version 4.0.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: propr
 Title: Calculating Proportionality Between Vectors of Compositional
         Data
-Version: 3.5.1
+Version: 4.0.0
 URL: http://github.com/tpq/propr
 BugReports: http://github.com/tpq/propr/issues
 Authors@R: c(
@@ -12,11 +12,9 @@ Authors@R: c(
     person("Greg", "Gloor", email = "ggloor@uwo.ca", 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. This includes, for example, biological count data
-    generated by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
-    ChIP-sequencing, Methyl-Capture sequencing, and other techniques. This package
-    implements several metrics for proportionality, including
+    correlation-based analyses. However, correlation lacks validity when
+    applied to relative data, including count data generated by next-generation
+    sequencing. This package implements several metrics for proportionality, including
     phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
     rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
     implements several metrics for differential proportionality. Unlike correlation,
@@ -27,17 +25,17 @@ VignetteBuilder: knitr
 RoxygenNote: 6.0.1
 Depends: methods, R (>= 3.2.2)
 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
+Suggests: ALDEx2, Biobase, cccrm, compositions, data.table, datasets,
+        grid, ggdendro, knitr, limma, plotly, reshape2, rgl, rmarkdown,
+        SDMTools, testthat
 LinkingTo: Rcpp
 NeedsCompilation: yes
-Packaged: 2018-05-09 01:48:34 UTC; thom
+Packaged: 2018-07-25 05:22:11 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: 2018-05-09 03:43:57 UTC
+Date/Publication: 2018-07-25 07:20:03 UTC

MD5

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+8338f7da4ae675b8053dd2c0adb12e05 *vignettes/b_visualization.Rmd
+ba49707d6dbc812c59c47da5b232f8ba *vignettes/d_advanced.Rmd
+4513109d7e5528ca0570ce5f5752a3c9 *vignettes/e_differential.Rmd
+9520b147409a3c4a92d4c4cb83625b54 *vignettes/f_moderation.Rmd
+e4d96faab6b6070aa12aff451115e357 *vignettes/g_questions.Rmd

NAMESPACE

@@ -1,8 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-export(abstract)
-export(adjacent)
 export(aldex.cor)
+export(aldex.glm)
 export(aldex2propr)
 export(bokeh)
 export(bowtie)
@@ -14,16 +13,19 @@ export(decomposed)
 export(dendrogram)
 export(gemini)
 export(geyser)
+export(ivar2index)
 export(lr2cor)
+export(lr2glm)
 export(pals)
 export(pca)
 export(perb)
 export(phis)
 export(phit)
 export(prism)
-export(prop2prob)
 export(propd)
 export(propd2propr)
+export(propr)
+export(qtheta)
 export(ratios)
 export(setActive)
 export(setDisjointed)
@@ -35,6 +37,8 @@ export(slice)
 export(smear)
 export(snapshot)
 export(updateCutoffs)
+export(updateCutoffs.propd)
+export(updateCutoffs.propr)
 export(updateF)
 exportClasses(propd)
 exportClasses(propr)
@@ -48,15 +52,16 @@ importFrom(methods,show)
 importFrom(stats,aov)
 importFrom(stats,as.dist)
 importFrom(stats,as.formula)
+importFrom(stats,coef)
 importFrom(stats,cor.test)
 importFrom(stats,cutree)
 importFrom(stats,dist)
+importFrom(stats,glm)
 importFrom(stats,kruskal.test)
 importFrom(stats,lm)
 importFrom(stats,p.adjust)
 importFrom(stats,pf)
-importFrom(stats,pnorm)
 importFrom(stats,prcomp)
+importFrom(stats,qf)
 importFrom(stats,var)
-importFrom(utils,head)
 useDynLib(propr, .registration = TRUE)

NEWS.md

@@ -1,3 +1,41 @@
+## propr 4.0.0
+---------------------
+* Update `ivar2index` method
+    * Now replaces zeros with 1 to calculate IQR (fixes "iqlr" bug for alpha > 0)
+* Update `propr` object backend and API
+    * Heavily revise documentation to harmonize `propd` with `propr`
+    * Create `propr` function to replace `perb`, `phit`, and `phis`
+    * Add `@results` slot for storing proportionality half-matrix
+    * Add `@permutes` slot for storing reproducible permutations
+    * Update `subset` and `[` to disable `@results` and `@permutes`
+    * Add `@fdr` slot for storing FDR results
+    * Add `alpha` argument
+        * Adjusts alpha-based VLR by var[(component^alpha - reference^alpha)/alpha]
+        * Saves `alpha` to `@alpha` and alpha-based counts to `@logratio`
+        * Note this is not yet technically equivalent to `propd` method
+    * Add `updateCutoffs` function to permute FDR for proportionality
+        * Add `@metric`, `@ivar` and `@alpha` slots to calculate metric exactly
+        * Count rho > cutoff and cor > cutoff as positive results
+        * Count phi < cutoff and phs < cutoff as positive results
+* Update `propd` object backend and API
+    * Heavily revise documentation to harmonize `propd` with `propr`
+    * Fix bug where zeros still get replaced for `lrm` calculation
+    * The `updateCutoffs` function is now an S4 method
+    * Turn `@theta` slot into `@results` slot
+    * Rebuild `pd.d` and `pd.e` objects
+* Update `aldex2propr` method
+    * Update `aldex2propr` and `[` to disable `@results` and `@permutes`
+    * Add `lr2glm` and `aldex.glm` functions
+* Add methods
+    * Add `qtheta` to calculate a cutoff of theta for a given p-value
+* Remove methods
+    * Remove `differentialCheck`
+    * Remove `prop2prob`
+    * Remove `abstract`
+    * Remove `initialize`
+    * Remove `adjacent`
+* Revise vignettes
+
 ## propr 3.5.1
 ---------------------
 * Update CITATION file and README
@@ -166,7 +204,7 @@
 ---------------------
 * Modified `propd` Class
     * Added `@weighted` slot now used by `updateCutoffs`
-* Implement # Initialize @theta for "weighted theta" calculation
+* Implement @theta for "weighted theta" calculation
     * Added `wtmRcpp` for weighted mean calculation
     * Added `wtvRcpp` for weighted variance calculation
     * Added `lrm` function with optional weighted calculations