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sim_data.html
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sim_data.html
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<!DOCTYPE html>
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<h1>Simulated conservation planning data</h1>
<small class="dont-index">Source: <a href="https://github.com/prioritizr/prioritizr/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="hidden name"><code>sim_data.Rd</code></div>
</div>
<div class="ref-description">
<p>Simulated data for making spatial prioritizations.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_polygons</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_zones_polygons</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_points</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_lines</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_sf</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_zones_sf</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_raster</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_locked_in_raster</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_locked_out_raster</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_zones_stack</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_features</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_features_zones</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_phylogeny</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
<dl><dt>sim_pu_polygons</dt>
<dd><p><code><a href="https://rdrr.io/pkg/sp/man/SpatialPolygonsDataFrame-class.html" class="external-link">SpatialPolygonsDataFrame</a></code>
object.</p></dd>
<dt>sim_pu_zones_polygons</dt>
<dd><p><code><a href="https://rdrr.io/pkg/sp/man/SpatialPolygonsDataFrame-class.html" class="external-link">SpatialPolygonsDataFrame</a></code> object.</p></dd>
<dt>sim_pu_sf</dt>
<dd><p><code><a href="https://r-spatial.github.io/sf/reference/sf.html" class="external-link">sf::sf()</a></code> object.</p></dd>
<dt>sim_pu_zones_sf</dt>
<dd><p><code><a href="https://r-spatial.github.io/sf/reference/sf.html" class="external-link">sf::sf()</a></code> object.</p></dd>
<dt>sim_pu_lines</dt>
<dd><p><code><a href="https://rdrr.io/pkg/sp/man/SpatialLinesDataFrame-class.html" class="external-link">SpatialLinesDataFrame</a></code> object.</p></dd>
<dt>sim_pu_points</dt>
<dd><p><code><a href="https://rdrr.io/pkg/sp/man/SpatialPointsDataFrame-class.html" class="external-link">SpatialPointsDataFrame</a></code>
object.</p></dd>
<dt>sim_pu_raster</dt>
<dd><p><code><a href="https://rdrr.io/pkg/raster/man/Raster-classes.html" class="external-link">RasterLayer</a></code> object.</p></dd>
<dt>sim_pu_zones_stack</dt>
<dd><p><code><a href="https://rdrr.io/pkg/raster/man/Raster-classes.html" class="external-link">RasterStack</a></code> object.</p></dd>
<dt>sim_locked_in_raster</dt>
<dd><p><code><a href="https://rdrr.io/pkg/raster/man/Raster-classes.html" class="external-link">RasterLayer</a></code>
object.</p></dd>
<dt>sim_locked_out_raster</dt>
<dd><p><code><a href="https://rdrr.io/pkg/raster/man/Raster-classes.html" class="external-link">RasterLayer</a></code>
object.</p></dd>
<dt>sim_features</dt>
<dd><p><code><a href="https://rdrr.io/pkg/raster/man/Raster-classes.html" class="external-link">RasterStack</a></code> object.</p></dd>
<dt>sim_features_zones</dt>
<dd><p><code><a href="zones.html">ZonesRaster()</a></code> object.</p></dd>
<dt>sim_phylogeny</dt>
<dd><p><code><a href="https://rdrr.io/pkg/ape/man/read.tree.html" class="external-link">ape::phylo()</a></code> object.</p></dd>
</dl></div>
<div id="details">
<h2>Details</h2>
<dl><dt><code>sim_pu_raster</code></dt>
<dd><p>Planning units are represented as raster data.
Pixel values indicate planning unit cost and <code>NA</code> values indicate
that a pixel is not a planning unit.</p></dd>
<dt><code>sim_pu_zones_stack</code></dt>
<dd><p>Planning units are represented as raster
stack data. Each layer indicates the cost for a different management
zone. Pixels with <code>NA</code> values in a given zone indicate that a
planning unit cannot be allocated to that zone in a solution.
Additionally, pixels with <code>NA</code> values in all layers are not a
planning unit.</p></dd>
<dt><code>sim_locked_in_raster</code></dt>
<dd><p>Planning units are represented as raster
data. Pixel values are binary and indicate if planning units should be
locked in to the solution.</p></dd>
<dt><code>sim_locked_out_raster</code></dt>
<dd><p>Planning units are represented as
raster data. Pixel values are binary and indicate if planning units
should be locked out from the solution.</p></dd>
<dt><code>sim_pu_polygons</code></dt>
<dd><p>Planning units represented as polygon data.
The attribute table contains fields (columns) indicating the expenditure
required for prioritizing each planning unit ("cost" field), if the
planning units should be selected in the solution ("locked_in" field),
and if the planning units should never be selected in the solution
("locked_out" field).</p></dd>
<dt><code>sim_pu_points</code></dt>
<dd><p>Planning units represented as point data.
The attribute table follows the same conventions as for
<code>sim_pu_polygons</code>.</p></dd>
<dt><code>sim_pu_lines</code></dt>
<dd><p>Planning units represented as line data.
The attribute table follows the same conventions as for
<code>sim_pu_polygons</code>.</p></dd>
<dt><code>sim_pu_sf</code></dt>
<dd><p>Planning units represented as polygon data
using the <code><a href="https://r-spatial.github.io/sf/reference/sf.html" class="external-link">sf::sf()</a></code> package.
The attribute table follows the same conventions as for
<code>sim_pu_polygons</code>.</p></dd>
<dt><code>sim_pu_zones_polygons</code></dt>
<dd><p>Planning units represented as polygon
data. The attribute table contains fields (columns) indicating the
expenditure required for prioritizing each planning unit under different
management zones ("cost_1", "cost_2", and "cost_3" fields), and a series
of fields indicating the value that each planning unit that should be
assigned in the solution ("locked_1", "locked_2", "locked_3" fields).
In these locked fields, planning units that should not be locked to a
specific value are assigned a <code>NA</code> value.</p></dd>
<dt><code>sim_pu_zones_sf</code></dt>
<dd><p>Planning units represented as polygon data
using the <code><a href="https://r-spatial.github.io/sf/reference/sf.html" class="external-link">sf::sf()</a></code> package. The attribute tables follows
the same conventions as for <code>sim_pu_zone_polygons</code>.</p></dd>
<dt><code>sim_features</code></dt>
<dd><p>The simulated distribution of ten species.
Pixel values indicate habitat suitability.</p></dd>
<dt><code>sim_features_zones</code></dt>
<dd><p>The simulated distribution for five
species under three different management zones.</p></dd>
<dt><code>sim_phylogeny</code></dt>
<dd><p>The phylogenetic tree for the ten species.</p></dd>
</dl></div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># load data</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_polygons</span>, <span class="va">sim_pu_lines</span>, <span class="va">sim_pu_points</span>, <span class="va">sim_pu_raster</span>,</span></span>
<span class="r-in"><span> <span class="va">sim_locked_in_raster</span>, <span class="va">sim_locked_out_raster</span>, <span class="va">sim_phylogeny</span>,</span></span>
<span class="r-in"><span> <span class="va">sim_features</span>, <span class="va">sim_pu_sf</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot example Spatial-class planning unit data</span></span></span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>mfrow <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">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_pu_raster</span>, main <span class="op">=</span> <span class="st">"planning units (raster)"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_locked_in_raster</span>, main <span class="op">=</span> <span class="st">"locked in units (raster)"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_locked_out_raster</span>, main <span class="op">=</span> <span class="st">"locked out units (raster)"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_pu_polygons</span>, main <span class="op">=</span> <span class="st">"planning units (polygons)"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_pu_lines</span>, main <span class="op">=</span> <span class="st">"planning units (lines)"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_pu_points</span>, main <span class="op">=</span> <span class="st">"planning units (points)"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="sim_data-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot example sf-class planning unit data</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_pu_sf</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="sim_data-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot example phylogeny data</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>mfrow <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">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">ape</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/ape/man/plot.phylo.html" class="external-link">plot.phylo</a></span><span class="op">(</span><span class="va">sim_phylogeny</span>, main <span class="op">=</span> <span class="st">"simulated phylogeny"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="sim_data-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot example feature data</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>mfrow <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">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_features</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="sim_data-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot example management zone cost data</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/par.html" class="external-link">par</a></span><span class="op">(</span>mfrow <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">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sim_pu_zones_stack</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="sim_data-5.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot example feature data for each management zone</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/do.call.html" class="external-link">do.call</a></span><span class="op">(</span><span class="va">stack</span>, <span class="va">sim_features_zones</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Species "</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fu"><a href="number_of_zones.html">number_of_zones</a></span><span class="op">(</span><span class="va">sim_features_zones</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="number_of_features.html">number_of_features</a></span><span class="op">(</span><span class="va">sim_features_zones</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="st">" (zone "</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fu"><a href="number_of_features.html">number_of_features</a></span><span class="op">(</span><span class="va">sim_features_zones</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> each <span class="op">=</span> <span class="fu"><a href="number_of_zones.html">number_of_zones</a></span><span class="op">(</span><span class="va">sim_features_zones</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="st">")"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="sim_data-6.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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