From 489bb6e967854e0e3517ae171e7d1197bb55fff6 Mon Sep 17 00:00:00 2001
From: "Liam J. Revell" <liam.revell@umb.edu>
Date: Tue, 7 Jun 2016 15:59:37 -0400
Subject: [PATCH] handy fix to contMap & densityMap for short internal edges

---
 R/contMap.R    | 3 ++-
 R/densityMap.R | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/contMap.R b/R/contMap.R
index 0f574443..80caba74 100644
--- a/R/contMap.R
+++ b/R/contMap.R
@@ -1,5 +1,5 @@
 # function plots reconstructed values for ancestral characters along the edges of the tree
-# written by Liam J. Revell 2012, 2013, 2014, 2015
+# written by Liam J. Revell 2012, 2013, 2014, 2015, 2016
 contMap<-function(tree,x,res=100,fsize=NULL,ftype=NULL,lwd=4,legend=NULL,
 	lims=NULL,outline=TRUE,sig=3,type="phylogram",direction="rightwards",
 	plot=TRUE,...){
@@ -53,6 +53,7 @@ contMap<-function(tree,x,res=100,fsize=NULL,ftype=NULL,lwd=4,legend=NULL,
 	if(is.null(lims)) lims<-c(min(y),max(y))
 	trans<-0:1000/1000*(lims[2]-lims[1])+lims[1]
 	names(trans)<-0:1000
+	tree$maps<-vector(mode="list",length=nrow(tree$edge))
 	for(i in 1:nrow(tree$edge)){
 		XX<-cbind(c(H[i,1],steps[intersect(which(steps>H[i,1]),which(steps<H[i,2]))]),
 			c(steps[intersect(which(steps>H[i,1]),which(steps<H[i,2]))],H[i,2]))-H[i,1]
diff --git a/R/densityMap.R b/R/densityMap.R
index fb6e6d32..1c61a8cf 100644
--- a/R/densityMap.R
+++ b/R/densityMap.R
@@ -38,6 +38,7 @@ densityMap<-function(trees,res=100,fsize=NULL,ftype=NULL,lwd=3,check=FALSE,legen
 	}	
 	H<-nodeHeights(tree)
 	message("sorry - this might take a while; please be patient")
+	tree$maps<-vector(mode="list",length=nrow(tree$edge))
 	for(i in 1:nrow(tree$edge)){
 		YY<-cbind(c(H[i,1],steps[intersect(which(steps>H[i,1]),which(steps<H[i,2]))]),
 			c(steps[intersect(which(steps>H[i,1]),which(steps<H[i,2]))],H[i,2]))-H[i,1]