version 3.0.4

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: propr
 Title: Calculating Proportionality Between Vectors of Compositional
         Data
-Version: 2.2.0
+Version: 3.0.4
 URL: http://github.com/tpq/propr
 BugReports: http://github.com/tpq/propr/issues
 Authors@R: c(
     person("Thomas", "Quinn", email = "contacttomquinn@gmail.com", role = c("aut", "cre")),
     person("David", "Lovell", email = "david.lovell@qut.edu.au", role = "aut"),
-    person("Ionas", "Erb", email = "ionas.erb@crg.eu", role = "ctb"),
+    person("Ionas", "Erb", email = "ionas.erb@crg.eu", role = "aut"),
     person("Anders", "Bilgrau", email = "anders.ellern.bilgrau@gmail.com", role = "ctb"),
     person("Greg", "Gloor", email = "ggloor@uwo.ca", role = "ctb")
     )
@@ -27,17 +27,18 @@ LazyData: true
 VignetteBuilder: knitr
 RoxygenNote: 6.0.1
 Depends: methods, R (>= 3.2.2)
-Imports: fastcluster, ggplot2, igraph, Rcpp, stats, utils
-Suggests: ALDEx2, cccrm, compositions, data.table, grid, ggdendro,
-        knitr, plotly, reshape2, rgl, rmarkdown, testthat
+Imports: fastcluster, ggplot2, grDevices, igraph, Rcpp, stats, utils
+Suggests: ALDEx2, cccrm, compositions, data.table, datasets,
+        directlabels, grid, ggdendro, knitr, limma, plotly, reshape2,
+        rgl, rmarkdown, SDMTools, testthat
 LinkingTo: Rcpp
 NeedsCompilation: yes
-Packaged: 2017-04-19 00:49:55 UTC; thom
+Packaged: 2017-06-02 00:42:48 UTC; thom
 Author: Thomas Quinn [aut, cre],
   David Lovell [aut],
-  Ionas Erb [ctb],
+  Ionas Erb [aut],
   Anders Bilgrau [ctb],
   Greg Gloor [ctb]
 Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
 Repository: CRAN
-Date/Publication: 2017-04-19 03:58:50 UTC
+Date/Publication: 2017-06-02 05:26:33 UTC

MD5

@@ -1,82 +1,117 @@
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-a2082244eaaad50faf69f348fdb88685 *NAMESPACE
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+63d12e493009299a1aba9d785e5f27fd *vignettes/b_visualization.Rmd
+c0f8a55ce971fb97e30cdd76079ed2d1 *vignettes/c_cutoffs.Rmd
+33a64e291aa4529e2364d09fd4cf2bd1 *vignettes/d_differential.Rmd
+dfca65f33963b1461c56c5271db4921a *vignettes/e_questions.Rmd

NAMESPACE

@@ -5,20 +5,35 @@ export(adjacent)
 export(aldex.cor)
 export(aldex2propr)
 export(bokeh)
+export(bowtie)
 export(bucket)
+export(calculateTheta)
 export(cytescape)
+export(decomposed)
 export(dendrogram)
+export(geiser)
+export(gemini)
 export(lr2cor)
+export(pals)
 export(pca)
 export(perb)
 export(phis)
 export(phit)
 export(prism)
 export(prop2prob)
+export(propd)
+export(propd2propr)
+export(setActive)
+export(setDisjointed)
+export(setEmergent)
+export(shale)
 export(simplify)
 export(slate)
+export(slice)
 export(smear)
 export(snapshot)
+export(updateCutoffs)
+exportClasses(propd)
 exportClasses(propr)
 exportMethods("[")
 exportMethods(plot)
@@ -39,4 +54,5 @@ importFrom(stats,p.adjust)
 importFrom(stats,pnorm)
 importFrom(stats,prcomp)
 importFrom(stats,var)
+importFrom(utils,head)
 useDynLib(propr, .registration = TRUE)

NEWS.md

@@ -1,3 +1,61 @@
+## propr 3.0.4
+---------------------
+* Modified `calculateTheta`
+    * Now saves log-ratio variance (LRV) modifier in output
+* Modified visualization tools
+    * New `decomposed` function for LRV decomposition
+    * Uses LRV modifier for weighted theta types
+
+## propr 3.0.3
+---------------------
+* Modified visualization tools
+    * Updated `plot.propd` method to display `theta_f`
+
+## propr 3.0.2
+---------------------
+* Modified `propd` Class
+    * Added `@weighted` slot now used by `updateCutoffs`
+* Implement backend for "weighted theta" calculation
+    * Added `wtmRcpp` for weighted mean calculation
+    * Added `wtvRcpp` for weighted variance calculation
+    * Added `lrm` function with optional weighted calculations
+    * Added `lrv` function with optional weighted calculations
+* Implement "weighted theta" calculation
+    * Added `calculateThetaW_old` for unit testing
+    * Added weighted lrv calculation
+* Modified `calculateTheta`
+    * Moved log-ratio mean calculations here
+    * Added weighted lrm calculation
+
+## propr 3.0.1
+---------------------
+* Modified `propd` Class
+    * Added `@active` slot now used by `updateCutoffs`
+    * Added `setActive` method to switch between theta types
+* Modified `calculateTheta`
+    * Added `theta_f` which equals `1 - theta_e`
+    * Added `only` argument to retrieve only one theta type
+
+## propr 3.0.0
+---------------------
+* Modified package skeleton
+    * Added differential proportionality article to CITATION
+    * Added propriety project pre-merger changelog to OLDNEWS.md
+* Manually merged R functions from propriety project
+    * New functions: `propd` and methods, `calculateTheta`, `updateCutoffs`
+    * Added deprecated functions anticipating unit tests
+* Manually merged C++ functions from propriety project
+    * New functions: `half2matrix`, `boxRcpp`, `ctzRcpp`, `lrmRcpp`
+    * Added deprecated functions anticipating unit tests
+* Modified unit tests
+    * Added `requireNamespace` check for `ALDEx2` tests
+    * Added unit tests from propriety project
+* Modified data
+    * Rebuilt `pd.d` and `pd.e` data
+    * Added `top.counts` as count data using filtered `caneToad.counts`
+    * Added `top.lr` as log-ratio data using filtered `caneToad.counts`
+    * Removed `top` data
+
 ## propr 2.2.0
 ---------------------
 * Modified data set from Rollins et al. 2015

R/RcppExports.R

@@ -61,6 +61,18 @@ labRcpp <- function(nfeats) {
     .Call('propr_labRcpp', PACKAGE = 'propr', nfeats)
 }
 
+half2mat <- function(X) {
+    .Call('propr_half2mat', PACKAGE = 'propr', X)
+}
+
+count_if <- function(x) {
+    .Call('propr_count_if', PACKAGE = 'propr', x)
+}
+
+pairmutate <- function(counts, group) {
+    .Call('propr_pairmutate', PACKAGE = 'propr', counts, group)
+}
+
 lr2vlr <- function(lr) {
     .Call('propr_lr2vlr', PACKAGE = 'propr', lr)
 }
@@ -77,3 +89,35 @@ lr2phs <- function(lr) {
     .Call('propr_lr2phs', PACKAGE = 'propr', lr)
 }
 
+boxRcpp <- function(X, a) {
+    .Call('propr_boxRcpp', PACKAGE = 'propr', X, a)
+}
+
+ctzRcpp <- function(X) {
+    .Call('propr_ctzRcpp', PACKAGE = 'propr', X)
+}
+
+lrmRcpp <- function(X) {
+    .Call('propr_lrmRcpp', PACKAGE = 'propr', X)
+}
+
+wtmRcpp <- function(x, w) {
+    .Call('propr_wtmRcpp', PACKAGE = 'propr', x, w)
+}
+
+wtvRcpp <- function(x, w) {
+    .Call('propr_wtvRcpp', PACKAGE = 'propr', x, w)
+}
+
+lrm <- function(X, W, weighted = FALSE) {
+    .Call('propr_lrm', PACKAGE = 'propr', X, W, weighted)
+}
+
+lrv <- function(X, W, weighted = FALSE) {
+    .Call('propr_lrv', PACKAGE = 'propr', X, W, weighted)
+}
+
+lrvMod <- function(X, W) {
+    .Call('propr_lrvMod', PACKAGE = 'propr', X, W)
+}
+