ROxygenized version incorporating code updates

ROxygenized the code to incorporate all updates including exports
of namePathsWSpecies and several plotting functions.

DESCRIPTION

@@ -2,13 +2,13 @@ Package: RERconverge
 Type: Package
 Title: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences
 Version: 0.1.0
-Authors: Maria Chikina, Nathan Clark, Amanda Kowalczyk, Weiguang (Wayne) Mao, Wynn Meyer, and Raghavendran Partha
+Author: Maria Chikina, Nathan Clark, Amanda Kowalczyk, Weiguang (Wayne) Mao, Wynn Meyer, and Raghavendran Partha
 Maintainer: Maria Chikina <mchikina@pitt.edu> / Nathan Clark <nclark@pitt.edu>
 Description: RERConverge is a set of software written in R that estimates the correlation between relative evolutionary rates of genes and the    evolution of a convergent binary or continuous trait across a phylogeny.
 License: GNU General Public License v3.0
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
 Depends: RColorBrewer, gplots,  phytools, geiger, knitr, Rcpp, RcppArmadillo, weights, phangorn, ggplot2, dplyr
 Imports: Rcpp (>= 0.11.0), ape
 LinkingTo: Rcpp, RcppArmadillo, ape

NAMESPACE

@@ -1,9 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-useDynLib(RERconverge, .registration=TRUE)
-importFrom(Rcpp, evalCpp)
-
-
 export(char2Paths)
 export(correlateWithBinaryPhenotype)
 export(correlateWithContinuousPhenotype)
@@ -13,8 +9,12 @@ export(foreground2Tree)
 export(getAllCor)
 export(getAllResiduals)
 export(makeBinaryPaths)
+export(namePathsWSpecies)
+export(plotRers)
+export(plotTreeHighlightBranches)
 export(pruneTree)
 export(readTrees)
 export(tree2Paths)
-export(plotTreeHighlightBranches)
-export(plotRers)
+import(Rcpp)
+importFrom(Rcpp,evalCpp)
+useDynLib(RERconverge)

R/RcppExports.R

@@ -2,50 +2,50 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 timesTwo <- function(x) {
-    .Call(`_RERconverge_timesTwo`, x)
+    .Call('_RERconverge_timesTwo', PACKAGE = 'RERconverge', x)
 }
 
 missingSampler <- function() {
-    .Call(`_RERconverge_missingSampler`)
+    .Call('_RERconverge_missingSampler', PACKAGE = 'RERconverge')
 }
 
 isNA <- function(x) {
-    .Call(`_RERconverge_isNA`, x)
+    .Call('_RERconverge_isNA', PACKAGE = 'RERconverge', x)
 }
 
 isNotNArowvec <- function(x) {
-    .Call(`_RERconverge_isNotNArowvec`, x)
+    .Call('_RERconverge_isNotNArowvec', PACKAGE = 'RERconverge', x)
 }
 
 fastLmResid <- function(Y, X) {
-    .Call(`_RERconverge_fastLmResid`, Y, X)
+    .Call('_RERconverge_fastLmResid', PACKAGE = 'RERconverge', Y, X)
 }
 
 fastLmPredicted <- function(Y, X) {
-    .Call(`_RERconverge_fastLmPredicted`, Y, X)
+    .Call('_RERconverge_fastLmPredicted', PACKAGE = 'RERconverge', Y, X)
 }
 
 fastLmResidWeighted <- function(Y, X, wa) {
-    .Call(`_RERconverge_fastLmResidWeighted`, Y, X, wa)
+    .Call('_RERconverge_fastLmResidWeighted', PACKAGE = 'RERconverge', Y, X, wa)
 }
 
 fastLm <- function(Y, X) {
-    .Call(`_RERconverge_fastLm`, Y, X)
+    .Call('_RERconverge_fastLm', PACKAGE = 'RERconverge', Y, X)
 }
 
 fastLmResidMat <- function(Y, X) {
-    .Call(`_RERconverge_fastLmResidMat`, Y, X)
+    .Call('_RERconverge_fastLmResidMat', PACKAGE = 'RERconverge', Y, X)
 }
 
 fastLmPredictedMat <- function(Y, X) {
-    .Call(`_RERconverge_fastLmPredictedMat`, Y, X)
+    .Call('_RERconverge_fastLmPredictedMat', PACKAGE = 'RERconverge', Y, X)
 }
 
 fastLmResidMatWeighted <- function(Y, X, W) {
-    .Call(`_RERconverge_fastLmResidMatWeighted`, Y, X, W)
+    .Call('_RERconverge_fastLmResidMatWeighted', PACKAGE = 'RERconverge', Y, X, W)
 }
 
 fastLmResidMatWeightedNoNACheck <- function(Y, X, W) {
-    .Call(`_RERconverge_fastLmResidMatWeightedNoNACheck`, Y, X, W)
+    .Call('_RERconverge_fastLmResidMatWeightedNoNACheck', PACKAGE = 'RERconverge', Y, X, W)
 }