogen pest invasions. functions geohabnet initially developed thinking cropland connectivity, users recommended first familiar concept looking Xing et al paper. nutshell, habitat connectivity analysis combines information maps host density, estimates relative likelihood pathogen movement habitat locations area interest, applies network analysis calculate connectivity habitat locations. functions geohabnet built conduct habitat connectivity analysis relying geographic parameters (spatial resolution spatial extent), dispersal parameters (two commonly used dispersal kernels: inverse power law negative exponential models), network parameters (link weight thresholds network metrics). functionality main extensions provided functions geohabnet habitat connectivity analysis ) Capability easily calculate connectivity locations landscape using single function, sensitivity_analysis() msean(). b) backbone datasets, geohabnet package supports use two publicly available global datasets calculate cropland density. backbone datasets geohabnet package include crop distribution maps Monfreda, C., N. Ramankutty, J. . Foley (2008) doi:10.1029/2007gb002947  \"Farming planet: 2. Geographic distribution crop areas, yields, physiological types, net primary production year 2000, Global Biogeochem. Cycles, 22, GB1022\" International Food Policy Research Institute (2019) doi:10.7910/DVN/PRFF8V  \"Global Spatially-Disaggregated Crop Production Statistics Data 2010 Version 2.0, Harvard Dataverse, V4\". Users can also provide geographic dataset represents host density. c) geohabnet package allows R users provide maps host density (originally Xing et al (2021)), host landscape density (representing geographic distribution either crops wild species), habitat distribution (host landscape density adjusted climate suitability) inputs, propose term habitat connectivity. d) geohabnet package allows R users customize parameter values habitat connectivity analysis, facilitating context-specific (pathogen- pest-specific) analyses. e) geohabnet package allows users automatically visualize maps habitat connectivity locations resulting sensitivity analysis across customized parameter combinations. primary function sean() sensitivity analysis(). functions geohabnet provide three main outcomes: ) map mean habitat connectivity across parameters selected user, ii) map variance habitat connectivity across selected parameters, iii) map difference ranks habitat connectivity habitat density. function can used generate maps 'final' outcomes. function can also provide intermediate outcomes, adjacency matrices built perform analysis, can used network analysis. Refer article https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html see examples function access outcome types. change parameter values, file called parameters.yaml stores parameters values, can accessed using get_parameters() set new parameter values set_parameters(). Users can modify ten parameters.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geohabnet-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"geohabnet: Geographical Risk Analysis Based on Habitat Connectivity — geohabnet-package","text":"Maintainer: Krishna Keshav kkeshav@ufl.edu Authors: Aaron Plex plexaaron@ufl.edu (ORCID) Karen Garrett karengarrett@ufl.edu (ORCID) contributors: Garrett Lab karengarrett@ufl.edu (https://garrettlab.com) [contributor] University Florida (https://www.ufl.edu) [copyright holder, funder]","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoModel-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GeoModel class — GeoModel-class","title":"GeoModel class — GeoModel-class","text":"ref class represent results dispersal models.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoModel-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"GeoModel class — GeoModel-class","text":"matrix adjacency matrix represent network.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GeoNetwork — GeoNetwork-class","title":"GeoNetwork — GeoNetwork-class","text":"S4 class representing network geographical data. wrap results risk analysis using sean() sensitivity_analysis(). class contains field Gmap class results form SpatRaster TIFF file.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GeoNetwork — GeoNetwork-class","text":"","code":"# S4 method for GeoNetwork host_density(x) <- value"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GeoNetwork — GeoNetwork-class","text":"x GeoNetwork. value SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GeoNetwork — GeoNetwork-class","text":"GeoNetwork.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoNetwork-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"GeoNetwork — GeoNetwork-class","text":"rasters list GeoRasters objects. host_density SpatRaster representing host density. me_rast raster representing mean risk index. me_out Character. file path mean risk index raster. diff_rast raster representing difference. diff_out Character. file path difference raster. var_rast raster representing variance. var_out Character. file path variance raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoRasters-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GeoRaster class — GeoRasters-class","title":"GeoRaster class — GeoRasters-class","text":"class represent raster vis--vis risk indices. class encapsulates results apply dispersal models metrics.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GeoRasters-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"GeoRaster class — GeoRasters-class","text":"host_density SpatRaster. spatial raster representing host density. rasters List. List raster representing risk indices. type GeoModels. global Boolean. True contains GlobalRast object, False otherwise.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":null,"dir":"Reference","previous_headings":"","what":"Get geographical scales from the parameters — geoscale_param","title":"Get geographical scales from the parameters — geoscale_param","text":"function returns list geographical scales set global custom extent parameters.yaml. global TRUE, CustomExt ignored.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get geographical scales from the parameters — geoscale_param","text":"","code":"geoscale_param(gparams = load_parameters())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get geographical scales from the parameters — geoscale_param","text":"gparams Optional. load_parameters() null","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/geoscale_param.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get geographical scales from the parameters — geoscale_param","text":"Vector. set geographical scales","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Parameters — get_parameters","title":"Get Parameters — get_parameters","text":"Retrieves parameters copies parameter file specified output path.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Parameters — get_parameters","text":"","code":"get_parameters(out_path = tempdir(), iwindow = FALSE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Parameters — get_parameters","text":"out_path character. output path parameter file copied. Default temporary directory tempdir() iwindow logical. TRUE, prompts user select output directory using file chooser window. Default FALSE","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Parameters — get_parameters","text":"character. path copied parameter file.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Parameters — get_parameters","text":"Using configuration file alternative sean()","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Parameters — get_parameters","text":"","code":"get_parameters() get_parameters(out = tempdir())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":null,"dir":"Reference","previous_headings":"","what":"Get rasters object from parameters — get_rasters","title":"Get rasters object from parameters — get_rasters","text":"Takes named list hosts input. See host object get_parameters() load_parameters(). also wrapper crops_rast(). Function creates 2 raster object - one sum crops specified sources using provided raster file. See tiff_torast()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get rasters object from parameters — get_rasters","text":"","code":"get_rasters(hosts)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get rasters object from parameters — get_rasters","text":"hosts List hosts values. synonym Hosts object parameters","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get rasters object from parameters — get_rasters","text":"List SpatRaster.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/get_rasters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get rasters object from parameters — get_rasters","text":"","code":"# Get default rasters if (FALSE) { get_rasters(list(mapspam2010 = c(\"wheat\"), monfreda = c(\"avocado\"), file = \"some_raster.tif\")) }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GlobalRast-class.html","id":null,"dir":"Reference","previous_headings":"","what":"GlobalRast class — GlobalRast-class","title":"GlobalRast class — GlobalRast-class","text":"class represent raster global scales. Global scales accessible using global_scales(). However, class encapsulates results apply dispersal models metrics.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/GlobalRast-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"GlobalRast class — GlobalRast-class","text":"east list raster eastern hemisphere. west list raster western hemisphere.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":null,"dir":"Reference","previous_headings":"","what":"Global geographical extent — global_scales","title":"Global geographical extent — global_scales","text":"See geographical extents used global analysis. Returns eastern western hemisphere extents. extent form c(Xmin, Xmax, Ymin, Ymax).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Global geographical extent — global_scales","text":"","code":"global_scales()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Global geographical extent — global_scales","text":"List. Named list scales eastern western hemisphere","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/global_scales.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Global geographical extent — global_scales","text":"Seperate analysis geographical scales eastern western hemisphere combined run global analysis.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Gmap class — Gmap-class","title":"Gmap class — Gmap-class","text":"S4 class represent various maps form SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gmap class — Gmap-class","text":"","code":"setmaps(x, me, vari, dif)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gmap class — Gmap-class","text":"x Gmap object. SpatRaster. raster representing mean risk index. vari SpatRaster. raster representing variance. dif SpatRaster. raster representing difference.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gmap class — Gmap-class","text":"Gmap object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/Gmap-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Gmap class — Gmap-class","text":"me_rast raster representing mean risk index. me_out Character. file path mean risk index raster. diff_rast raster representing difference. diff_out Character. file path difference raster. var_rast raster representing variance. var_out Character. file path variance raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot a Raster* object — gplot","title":"Plot a Raster* object — gplot","text":"wrapper terra::plot()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot a Raster* object — gplot","text":"","code":"gplot(x, ...)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot a Raster* object — gplot","text":"x Raster* object ... additional arguments passed terra::plot()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot a Raster* object — gplot","text":"plot","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/gplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot a Raster* object — gplot","text":"","code":"r <- terra::rast(nrows=108, ncols=21, xmin=0, xmax=10) gplot(r) gplot(r, col = \"red\") gplot(r, col = \"red\", breaks = 10)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate difference map — hci_diff","title":"Calculate difference map — hci_diff","text":"function produces map difference b/w mean sum indexes rank cropland harvested area fraction.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate difference map — hci_diff","text":"","code":"hci_diff(x, y, global, geoscale, res = reso(), outdir = tempdir())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate difference map — hci_diff","text":"x SpatRaster. y SpatRaster. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. geoscale Numeric vector. x cropped extent. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate difference map — hci_diff","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_diff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate difference map — hci_diff","text":"Ideally, function tested yield desired results length((y[] > 0)) > length((x[] > 0)).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate mean of raster objects — hci_mean","title":"Calculate mean of raster objects — hci_mean","text":"Wrapper terra::mean(). Calculates mean list rasters.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate mean of raster objects — hci_mean","text":"","code":"hci_mean(   indices,   global = FALSE,   east = NULL,   west = NULL,   geoscale = NULL,   res = reso(),   plt = TRUE,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate mean of raster objects — hci_mean","text":"indices List SpatRasters. input represents spatial raster collection mean calculated. global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). plt TRUE need plot mean map, FALSE otherwise. outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_mean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate mean of raster objects — hci_mean","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate variance of CCRI — hci_variance","title":"Calculate variance of CCRI — hci_variance","text":"function produces map variance CCRI based input parameters","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate variance of CCRI — hci_variance","text":"","code":"hci_variance(   indices,   rast,   global,   east = NULL,   west = NULL,   geoscale,   res = reso(),   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate variance of CCRI — hci_variance","text":"indices SpatRaster. Collection risk indices. rast SpatRaster. Template variance output global Logical. TRUE global analysis desired, FALSE otherwise. east west required TRUE. east SpatRaster. Collection risk indices eastern extent. west SpatRaster. Collection risk indices western extent. TRUE, geoscale ignored. Default TRUE. geoscale Vector. geographical scale. Default NULL. res Numeric. Map resolution. value used aggregation dis-aggregation operation. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/hci_variance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate variance of CCRI — hci_variance","text":"RiskMap. Contains result form SpatRaster objects file path saved maps.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/host_density-set.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the host density. — host_density<-","title":"Set the host density. — host_density<-","text":"Sets host density slot GeoNetwork object","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/host_density-set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the host density. — host_density<-","text":"","code":"host_density(x) <- value"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/host_density-set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the host density. — host_density<-","text":"x GeoNetwork object. value SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Load Parameters from YAML File — load_parameters","title":"Load Parameters from YAML File — load_parameters","text":"function loads parameters YAML file stores object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load Parameters from YAML File — load_parameters","text":"","code":"load_parameters(filepath = .param_fp())"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load Parameters from YAML File — load_parameters","text":"filepath Path YAML file containing parameters. default, takes value parameters.yaml R user's directory.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load Parameters from YAML File — load_parameters","text":"object parameters values","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/load_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load Parameters from YAML File — load_parameters","text":"","code":"# Load parameters from default file load_parameters()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/mapspam.html","id":null,"dir":"Reference","previous_headings":"","what":"Supported sources for Mapspam — mapspam","title":"Supported sources for Mapspam — mapspam","text":"Supported sources Mapspam","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/mapspam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supported sources for Mapspam — mapspam","text":"","code":"mapspam()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/monfreda.html","id":null,"dir":"Reference","previous_headings":"","what":"Supported sources for monfreda — monfreda","title":"Supported sources for monfreda — monfreda","text":"Supported sources monfreda","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/monfreda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supported sources for monfreda — monfreda","text":"","code":"monfreda()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculation on network metrics a.k.a centralities. — nn_sum","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"functions igraph package adapted calculate habitat connectivity. context habitat connectivity, functions can interpreted follows: [nn_sum()]: Calculates sum nearest neighbors igraph::graph.knn(). [node_strength()]: Calculates sum edge weights adjacent nodes igraph::graph.strength(). [betweeness()]: Calculates node betweenness based number shortest paths. igraph::betweenness() function igraph interprets link weights distances calculate shortest paths, betweenness() function geohabnet transforms link weights (relative likelihood pathogen pest movement) adjacency matrix higher link weight values shortest (likely) paths pathogen pest movement. [ev()]: Calculates eigenvector centrality positions within network igraph::evcent(). [closeness()]: measures many steps required access every vertex given vertex igraph::closeness(). igraph::closeness() function igraph interprets link weights distances calculate shortest paths, closeness() function geohabnet transforms link weights (relative likelihood pathogen pest movement) adjacency matrix higher link weight values shortest (likely) paths pathogen pest movement. [degree()]: number adjacent edges igraph::degree(). [pagerank()]: page rank score vertices igraph::page_rank().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"","code":"nn_sum(crop_dm, ...)  node_strength(crop_dm, ...)  betweeness(crop_dm, ...)  ev(crop_dm, ...)  degree(crop_dm, ...)  closeness(crop_dm, ...)  pagerank(crop_dm, ...)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"crop_dm square adjacency matrix, rows columns names represent nodes (locations) entry indicate relative likelihood pathogen pest movement pair nodes. internal workflow, adjacency matrix comes result operations within sean() function. weight represents importance network metric habitat connectivity analysis. ... arguments corresponding igraph fun","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/nn_sum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculation on network metrics a.k.a centralities. — nn_sum","text":"SpatRaster. Representing connectivity node location.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset parameters.yaml — reset_params","title":"Reset parameters.yaml — reset_params","text":"Resets values parameters.yaml file default initial values.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset parameters.yaml — reset_params","text":"","code":"reset_params()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset parameters.yaml — reset_params","text":"Logical. TRUE function successfully executed","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reset_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reset parameters.yaml — reset_params","text":"","code":"reset_params()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reso.html","id":null,"dir":"Reference","previous_headings":"","what":"Get resolution value — reso","title":"Get resolution value — reso","text":"Resolution stored parameter.yaml. present result default value.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reso.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get resolution value — reso","text":"","code":"reso()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/reso.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get resolution value — reso","text":"Numeric. Resolution parameters.yaml. Default 24.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/RiskMap-class.html","id":null,"dir":"Reference","previous_headings":"","what":"RiskMap class — RiskMap-class","title":"RiskMap class — RiskMap-class","text":"S4 class representing resulting maps specific operation type.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/RiskMap-class.html","id":"fields","dir":"Reference","previous_headings":"","what":"Fields","title":"RiskMap class — RiskMap-class","text":"map Character. file path map. riid SpatRaster. one risk maps. spr SpatRaster. spatial raster representing risk index. fp Character. file path risk index raster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Get risk indices — risk_indices","title":"Get risk indices — risk_indices","text":"Get risk indices GeoRasters object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get risk indices — risk_indices","text":"","code":"risk_indices(ri)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get risk indices — risk_indices","text":"ri GeoRasters object","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get risk indices — risk_indices","text":"List risk indices. ri global, list contain two elements, one hemisphere. e.g. list(east = list(), west = list()). ri global, list contain single element, e.g. list().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/risk_indices.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get risk indices — risk_indices","text":"function unpack SpatRasters GeoMadel thus future::future() safe.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":null,"dir":"Reference","previous_headings":"","what":"Run sensitivity analysis — sa_onrasters","title":"Run sensitivity analysis — sa_onrasters","text":"sensitivity_analysis() takes raster object parameters input. sa_onrasters() wrapper around sean() function. Takes raster object parameters input. msean_onrast() sa_onrasters(). Use side effects + results. Produces plots maps outcomes results returned object. produces plots maps outcomes results returned object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run sensitivity analysis — sa_onrasters","text":"","code":"sa_onrasters(rast, link_thresholds = c(0), hd_thresholds = c(0), ...)  msean_onrast(   global = TRUE,   geoscale = NULL,   res = reso(),   outdir = tempdir(),   ... )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run sensitivity analysis — sa_onrasters","text":"rast Raster object used analysis. link_thresholds Numeric vector. link threshold values hd_thresholds Numeric vector. host density threshold values ... Additional parameters passed sean(). global Logical. TRUE global analysis, FALSE otherwise. Default TRUE geoscale Numeric vector. Geographical coordinates form c(Xmin, Xmax, Ymin, Ymax) EPSG:4326 coordinate reference system. geoscale NuLL, extent extracted rast(SpatRaster) using terra::ext(). res Numeric. Resolution raster. Default reso(). outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run sensitivity analysis — sa_onrasters","text":"list calculated CCRI indices operations. index generated combination paramters. One combination equivalent sean() function.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Run sensitivity analysis — sa_onrasters","text":"Error handled non-overlapping extents.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Run sensitivity analysis — sa_onrasters","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sa_onrasters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run sensitivity analysis — sa_onrasters","text":"","code":"# \\donttest{ rr <- get_rasters(list(monfreda = c(\"avocado\"))) res1 <- sa_onrasters(rr[[1]],             global = FALSE,             geoscale = c(-115, -75, 5, 32),             c(0.0001, 0.00004),             c(0.0001, 0.00005),             c(\"sum\", \"mean\"),             res = 12) res2 <- sa_onrasters(rr[[1]],             global = TRUE,             link_thresholds = c(0.000001),             hd_thresholds = c(0.00015),             agg_methods = c(\"sum\"),             res = 12) res3 <- msean_onrast(rast = rr[[1]],           link_thresholds = c(0.000001),           hd_thresholds = c(0.00015)) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/scales.html","id":null,"dir":"Reference","previous_headings":"","what":"Only meant to global variables — scales","title":"Only meant to global variables — scales","text":"meant global variables","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/scales.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Only meant to global variables — scales","text":"","code":"scales"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/scales.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Only meant to global variables — scales","text":"object class environment length 2.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":null,"dir":"Reference","previous_headings":"","what":"Sensitivity analysis across maps of habitat connectivity — sean","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"function performs sensitivity analysis across different values habitat connectivity location map. combination selected parameters, index habitat connectivity calculated. sensitivity_analysis() wrapper around sean() function. msean() wrapper around sean() function. additional argument specify maps calculated using connectivity() function. maps essentially risk network.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"","code":"sean(   rast,   global = TRUE,   geoscale = NULL,   agg_methods = c(\"sum\", \"mean\"),   dist_method = \"geodesic\",   link_threshold = 0,   hd_threshold = 0,   res = reso(),   inv_pl = inv_powerlaw(NULL, betas = c(0.5, 1, 1.5), mets = c(\"betweeness\",     \"NODE_STRENGTH\", \"Sum_of_nearest_neighbors\", \"eigenVector_centrAlitY\"), we = c(50,     15, 15, 20), linkcutoff = -1),   neg_exp = neg_expo(NULL, gammas = c(0.05, 1, 0.2, 0.3), mets = c(\"betweeness\",     \"NODE_STRENGTH\", \"Sum_of_nearest_neighbors\", \"eigenVector_centrAlitY\"), we = c(50,     15, 15, 20), linkcutoff = -1) )  msean(   rast,   global = TRUE,   geoscale = NULL,   res = reso(),   ...,   outdir = tempdir() )"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"rast Raster object used analysis. global Logical. TRUE global analysis, FALSE otherwise. Default TRUE geoscale Numeric vector. Geographical coordinates form c(Xmin, Xmax, Ymin, Ymax) EPSG:4326 coordinate reference system. geoscale NuLL, extent extracted rast(SpatRaster) using terra::ext(). agg_methods Character. One values - SUM, MEAN. Aggregation strategy scaling input raster desired resolution. dist_method Character. method calculate distance matrix. link_threshold Numeric. threshold value link weight. link weights threshold replaced zero connectivity analysis. Link weights represent relative likelihood pathogen, pest, invasive species movement pair host locations, calculated using gravity models based host density (availability) dispersal kernels. hd_threshold Numeric. threshold value host density. locations host density selected threshold excluded connectivity analysis, focuses analysis important locations. values host density threshold can range 0 1; value 1, locations excluded analysis 0 include locations analysis. Selecting threshold host density requires least knowing maximum value host density map avoid excluding locations analysis. value 1, locations excluded analysis 0 include locations analysis. Selecting threshold host density requires least knowing maximum value host density map avoid excluding locations analysis. res Numeric. Resolution raster. Default reso(). inv_pl List. named list parameters inverse power law. See details. neg_exp List. named list parameters inverse negative exponential. See details. locations host density selected threshold excluded connectivity analysis, focuses analysis important locations. values host density threshold can range 0 1; ... arguments passed sean() outdir Character. Output directory saving raster TIFF format. Default tempdir().","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"GeoRasters. GeoNetwork.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"global = TRUE, geoscale ignored global_scales() used default. functions sean() msean() perform sensitivity analysis, differ return value. return value msean() GeoNetwork, contains result applying connectivity() function habitat connectivity indexes. Essentially, risk maps. neither inverse power law negative exponential dispersal kernel specified, function return error. msean(), three spatRasters produced following values. location area interest, mean habitat connectivity across selected parameters calculated. location area interest, variance habitat connectivity across selected parameters calculated. location area interest, difference rank habitat connectivity rank host density calculated. default, spatRasters plotted visualization.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sensitivity analysis across maps of habitat connectivity — sean","text":"","code":"# \\donttest{ avocado <- cropharvest_rast(\"avocado\", \"monfreda\")  # global ri <- sean(avocado) # returns a list of GeoRasters mri <- msean(rast = avocado) # returns GeoNetwork object  # non-global # geoscale is a vector of xmin, xmax, ymin, ymax  # returns GeoRasters object ri <- sean(avocado, global = FALSE, geoscale = c(-115, -75, 5, 32)) ri  # returns GeoNetwork object mri <- msean(rast = avocado, global = FALSE, geoscale = c(-115, -75, 5, 32)) mri # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":null,"dir":"Reference","previous_headings":"","what":"Search for crop — search_crop","title":"Search for crop — search_crop","text":"returns dataset sources crop data available. Essentially, wrapper around geodata::spamCrops() geodata::monfredaCrops()","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search for crop — search_crop","text":"","code":"search_crop(name)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search for crop — search_crop","text":"name name crop","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search for crop — search_crop","text":"Logical. Sources iin crop data available.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/search_crop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search for crop — search_crop","text":"","code":"search_crop(\"coffee\") search_crop(\"wheat\") # \\donttest{ search_crop(\"jackfruit\") # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"function runs sensitivity analysis habitat connectivity calculated based every combination selected parameters. Parameter values sensitivity_analysis() provided using function set_parameters(). parameters provided, sensitivity_analysis() function run sensitivity analysis using default set parameter values, accessible function get_parameters(). customize parameter values, open parameters.yaml automatically downloaded geohabnet installed, change, remove, add parameter values directly parameters.yaml save . values changed manually, run set_parameters() set new parameter values, return TRUE parameters set successfully.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"","code":"sensitivity_analysis(maps = TRUE, alert = TRUE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"maps logical. TRUE maps outcomes plotted, FALSE otherwise. TRUE, three maps possible: map mean habitat connectivity, map variance habitat connectivity, map difference ranks habitat connectivity habitat density. alert logical. TRUE beep sound played analysis completed, FALSE otherwise","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"GeoNetwork. Errors handled.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"location region, sensitivity_analysis() calculates habitat connectivity risk index (CCRI) proposed Xing et al. (2021). default, sensitivity_analysis() runs sensitivity analysis global extent, see global_scales() details. function also plots maps outcomes automatically, suppress maps outcomes maps = FALSE interactive() FALSE. returned object class GeoNetwork, contains two types outcomes. One outcome type corresponds spatRasters representing maps habitat connectivity. second type corresponds adjacency matrices used calculate habitat connectivity, columns rows represent locations maps entries relative likelihood pathogen pest movement pair nodes.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"Yanru Xing, John F Hernandez Nopsa, Kelsey F Andersen, Jorge L Andrade-Piedra, Fenton D Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny L Coyne, Wilmer J Cuellar, Gregory Forbes, Jan F Kreuze, Jürgen Kroschel, P Lava Kumar, James P Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen Garrett, Global Cropland .connectivity: Risk Factor Invasion Saturation Emerging Pathogens Pests, BioScience, Volume 70, Issue 9, September 2020, Pages 744–758, doi:10.1093/biosci/biaa067 Hijmans R (2023). terra: Spatial Data Analysis. R package version 1.7-46, https://CRAN.R-project.org/package=terra","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sensitivity_analysis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sensitivity analysis for habitat connectivity — sensitivity_analysis","text":"","code":"# \\donttest{ # Run analysis on specified parameters.yaml ss1 <- sensitivity_analysis() ss2 <- sensitivity_analysis(FALSE, FALSE) ss3 <- sensitivity_analysis(TRUE, FALSE) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"wraps results(SpatRasters) risk analysis.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"","code":"# S4 method for Gmap setmaps(x, me, vari, dif)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"x Gmap object. GeoRaster object representing mean risk index. vari GeoRaster object representing variance. dif GeoRaster object representing difference.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/setmaps-Gmap-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets the map slots in the Gmap object. — setmaps,Gmap-method","text":"Gmap object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":null,"dir":"Reference","previous_headings":"","what":"Set global geographical extent — set_global_scales","title":"Set global geographical extent — set_global_scales","text":"Set geographical extents used global analysis. extent form c(Xmin, Xmax, Ymin, Ymax)","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set global geographical extent — set_global_scales","text":"","code":"set_global_scales(value)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set global geographical extent — set_global_scales","text":"value list. Named list eastern western hemisphere extents. See usage.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set global geographical extent — set_global_scales","text":"List. Named list scales eastern western hemisphere","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_global_scales.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set global geographical extent — set_global_scales","text":"","code":"set_global_scales(list(east = c(-24, 180, -58, 60), west = c(-140, -34, -58, 60)))"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Parameters — set_parameters","title":"Set Parameters — set_parameters","text":"function allows set parameters replacing existing parameters file new one. Use get_parameters() modify parameter values.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Parameters — set_parameters","text":"","code":"set_parameters(new_params, iwindow = FALSE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Parameters — set_parameters","text":"new_params path new parameters file. iwindow Logical indicating whether prompt user select new parameters file using file selection window. Defaults FALSE.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Parameters — set_parameters","text":"None","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/set_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Parameters — set_parameters","text":"","code":"param_fp <- get_parameters() set_parameters(param_fp)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Raster for mapspam crop. — sp_rast","title":"Raster for mapspam crop. — sp_rast","text":"get raster crop mapspam dataset","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raster for mapspam crop. — sp_rast","text":"","code":"sp_rast(crp, africa = FALSE)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raster for mapspam crop. — sp_rast","text":"crp character. name crop. Case-insensitive. africa Fetch 2017 Mpaspam crop data Africa. Default FALSE.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Raster for mapspam crop. — sp_rast","text":"SpatRaster","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Raster for mapspam crop. — sp_rast","text":"See geodata::spamCrops() supported crops.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Raster for mapspam crop. — sp_rast","text":"International Food Policy Research Institute, 2020. Spatially-Disaggregated Crop Production Statistics Data Africa South Sahara 2017. <doi: 10.7910/DVN/FSSKBW>, Harvard Dataverse, V2","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/sp_rast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Raster for mapspam crop. — sp_rast","text":"","code":"# \\donttest{ sp_rast(\"potato\") sp_rast(\"potato\", TRUE) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_BETWEENNESS.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","title":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_BETWEENNESS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","text":"","code":"STR_BETWEENNESS"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_BETWEENNESS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_BETWEENNESS","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_CLOSENESS_CENTRALITY.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","title":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_CLOSENESS_CENTRALITY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","text":"","code":"STR_CLOSENESS_CENTRALITY"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_CLOSENESS_CENTRALITY.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_CLOSENESS_CENTRALITY","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DEGREE.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_DEGREE","title":"global variable containing string. Not intended to modify. — STR_DEGREE","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DEGREE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_DEGREE","text":"","code":"STR_DEGREE"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DEGREE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_DEGREE","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DISTANCE_MATRIX.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","title":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DISTANCE_MATRIX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","text":"","code":"STR_DISTANCE_MATRIX"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_DISTANCE_MATRIX.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_DISTANCE_MATRIX","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EAST.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_EAST","title":"global variable containing string. Not intended to modify. — STR_EAST","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EAST.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_EAST","text":"","code":"STR_EAST"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EAST.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_EAST","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EIGEN_VECTOR_CENTRALITY.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","title":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EIGEN_VECTOR_CENTRALITY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","text":"","code":"STR_EIGEN_VECTOR_CENTRALITY"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_EIGEN_VECTOR_CENTRALITY.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_EIGEN_VECTOR_CENTRALITY","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NEAREST_NEIGHBORS_SUM.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","title":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NEAREST_NEIGHBORS_SUM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","text":"","code":"STR_NEAREST_NEIGHBORS_SUM"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NEAREST_NEIGHBORS_SUM.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_NEAREST_NEIGHBORS_SUM","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NODE_STRENGTH.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","title":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NODE_STRENGTH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","text":"","code":"STR_NODE_STRENGTH"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_NODE_STRENGTH.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_NODE_STRENGTH","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_PAGE_RANK.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","title":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_PAGE_RANK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","text":"","code":"STR_PAGE_RANK"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_PAGE_RANK.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_PAGE_RANK","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_WEST.html","id":null,"dir":"Reference","previous_headings":"","what":"global variable containing string. Not intended to modify. — STR_WEST","title":"global variable containing string. Not intended to modify. — STR_WEST","text":"global variable containing string. intended modify.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_WEST.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"global variable containing string. Not intended to modify. — STR_WEST","text":"","code":"STR_WEST"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/STR_WEST.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"global variable containing string. Not intended to modify. — STR_WEST","text":"object class character length 1.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns metrics currently supported in the analysis. — supported_metrics","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"Returns metrics currently supported analysis.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"","code":"supported_metrics()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"vector supported metrics.","code":""},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_metrics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Returns metrics currently supported in the analysis. — supported_metrics","text":"","code":"supported_metrics()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":null,"dir":"Reference","previous_headings":"","what":"Get supported sources of crops — supported_sources","title":"Get supported sources of crops — supported_sources","text":"provided, cropharvest_rast() look cropland data specific source.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get supported sources of crops — supported_sources","text":"","code":"supported_sources()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get supported sources of crops — supported_sources","text":"Vector supported sources. Also used lookup find get raster object.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/supported_sources.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get supported sources of crops — supported_sources","text":"","code":"# Get currently supported sources supported_sources()"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":null,"dir":"Reference","previous_headings":"","what":"Get raster object from tif file — tiff_torast","title":"Get raster object from tif file — tiff_torast","text":"wrapper terra::rast() generates raster object provided TIF file.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get raster object from tif file — tiff_torast","text":"","code":"tiff_torast(path_to_tif)"},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get raster object from tif file — tiff_torast","text":"path_to_tif TIFF file. encoding map raster format.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get raster object from tif file — tiff_torast","text":"SpatRaster.","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/reference/tiff_torast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get raster object from tif file — tiff_torast","text":"","code":"# \\donttest{ # Generate raster for usage fp <- paste(tempfile(), \".tif\", sep = \"\") ret <- utils::download.file( \"https://geohabnet.s3.us-east-2.amazonaws.com/util-rasters/avocado_HarvestedAreaFraction.tif\", destfile = fp, method = \"auto\", mode = \"wb\") tiff_torast(fp) # }"},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-211","dir":"Changelog","previous_headings":"","what":"geohabnet 2.1.1","title":"geohabnet 2.1.1","text":"Removed dependency Amazon S3","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-210","dir":"Changelog","previous_headings":"","what":"geohabnet 2.1.0","title":"geohabnet 2.1.0","text":"CRAN release: 2024-03-28 Dispersal kernels can now either Inverse Power Law Exponential Renamed CCRI HCI","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-200","dir":"Changelog","previous_headings":"","what":"geohabnet 2.0.0","title":"geohabnet 2.0.0","text":"CRAN release: 2024-02-27 Adoption habitat connectivity Corrected difference map Added support mapspam 2010 2017 Africa data Corrected weight transformation closeness betweenness Removed global variables Fixed bugs New functions - msean() New parameters Returning objects S4 classes sensitivity_analysis() include Adjacency matrix Supports parallel processing future package functions support risk parameters New/updated vignette New/updated examples New tests New/updated documentation","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-101","dir":"Changelog","previous_headings":"","what":"geohabnet 1.0.1","title":"geohabnet 1.0.1","text":"CRAN release: 2023-10-31","code":""},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-100","dir":"Changelog","previous_headings":"","what":"geohabnet 1.0.0","title":"geohabnet 1.0.0","text":"CRAN release: 2023-10-20","code":""},{"path":[]},{"path":[]},{"path":"https://garrettlab.github.io/HabitatConnectivity/news/index.html","id":"geohabnet-0009000","dir":"Changelog","previous_headings":"","what":"geohabnet 0.0.0.9000","title":"geohabnet 0.0.0.9000","text":"Added NEWS.md file track changes package.","code":""}]
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