[Picante-commits] r199 - branches/will/man

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

Author: will_cornwell
Date: 2009-11-19 01:32:34 +0100 (Thu, 19 Nov 2009)
New Revision: 199

Removed:
   branches/will/man/spp.evol.history.Rd
Modified:
   branches/will/man/evol.distinct.Rd
Log:
fixed bugs in documentation

Modified: branches/will/man/evol.distinct.Rd
===================================================================
--- branches/will/man/evol.distinct.Rd	2009-11-19 00:26:45 UTC (rev 198)
+++ branches/will/man/evol.distinct.Rd	2009-11-19 00:32:34 UTC (rev 199)
@@ -9,7 +9,7 @@
 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.
 }
 \usage{
-spp.evol.history(tree, type = c("equal.splits", "fair.proportion"), scale = F, use.branch.lengths = TRUE)
+evol.distinct(tree, type = c("equal.splits", "fair.proportion"), scale = F, use.branch.lengths = TRUE)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

Deleted: branches/will/man/spp.evol.history.Rd
===================================================================
--- branches/will/man/spp.evol.history.Rd	2009-11-19 00:26:45 UTC (rev 198)
+++ branches/will/man/spp.evol.history.Rd	2009-11-19 00:32:34 UTC (rev 199)
@@ -1,116 +0,0 @@
-\name{spp.evol.history}
-\Rdversion{1.1}
-\alias{spp.evol.history}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-Evolutionary distinctiveness
-}
-\description{
-Evolutionary distinctiveness by: a) equal splits (Redding and Mooers 2006) b) fair proportions (Isaac et al., 2007). Returns a vector of species scores.
-}
-\usage{
-spp.evol.history(tree, type = c("equal.splits", "fair.proportion"), scale = F, use.branch.lengths = TRUE)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{tree}{
-a .phylo "APE" tree}
-  \item{type}{
-a) equal splits (Redding and Mooers 2006) or b) fair proportions (Isaac et al., 2007)
-}
-  \item{scale}{
-%%     The scale option refers to whether or not the phylogeny should be scaled to a depth of 1 or, in the case of an ultrametric tree,  scaled such that branch lengths are relative.
-}
-  \item{use.branch.lengths}{
-If use.branch.lengths=FALSE, then all branch lengths are changed to 1.
-}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-}
-\value{
-%%  ~Describe the value returned
-%%  If it is a LIST, use
-%%  \item{comp1 }{Description of 'comp1'}
-%%  \item{comp2 }{Description of 'comp2'}
-%% ...
-}
-\references{
-Redding, D.W. and Mooers, A.O. (2006). Incorporating evolutionary measures into conservation
-prioritisation. Conservation Biology, 20, 1670-1678.
-
-Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. and Baillie, J.E.M. (2007). Mammals on
-the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.
-}
-\author{
-Karen Magnuson-Ford 
-Will Cornwell
-Arne Mooers
-Mark Vellend}
-\note{
-%%  ~~further notes~~
-}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-}
-\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, type=c("equal.splits", "fair.proportion"), scale=F, use.branch.lengths=TRUE){
-
-if(is.rooted(tree)==FALSE)
-warning("A rooted phylogeny is required for meaningful output of this function", call.=FALSE)
-
-if(scale==TRUE){
-#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/sum(tree$edge.length)
-  }
-
-if(use.branch.lengths==FALSE)
-tree<- speciationalTree(tree)
-
-for(i in 1:length(tree$tip.label)){
-	spp<- tree$tip.label[i]
-	nodes<- get.nodes(tree, spp)
-	#get rid of root node
-	nodes<- nodes[1:(length(nodes)-1)]
-	
-	internal.brlen<- tree$edge.length[which(tree$edge[,2] \%in\% nodes)]
-
-#apportion internal branch lengths appropriately
-if(length(internal.brlen)!=0){
-internal.brlen<- internal.brlen*switch(type,
-	"equal.splits"=	sort(rep(.5,length(internal.brlen))^c(1:length(internal.brlen))),
-	"fair.proportion"= 1/for(j in 1:length(nodes)){
-		n.descendents<- length(node.leaves(tree, nodes[j]))
-		if(j==1)
-		portion<- n.descendents else
-		portion<- c(n.descendents, portion)
-		})}
-	
-	#sum internal branch lengths with the pendant edge
-	ED<- sum(internal.brlen, tree$edge.length[which.edge(tree, spp)])
-	
-	if(i==1)
-	w<- ED else
-	w<- c(w, ED)
-	}
-results<- cbind(tree$tip.label, as.data.frame(w))
-names(results)<- c("Species", "w")
-results
-	
-	}
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line