diff --git a/.DS_Store b/.DS_Store
index b11ca5d..4ee3ae6 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/DESCRIPTION b/DESCRIPTION
index 864e04f..1032a38 100644
--- a/DESCRIPTION
+++ b/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
diff --git a/NAMESPACE b/NAMESPACE
index 3abb6a1..7d60d82 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/RcppExports.R b/R/RcppExports.R
index da34cfd..03501d0 100644
--- a/R/RcppExports.R
+++ b/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)
 }
 
diff --git a/man/RERconverge.Rd b/man/RERconverge.Rd
new file mode 100644
index 0000000..fce93c7
--- /dev/null
+++ b/man/RERconverge.Rd
@@ -0,0 +1,10 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RERfuncs.R
+\docType{package}
+\name{RERconverge}
+\alias{RERconverge}
+\alias{RERconverge-package}
+\title{RERconverge}
+\description{
+RERconverge
+}
diff --git a/man/correlateWithContinuousPhenotype.Rd b/man/correlateWithContinuousPhenotype.Rd
index ce54481..19fe5f2 100644
--- a/man/correlateWithContinuousPhenotype.Rd
+++ b/man/correlateWithContinuousPhenotype.Rd
@@ -4,7 +4,7 @@
 \alias{correlateWithContinuousPhenotype}
 \title{Computes the association statistics between RER from \code{\link{getAllResiduals}} and a phenotype paths vector for a continuous phenotype made with \code{\link{char2Paths}}}
 \usage{
-correlateWithContinuousPhenotype(RERmat, charP, min.sp = 10, min.pos = 2,
+correlateWithContinuousPhenotype(RERmat, charP, min.sp = 10,
   winsorize = 3)
 }
 \arguments{
diff --git a/man/foreground2Tree.Rd b/man/foreground2Tree.Rd
index 98d32a7..aedcc1b 100644
--- a/man/foreground2Tree.Rd
+++ b/man/foreground2Tree.Rd
@@ -2,23 +2,31 @@
 % Please edit documentation in R/RERfuncs.R
 \name{foreground2Tree}
 \alias{foreground2Tree}
-\title{Creates a tree form a set of foreground species}
+\title{Creates a tree from a set of foreground species}
 \usage{
 foreground2Tree(foreground, treesObj, collapse2anc = T, plotTree = T,
-  wholeClade = F)
+  wholeClade = F, clade = c("ancestral", "terminal", "all",
+  "weighted"))
 }
 \arguments{
 \item{treesObj}{A treesObj created by \code{\link{readTrees}}}
 
-\item{collapse2anc}{Put all the weight on the ancestral branch when the trait appears on a while clade}
+\item{collapse2anc}{Put all the weight on the ancestral branch when the trait appears on a whole clade (redundant to "clade", kept for backwards compatibility)}
 
 \item{plotTree}{Plot a tree representation of the result}
 
+\item{wholeClade}{Whether to implement the weighted edge option across
+all members of a foreground clade (redundant to "clade", kept for backwards compatibility)}
+
+\item{clade}{A character string indicating which branches within the clade
+containing the foreground species should be set to foreground. Must be one
+of the strings "ancestral", "terminal", "all", or "weighted".}
+
 \item{foreground.}{A character vector containing the foreground species}
 }
 \value{
 A tree with edge.lengths representing phenotypic states
 }
 \description{
-Creates a tree form a set of foreground species
+Creates a tree from a set of foreground species
 }
diff --git a/man/getAllResiduals.Rd b/man/getAllResiduals.Rd
index 118ff49..64daba7 100644
--- a/man/getAllResiduals.Rd
+++ b/man/getAllResiduals.Rd
@@ -4,9 +4,9 @@
 \alias{getAllResiduals}
 \title{main RER computation function}
 \usage{
-getAllResiduals(treesObj, cutoff = NULL, transform = "sqrt", weighted = T,
-  useSpecies = NULL, min.sp = 10, scale = T, doOnly = NULL,
-  maxT = NULL, scaleForPproj = F, mean.trim = 0.05)
+getAllResiduals(treesObj, cutoff = NULL, transform = "sqrt",
+  weighted = T, useSpecies = NULL, min.sp = 10, scale = T,
+  doOnly = NULL, maxT = NULL, scaleForPproj = F, mean.trim = 0.05)
 }
 \arguments{
 \item{treesObj}{A treesObj created by \code{\link{readTrees}}}
diff --git a/man/namePathsWSpecies.Rd b/man/namePathsWSpecies.Rd
new file mode 100644
index 0000000..f203b39
--- /dev/null
+++ b/man/namePathsWSpecies.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RERfuncs.R
+\name{namePathsWSpecies}
+\alias{namePathsWSpecies}
+\title{Provides names for paths/RERs representing terminal branches for plotting
+Originally an internal function but necessary for the vignette/walk-through}
+\usage{
+namePathsWSpecies(masterTree)
+}
+\arguments{
+\item{masterTree}{The master tree used for analysis}
+}
+\value{
+Names corresponding to the paths/RERs for terminal branches
+}
+\description{
+Provides names for paths/RERs representing terminal branches for plotting
+Originally an internal function but necessary for the vignette/walk-through
+}
diff --git a/man/plotTreeHighlightBranches.Rd b/man/plotTreeHighlightBranches.Rd
index d667554..10e818f 100644
--- a/man/plotTreeHighlightBranches.Rd
+++ b/man/plotTreeHighlightBranches.Rd
@@ -4,7 +4,8 @@
 \alias{plotTreeHighlightBranches}
 \title{Plot the provided tree, (optionally) rerooted, with specified branches highlighted}
 \usage{
-plotTreeHighlightBranches(tree, outgroup=NULL, hlspecies, hlcols=NULL, main="")
+plotTreeHighlightBranches(tree, outgroup = NULL, hlspecies,
+  hlcols = NULL, main = "")
 }
 \arguments{
 \item{tree.}{A tree object.}
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