version 3.0.7

cran · Sep 7, 2017 · e152cbb · e152cbb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: propr
 Title: Calculating Proportionality Between Vectors of Compositional
         Data
-Version: 3.0.6
+Version: 3.0.7
 URL: http://github.com/tpq/propr
 BugReports: http://github.com/tpq/propr/issues
 Authors@R: c(
@@ -32,12 +32,12 @@ Suggests: ALDEx2, cccrm, compositions, data.table, datasets,
         rgl, rmarkdown, SDMTools, testthat
 LinkingTo: Rcpp
 NeedsCompilation: yes
-Packaged: 2017-08-01 02:13:07 UTC; thom
+Packaged: 2017-09-07 01:01:29 UTC; thom
 Author: Thomas Quinn [aut, cre],
   David Lovell [aut],
   Ionas Erb [aut],
   Anders Bilgrau [ctb],
   Greg Gloor [ctb]
 Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
 Repository: CRAN
-Date/Publication: 2017-08-01 04:54:56 UTC
+Date/Publication: 2017-09-07 03:16:58 UTC
diff --git a/MD5 b/MD5
@@ -1,6 +1,6 @@
-721897edcdb7dbcef8a41929f8723a5c *DESCRIPTION
-d565bb7f4ec66a88641100af299a0e1d *NAMESPACE
-05bdec3ed057f9049a9082c712aa489b *NEWS.md
+e7cd3c5920dbab73d42c9326c7191c6a *DESCRIPTION
+acc229b4b3fc7470268ec9bd45855671 *NAMESPACE
+fa6c8f8afe174cb3fa4f3f905e43cd65 *NEWS.md
 81c9b019b2c16e5c7124a36614f6b71e *R/RcppExports.R
 01cde507c5d5e55e797ad1139adeed3e *R/aldex2propr.R
 b887c19bf022fe5fe5cdc8565d3c0531 *R/deprecated.R
@@ -10,11 +10,11 @@ ad9bac9121a00d2bc230ecd205f05cef *R/deprecated2.R
 0b4893e99cb5bc7cfd80236b7a2d9337 *R/prop2prob.R
 4474f46962ee8df30f3fa4b02e04a29f *R/propd.R
 f164508ea487664433e258a0fa7834e8 *R/propdViz.R
-fa6205626e683e0ec43b41e0acafa57d *R/propr.R
+6b54592b1a5bc83247a41bec46674228 *R/propr.R
 da5d625b63179c066372091aa823c932 *R/proprViz.R
 641e20cada832fc8982131ccc7bda490 *R/theta.R
 87938842c4ac82eaaf773e687768a419 *README.md
-5ce8b577741214ef5e1b05c9a8acc9ba *build/vignette.rds
+dcd734a88ad745b1f6ba258b88a90359 *build/vignette.rds
 85afe8e966882d64a79de4ad8f198689 *data/caneToad.counts.rda
 73203b36c5c9e855bd52d9beefaf5195 *data/caneToad.groups.rda
 f937a82f42500a3aec725965e09b3ac8 *data/datalist
@@ -27,22 +27,22 @@ ed6a318a02091045e6fd3b1064cd7929 *data/top.lr.rda
 7300a38fd7b1982307c40dbe372b051b *inst/CITATION
 0d3367acb9f2735c5ccf15cd4bf2994b *inst/doc/a_introduction.R
 de5ea8db708de283072c01540f4c20dc *inst/doc/a_introduction.Rmd
-b8521d647c00f14667d48c1db2695283 *inst/doc/a_introduction.html
+c8b10c046c0633cf83257c0401ecdf70 *inst/doc/a_introduction.html
 4ed6a9581eba3ae5c93b78ba0e73ed3f *inst/doc/b_visualization.R
 fa77645fd963270253ff4ca76493dc21 *inst/doc/b_visualization.Rmd
-7f3d8f531a32df33fe523ffae44f3898 *inst/doc/b_visualization.html
+1a115621af15ce0660111f21fa11a241 *inst/doc/b_visualization.html
 d1ad2bea45ee5bd03f5c30ff5408af8c *inst/doc/c_indexing.R
 c1df1951c507a95db25c2d90aa75aea0 *inst/doc/c_indexing.Rmd
-e9a356bf0a67664a9e37ef1bf99476ab *inst/doc/c_indexing.html
+e6b316db5726d2102d592b5099a9cb96 *inst/doc/c_indexing.html
 fbbe4b58eb9d04467b6fa097c4923550 *inst/doc/d_advanced.R
 91bd664bd397584c83393e0678fdb677 *inst/doc/d_advanced.Rmd
-2245f5336e2597c47462e5942619240a *inst/doc/d_advanced.html
+e4c7b02b182b6acdde06628c33559deb *inst/doc/d_advanced.html
 483013ee2dc09c151cb69c13a0df97fd *inst/doc/e_differential.R
-a0a341b6babeb16abb8b7f092d1fdaa0 *inst/doc/e_differential.Rmd
-e1db979b7f39612b965b30f3ae93fd14 *inst/doc/e_differential.html
+6bfec570b198e0e2d33d6db0bca90efd *inst/doc/e_differential.Rmd
+93614a99f45d12ba75f2c27d94dca2f3 *inst/doc/e_differential.html
 33a9bed57d1e32b52a309e6280fd2ddd *inst/doc/f_questions.R
 85d948cd2caf933f952c47ca945044d1 *inst/doc/f_questions.Rmd
-dc9c10d046f0b012a765806e84108c69 *inst/doc/f_questions.html
+a98faba3614134a302a82679e5a1475f *inst/doc/f_questions.html
 427a5e0e1922bf1f26ffcf145b0f2514 *man/abstract.Rd
 fd9e9ce2d1945ebda1a16405a88dc8e3 *man/aldex.cor.Rd
 2f058dcf3c697dc7d60c76b6b76c4efc *man/aldex2propr.Rd
@@ -77,7 +77,7 @@ c9baab60334ab67c888875a85cf35a45 *man/permuteTheta_false.Rd
 fba2ae11371baae737b38b4cdc1704a1 *man/promptCheck.Rd
 60af8c378f8a0f7999220bc348a8e68d *man/prop2prob.Rd
 f22a3a3d9c2dd7058061704f71b54fb1 *man/propd.Rd
-e924e970e26943209ea1eda629497044 *man/proportionality.Rd
+423a58de9432ce021cd9838044ea0307 *man/proportionality.Rd
 d6a51e7e86e61af949fa850daf23acfb *man/propr.Rd
 69e193aa9e879f1bf164ce7a3a086788 *man/proprALR.Rd
 10ef4645cb4e6684df607c7e888f5d6d *man/proprCLR.Rd
@@ -117,5 +117,5 @@ de5ea8db708de283072c01540f4c20dc *vignettes/a_introduction.Rmd
 fa77645fd963270253ff4ca76493dc21 *vignettes/b_visualization.Rmd
 c1df1951c507a95db25c2d90aa75aea0 *vignettes/c_indexing.Rmd
 91bd664bd397584c83393e0678fdb677 *vignettes/d_advanced.Rmd
-a0a341b6babeb16abb8b7f092d1fdaa0 *vignettes/e_differential.Rmd
+6bfec570b198e0e2d33d6db0bca90efd *vignettes/e_differential.Rmd
 85d948cd2caf933f952c47ca945044d1 *vignettes/f_questions.Rmd
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,7 @@ export(bokeh)
 export(bowtie)
 export(bucket)
 export(calculateTheta)
+export(corr)
 export(cytescape)
 export(decomposed)
 export(dendrogram)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+## propr 3.0.7
+---------------------
+* New `corr` function calculates log-ratio based correlation
+* Fixed mistake with vignette indexing
+
 ## propr 3.0.6
 ---------------------
 * Modified visualization tools

diff --git a/R/propr.R b/R/propr.R
@@ -12,6 +12,8 @@
 #' 	analogous to a correlation matrix.
 #' 	For phs, the result of \code{phis}, one can think of the resultant matrix as
 #' 	either a naturally symmetric variant of phi or a monotonic variant of rho.
+#' 	Another function, \code{corr}, calculates Pearsons' correlation using
+#' 	log-ratio transformed data.
 #'
 #' These methods all use the centered log-ratio transformation by default,
 #'  but will use an additive log-ratio transformation instead if a scalar
@@ -161,3 +163,12 @@ phis <- function(counts, ivar = 0, select){
   prop@matrix <- lr2phs(prop@logratio)
   return(prop)
 }
+
+#' @rdname proportionality
+#' @export
+corr <- function(counts, ivar = 0, select){
+
+  prop <- new("propr", counts = counts, ivar = ivar, select = select)
+  prop@matrix <- stats::cor(prop@logratio)
+  return(prop)
+}
diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/doc/a_introduction.html b/inst/doc/a_introduction.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Thomas Quinn" />
 
-<meta name="date" content="2017-08-01" />
+<meta name="date" content="2017-09-07" />
 
 <title>An Introduction to Proportionality</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">An Introduction to Proportionality</h1>
 <h4 class="author"><em>Thomas Quinn</em></h4>
-<h4 class="date"><em>2017-08-01</em></h4>
+<h4 class="date"><em>2017-09-07</em></h4>
 
 
 

diff --git a/inst/doc/b_visualization.html b/inst/doc/b_visualization.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Thomas Quinn" />
 
-<meta name="date" content="2017-08-01" />
+<meta name="date" content="2017-09-07" />
 
 <title>Understanding Proportionality through Visualization</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Understanding Proportionality through Visualization</h1>
 <h4 class="author"><em>Thomas Quinn</em></h4>
-<h4 class="date"><em>2017-08-01</em></h4>
+<h4 class="date"><em>2017-09-07</em></h4>
 
 
 

diff --git a/inst/doc/c_indexing.html b/inst/doc/c_indexing.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Thomas Quinn" />
 
-<meta name="date" content="2017-08-01" />
+<meta name="date" content="2017-09-07" />
 
 <title>How Proportional Is Proportional Enough?</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">How Proportional Is Proportional Enough?</h1>
 <h4 class="author"><em>Thomas Quinn</em></h4>
-<h4 class="date"><em>2017-08-01</em></h4>
+<h4 class="date"><em>2017-09-07</em></h4>
 
 
 

diff --git a/inst/doc/d_advanced.html b/inst/doc/d_advanced.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Thomas Quinn" />
 
-<meta name="date" content="2017-08-01" />
+<meta name="date" content="2017-09-07" />
 
 <title>A Brief Critique of Proportionality</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">A Brief Critique of Proportionality</h1>
 <h4 class="author"><em>Thomas Quinn</em></h4>
-<h4 class="date"><em>2017-08-01</em></h4>
+<h4 class="date"><em>2017-09-07</em></h4>
 
 
 

diff --git a/inst/doc/e_differential.Rmd b/inst/doc/e_differential.Rmd
@@ -4,7 +4,7 @@ author: "Thomas Quinn & Ionas Erb"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{4. Calculating Differential Proportionality}
+  %\VignetteIndexEntry{5. Calculating Differential Proportionality}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/inst/doc/e_differential.html b/inst/doc/e_differential.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Thomas Quinn &amp; Ionas Erb" />
 
-<meta name="date" content="2017-08-01" />
+<meta name="date" content="2017-09-07" />
 
 <title>Calculating Differential Proportionality</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Calculating Differential Proportionality</h1>
 <h4 class="author"><em>Thomas Quinn &amp; Ionas Erb</em></h4>
-<h4 class="date"><em>2017-08-01</em></h4>
+<h4 class="date"><em>2017-09-07</em></h4>
 
 
 

diff --git a/inst/doc/f_questions.html b/inst/doc/f_questions.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Thomas Quinn" />
 
-<meta name="date" content="2017-08-01" />
+<meta name="date" content="2017-09-07" />
 
 <title>Frequently Asked Questions</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Frequently Asked Questions</h1>
 <h4 class="author"><em>Thomas Quinn</em></h4>
-<h4 class="date"><em>2017-08-01</em></h4>
+<h4 class="date"><em>2017-09-07</em></h4>
 
 
 

diff --git a/man/proportionality.Rd b/man/proportionality.Rd
diff --git a/vignettes/e_differential.Rmd b/vignettes/e_differential.Rmd
@@ -4,7 +4,7 @@ author: "Thomas Quinn & Ionas Erb"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{4. Calculating Differential Proportionality}
+  %\VignetteIndexEntry{5. Calculating Differential Proportionality}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---