version 2.1.1

DESCRIPTION

@@ -1,36 +1,41 @@
 Package: propr
 Title: Calculating Proportionality Between Vectors of Compositional
         Data
-Version: 2.0.4
+Version: 2.1.1
 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("David", "Lovell", email = "david.lovell@qut.edu.au", role = "aut"),
+    person("Anders", "Bilgrau", email = "anders.ellern.bilgrau@gmail.com", role = "ctb"),
+    person("Ionas", "Erb", email = "ionas.erb@crg.eu", role = "ctb")
     )
 Description: The bioinformatic evaluation of gene co-expression often begins with
     correlation-based analyses. However, this approach lacks statistical validity
-    when applied to relative data, including those biological count data produced by
-    microarray assays or high-throughput RNA-sequencing. Two metrics of proportionality,
-    phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and
-    Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived from compositional
-    data analysis, a branch of math dealing specifically with relative data,
-    represent novel alternatives to correlation. This package introduces a programmatic
-    framework for the calculation of feature dependence through proportionality, as
-    discussed in the cited publications.
+    when applied to relative count data. This includes, for example, biological data
+    produced by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
+    ChIP-sequencing, Methyl-Capture sequencing, and other techniques. Two metrics of
+    proportionality, phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>]
+    and rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived
+    from compositional data analysis, a branch of math dealing specifically with
+    relative data, represent novel alternatives to correlation. This package
+    introduces a programmatic framework for calculating feature dependence through
+    proportionality, as discussed in the cited publications.
 License: GPL-2
 LazyData: true
 VignetteBuilder: knitr
 RoxygenNote: 5.0.1
 Depends: R (>= 3.2.2)
-Imports: methods, Rcpp, stats
-Suggests: compositions, dendextend, fastcluster, ggplot2, ggthemes,
-        knitr, rmarkdown, testthat
+Imports: fastcluster, ggplot2, methods, Rcpp, stats, utils
+Suggests: cccrm, compositions, data.table, grid, ggdendro, igraph,
+        knitr, plotly, reshape2, rmarkdown, testthat
 LinkingTo: Rcpp
 NeedsCompilation: yes
-Packaged: 2016-10-31 02:33:12 UTC; thom
+Packaged: 2016-12-21 23:36:24 UTC; thom
 Author: Thomas Quinn [aut, cre],
-  David Lovell [aut]
+  David Lovell [aut],
+  Anders Bilgrau [ctb],
+  Ionas Erb [ctb]
 Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
 Repository: CRAN
-Date/Publication: 2016-10-31 07:57:10
+Date/Publication: 2016-12-22 00:50:40

MD5

@@ -1,57 +1,65 @@
-dd982525fb104b6a9cd05f7df2645519 *DESCRIPTION
-e812610c4a7d9dad42c1cffb6ea44962 *NAMESPACE
-9400d978ed79209096b3a8d1e4b45a57 *NEWS.md
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 3fdfd61583aba938c37c6184419cf768 *data/top.rda
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 2379613006c2a437ec70672e4bc9fe1b *man/proprPairs.Rd
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 9ee2ccbaf0706afa7fff9a61c5057e55 *man/proprSym.Rd
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-ea4d9fac6df9e8b31fc765e53c00ca99 *src/RcppExports.cpp
-1719a0b39402e976bc204649c184770d *src/backend.cpp
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+eab613fd6412716f6f8bdf4fc0bea293 *src/backend.cpp
 38a416384180a93d31020bdffb37ccee *tests/testthat.R
 63a47970d0a27f348d7dcc4e87df739a *tests/testthat/test-Rcpp.R
+3f501b827c157ac04f2ca4fd6d8c0086 *tests/testthat/test-linRcpp.R
 fc05d9b4d260a59e5ee9868520801bd6 *tests/testthat/test-logratio.R
+7e1bb5475426feec65cea8b58275f890 *tests/testthat/test-lrmodel.R
 8e71cb6dbce34a9dce413e4c707b429b *tests/testthat/test-perb.R
+26849f406bac6e67a33e71150a8f34e2 *tests/testthat/test-phis.R
 fb995286047319340ea951b7fb50b49a *tests/testthat/test-phit.R
+47e7353c4b2bd47309a12835b1770442 *tests/testthat/test-prop2prob.R
 b8ad11479a5be8cf446e974854a586d8 *tests/testthat/test-simplify.R
 23378d943d79a9bf3fb14ed100337e57 *tests/testthat/test-vlr.R
-8fb1dc176dacbc5d91c804337137d1ec *vignettes/introduction.Rmd
-0b74606e9ae952e188b93ebd604e90a5 *vignettes/visualize.Rmd
+a8de2cad2a05aee92f8b85e047d933ca *vignettes/introduction.Rmd
+f5ce72827d06f5aaac0b15ede77179d3 *vignettes/visualize.Rmd

NAMESPACE

@@ -1,32 +1,40 @@
 # Generated by roxygen2: do not edit by hand
 
+export(abstract)
+export(adjacent)
 export(bokeh)
 export(bucket)
+export(cytescape)
 export(dendrogram)
 export(mds)
+export(modelCLR)
 export(perb)
+export(phis)
 export(phit)
 export(prism)
+export(prop2prob)
 export(simplify)
 export(slate)
+export(smear)
 export(snapshot)
+exportClasses(lrmodel)
 exportClasses(propr)
 exportMethods("[")
 exportMethods(plot)
+exportMethods(predict)
 exportMethods(show)
 exportMethods(subset)
 importFrom(Rcpp,sourceCpp)
-importFrom(grDevices,rainbow)
 importFrom(methods,new)
 importFrom(methods,show)
 importFrom(stats,aov)
-importFrom(stats,as.dendrogram)
 importFrom(stats,as.dist)
 importFrom(stats,as.formula)
 importFrom(stats,cutree)
-importFrom(stats,heatmap)
+importFrom(stats,dist)
 importFrom(stats,lm)
-importFrom(stats,order.dendrogram)
+importFrom(stats,p.adjust)
+importFrom(stats,pnorm)
 importFrom(stats,prcomp)
 importFrom(stats,var)
 useDynLib(propr)

NEWS.md

@@ -1,3 +1,85 @@
+## propr 2.1.1
+---------------------
+* Modified `propr` Class
+  * Merged `propr-class` and `propr` documentation
+* Modified `phit`, `perb` functions
+  * Merged `phit` and `perb` documentation
+  * New `phis` function returns `(1 - rho) / (1 + rho)`
+  * NAs in count matrix now throw error
+  * 0s now replaced with 1s
+* Modified visualization tools
+  * Merged documentation
+
+## propr 2.1.0
+---------------------
+* Modified `[` method
+  * Now joins newly indexed pairs with any existing index
+* New `cytescape` function
+  * Uses `@pairs` slot to build an interaction network
+
+## propr 2.0.9
+---------------------
+* Modified visualization tools
+  * Courtesy `prompt` argument extended to `smear` and `dendrogram`
+  * Improved error handling and documentation
+* Modified `abstract` function
+  * New `dt` argument indexes significant results in `@pairs`
+* Modified `simplify` function
+  * Now builds index of lower left triangle of matrix
+* New `adjacent` function
+  * Uses `@pairs` slot to build an adjacency matrix
+
+## propr 2.0.8
+---------------------
+* Modified visualization tools
+  * `bucket` now depends on `slate` function
+* Modified backend code
+  * New `coordToIndex` performs inverse of `indexToCoord`
+* Modified `prop2prob` function
+  * Return p-values as a sorted `data.table`
+  * Now lets user select `method` for p-value adjustment
+  * New `prompt` argument turns off big data prompt
+  * Fix pass by reference bug in `linRcpp`
+* New `abstract` function
+  * Combines two `propr` objects into one
+
+## propr 2.0.7
+---------------------
+* New `lrmodel` class
+  * Use `modelCLR` to capture the clr-transformation rule
+  * Use `predict` to deploy this rule to new data
+* Modified backend code
+  * Added `corRcpp` function from `correlateR` package
+  * Added `linRcpp` function for Z-transformation
+  * Added `lltRcpp` and `urtRcpp` to retrieve a half-matrix
+  * Added `labRcpp` to label a half-matrix
+* New `prop2prob` function
+  * Allows hypothesis testing of rho equals naught
+  * Tests differential proportionality
+
+## propr 2.0.6
+---------------------
+* Modified visualization tools
+  * `plotCheck` extended to all plot functions
+  * `plot` method now calls `smear` function
+  * `dendrogram` plot now rendered using `ggplot2`
+  * `snapshot` plot now rendered using `ggplot2`
+  * `bokeh` plot now on positive log scale
+  * `plotly` support added
+* Modified backend code
+  * Temporarily removed `a_bool` function
+* Modified `[` method
+  * Removed `bool` and `copy` arguments
+
+## propr 2.0.5
+---------------------
+* Modified backend code
+  * New `a_bool` function returns thresholded boolean matrix
+* Modified `[` method
+  * New `bool` argument toggles whether to use `a_bool`
+  * New `tiny` argument toggles whether to use `simplify`
+  * New `copy` argument toggles `a_bool` copy-on-modify
+
 ## propr 2.0.4
 ---------------------
 * New visualization tools
@@ -86,10 +168,10 @@
 ## propr 1.0.0
 ---------------------
 * Introduced `phit` function
-  * Implements Lovell's \phi proportionality metric
+  * Implements Lovell's phi proportionality metric
   * Returns object of class `propr`
 * Introduced `perb` function
-  * Implements Erb's \rho proportionality metric
+  * Implements Erb's rho proportionality metric
   * Returns object of class `propr`
 * Introduced `propr` Class
   * `show` method

R/RcppExports.R

@@ -1,6 +1,10 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+corRcpp <- function(X) {
+    .Call('propr_corRcpp', PACKAGE = 'propr', X)
+}
+
 covRcpp <- function(X, norm_type = 0L) {
     .Call('propr_covRcpp', PACKAGE = 'propr', X, norm_type)
 }
@@ -37,3 +41,27 @@ indexToCoord <- function(V, N) {
     .Call('propr_indexToCoord', PACKAGE = 'propr', V, N)
 }
 
+coordToIndex <- function(row, col, N) {
+    .Call('propr_coordToIndex', PACKAGE = 'propr', row, col, N)
+}
+
+linRcpp <- function(rho, lr) {
+    .Call('propr_linRcpp', PACKAGE = 'propr', rho, lr)
+}
+
+lltRcpp <- function(X) {
+    .Call('propr_lltRcpp', PACKAGE = 'propr', X)
+}
+
+urtRcpp <- function(X) {
+    .Call('propr_urtRcpp', PACKAGE = 'propr', X)
+}
+
+labRcpp <- function(nfeats) {
+    .Call('propr_labRcpp', PACKAGE = 'propr', nfeats)
+}
+
+rhoToPhs <- function(X) {
+    .Call('propr_rhoToPhs', PACKAGE = 'propr', X)
+}
+