[Picante-commits] r200 - in branches/will: R man

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

Author: will_cornwell
Date: 2009-11-19 01:37:08 +0100 (Thu, 19 Nov 2009)
New Revision: 200

Modified:
   branches/will/R/evol.distinct.R
   branches/will/man/evol.distinct.Rd
Log:
minor changes

Modified: branches/will/R/evol.distinct.R
===================================================================
--- branches/will/R/evol.distinct.R	2009-11-19 00:32:34 UTC (rev 199)
+++ branches/will/R/evol.distinct.R	2009-11-19 00:37:08 UTC (rev 200)
@@ -4,7 +4,7 @@
 #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.
 #If use.branch.lengths=FALSE, then all branch lengths are changed to 1.
 
-evol.distinct<- function(tree, type=c("equal.splits", "fair.proportion"), scale=F, use.branch.lengths=TRUE){
+evol.distinct<- function(tree, type=c("equal.splits", "fair.proportion"), scale=FALSE, use.branch.lengths=TRUE){
 
 if(is.rooted(tree)==FALSE)
 warning("A rooted phylogeny is required for meaningful output of this function", call.=FALSE)

Modified: branches/will/man/evol.distinct.Rd
===================================================================
--- branches/will/man/evol.distinct.Rd	2009-11-19 00:32:34 UTC (rev 199)
+++ branches/will/man/evol.distinct.Rd	2009-11-19 00:37:08 UTC (rev 200)
@@ -6,7 +6,7 @@
 Species' evolutionary distinctiveness
 }
 \description{
-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 vector of species scores.
 }
 \usage{
 evol.distinct(tree, type = c("equal.splits", "fair.proportion"), scale = F, use.branch.lengths = TRUE)
@@ -25,16 +25,7 @@
 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.
@@ -53,16 +44,7 @@
 will provide very different outputs.  
 }
 
-%% ~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){