[Picante-commits] r207 - in branches/will: . R man

[noreply at r-forge.r-project.org]

Author: will_cornwell
Date: 2009-11-20 06:10:24 +0100 (Fri, 20 Nov 2009)
New Revision: 207

Modified:
   branches/will/DESCRIPTION
   branches/will/R/evol.distinct.R
   branches/will/man/evol.distinct.Rd
   branches/will/man/get.nodes.Rd
   branches/will/man/tax.distinctiveness.Rd
Log:
removing Geiger dependancy

Modified: branches/will/DESCRIPTION
===================================================================
--- branches/will/DESCRIPTION	2009-11-19 01:17:54 UTC (rev 206)
+++ branches/will/DESCRIPTION	2009-11-20 05:10:24 UTC (rev 207)
@@ -3,9 +3,9 @@
 Title: R tools for integrating phylogenies and ecology
 Version: 0.6-1
 Date: 2009-3-18
-Author: Steven Kembel <skembel at uoregon.edu>, David Ackerly <dackerly at berkeley.edu>, Simon Blomberg <s.blomberg1 at uq.edu.au>, Peter Cowan <pdc at berkeley.edu>, Matthew Helmus <mrhelmus at wisc.edu>, Helene Morlon  <morlon.helene at gmail.com>, Campbell Webb <cwebb at oeb.harvard.edu>, Will Cornwell <wcornwell at zoology.ubc.ca>
+Author: Steven Kembel <skembel at uoregon.edu>, David Ackerly <dackerly at berkeley.edu>, Simon Blomberg <s.blomberg1 at uq.edu.au>, Peter Cowan <pdc at berkeley.edu>, Matthew Helmus <mrhelmus at wisc.edu>, Helene Morlon  <morlon.helene at gmail.com>, Campbell Webb <cwebb at oeb.harvard.edu>, Will Cornwell <cornwell at zoology.ubc.ca>
 Maintainer: Steven Kembel <skembel at uoregon.edu>
-Depends: ape, vegan, nlme, geiger
+Depends: ape, vegan, nlme
 Suggests: brglm, circular
 Description: Phylocom integration, community analyses, null-models, traits and evolution in R
 License: GPL-2

Modified: branches/will/R/evol.distinct.R
===================================================================
--- branches/will/R/evol.distinct.R	2009-11-19 01:17:54 UTC (rev 206)
+++ branches/will/R/evol.distinct.R	2009-11-20 05:10:24 UTC (rev 207)
@@ -13,13 +13,14 @@
 #Scale tree to have unit depth (for an ultrametric tree) or scale all branches to unit length (for an additive tree)
 
 if(is.ultrametric(tree)==TRUE)
-tree<- rescaleTree(tree, 1) else 
+tree$edge.length<- tree$edge.length/(as.numeric(branching.times(tree)[1])) else 
 tree$edge.length<- tree$edge.length/sum(tree$edge.length)
 }
 
 if(use.branch.lengths==FALSE)
-tree<- speciationalTree(tree)
+tree$edge.length<- rep(1, length(tree$edge.length))
 
+
 for(i in 1:length(tree$tip.label)){
 	spp<- tree$tip.label[i]
 	nodes<- get.nodes(tree, spp)
@@ -33,7 +34,8 @@
 internal.brlen<- internal.brlen*switch(type,
 	"equal.splits"=	sort(rep(.5,length(internal.brlen))^c(1:length(internal.brlen))),
 	"fair.proportion"= 1/for(j in 1:length(nodes)){
-		n.descendents<- length(node.leaves(tree, nodes[j]))
+		sons<-node.desc(tree, nodes[j])
+		n.descendents<- length(sons$tips)
 		if(j==1)
 		portion<- n.descendents else
 		portion<- c(n.descendents, portion)

Modified: branches/will/man/evol.distinct.Rd
===================================================================
--- branches/will/man/evol.distinct.Rd	2009-11-19 01:17:54 UTC (rev 206)
+++ branches/will/man/evol.distinct.Rd	2009-11-20 05:10:24 UTC (rev 207)
@@ -7,7 +7,7 @@
 Species' evolutionary distinctiveness
 }
 \description{
-Calculates evolutionary distinctiveness measures for a suite of species by: a) equal splits (Redding and Mooers 2006) b) fair proportions (Isaac et al., 2007). Returns a vector of species scores.
+Calculates evolutionary distinctiveness measures for a suite of species by: a) equal splits (Redding and Mooers 2006) b) fair proportions (Isaac et al., 2007). Returns a datafram with species identifiers and species scores.
 }
 \usage{
 evol.distinct(tree, type = c("equal.splits", "fair.proportion"), scale = FALSE, use.branch.lengths = TRUE)
@@ -15,7 +15,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{tree}{
-a .phylo "APE" tree}
+an object of class phylo}
   \item{type}{
 a) equal splits (Redding and Mooers 2006) or b) fair proportions (Isaac et al., 2007)
 }

Modified: branches/will/man/get.nodes.Rd
===================================================================
--- branches/will/man/get.nodes.Rd	2009-11-19 01:17:54 UTC (rev 206)
+++ branches/will/man/get.nodes.Rd	2009-11-20 05:10:24 UTC (rev 207)
@@ -30,28 +30,4 @@
 }
 
 
-%% ~Make other sections like Warning with \section{Warning }{....} ~
 
-
-\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==>  Define data, use random,
-##--	or do  help(data=index)  for the standard data sets.
-
-## The function is currently defined as
-function(tree, spp){
-	edge<- which.edge(tree, spp)
-	nodes<- tree$edge[edge,1] 
-	root.edge<- which(tree$edge[,1]==(length(tree$tip.label)+1))
-while(!(edge \%in\% root.edge)){
-	edge<- which.edge(tree, tree$edge[edge,1])
-	next.node<- tree$edge[edge,1]
-	nodes<- c(nodes, next.node)
-	}
-	nodes
-	}
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

Modified: branches/will/man/tax.distinctiveness.Rd
===================================================================
--- branches/will/man/tax.distinctiveness.Rd	2009-11-19 01:17:54 UTC (rev 206)
+++ branches/will/man/tax.distinctiveness.Rd	2009-11-20 05:10:24 UTC (rev 207)
@@ -14,7 +14,7 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{tree}{
-phylogeny in ape format
+an object of class phylo
 }
   \item{type}{
 specify "Vane-Wright" or "May"