[Picante-commits] r229 - pkg pkg/R pkg/inst/doc pkg/man www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri May 21 22:52:08 CEST 2010
Author: skembel
Date: 2010-05-21 22:52:08 +0200 (Fri, 21 May 2010)
New Revision: 229
Removed:
pkg/man/evolve.brownian.Rd
Modified:
pkg/DESCRIPTION
pkg/R/evolve.trait.R
pkg/inst/doc/picante-intro.pdf
pkg/man/IvesGodfray.Rd
pkg/man/Kcalc.Rd
pkg/man/phylosignal.Rd
pkg/man/pic3.Rd
pkg/man/picante-package.Rd
pkg/man/traitgram.Rd
www/index.php
Log:
1.1-1 update addresses problems introduced by deprecation of ape::evolve.phylo function
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/DESCRIPTION 2010-05-21 20:52:08 UTC (rev 229)
@@ -1,8 +1,8 @@
Package: picante
Type: Package
Title: R tools for integrating phylogenies and ecology
-Version: 1.1-0
-Date: 2010-4-9
+Version: 1.1-1
+Date: 2010-5-18
Author: Steven W. Kembel <skembel at uoregon.edu>, David D. Ackerly <dackerly at berkeley.edu>, Simon P. Blomberg <s.blomberg1 at uq.edu.au>, Will K. Cornwell <cornwell at zoology.ubc.ca>, Peter D. Cowan <pdc at berkeley.edu>, Matthew R. Helmus <mrhelmus at wisc.edu>, Helene Morlon <morlon.helene at gmail.com>, Campbell O. Webb <cwebb at oeb.harvard.edu>
Maintainer: Steven W. Kembel <skembel at uoregon.edu>
Depends: ape, vegan, nlme
Modified: pkg/R/evolve.trait.R
===================================================================
--- pkg/R/evolve.trait.R 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/R/evolve.trait.R 2010-05-21 20:52:08 UTC (rev 229)
@@ -1,11 +1,3 @@
-`evolve.brownian` <-
-function(phy,value=0,var=1) {
- x <- as.vector(t(evolve.phylo(phy,value,var)$tip.character))
- names(x) <- phy$tip.label
- return(x)
-}
-
-
`.evolve.trait` <-
function(phy,
x.root=0, #root value
Modified: pkg/inst/doc/picante-intro.pdf
===================================================================
(Binary files differ)
Modified: pkg/man/IvesGodfray.Rd
===================================================================
--- pkg/man/IvesGodfray.Rd 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/man/IvesGodfray.Rd 2010-05-21 20:52:08 UTC (rev 229)
@@ -5,7 +5,7 @@
\description{
Data on the structure of a host-parasitoid food web from Ives & Godfray (2006). Includes information on phylogenetic covariances among 12 leaf-mining moth hosts and 27 species of parasitoid wasps.
}
-\usage{data(phylocom)}
+\usage{data(IvesGodfray)}
\format{
A list with three elements:
\itemize{
Modified: pkg/man/Kcalc.Rd
===================================================================
--- pkg/man/Kcalc.Rd 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/man/Kcalc.Rd 2010-05-21 20:52:08 UTC (rev 229)
@@ -27,7 +27,7 @@
\seealso{ \code{\link{phylosignal}} }
\examples{
randtree <- rcoal(20)
-randtraits <- evolve.brownian(randtree)
+randtraits <- rTraitCont(randtree)
Kcalc(randtraits[randtree$tip.label],randtree)
}
\keyword{univar}
Deleted: pkg/man/evolve.brownian.Rd
===================================================================
--- pkg/man/evolve.brownian.Rd 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/man/evolve.brownian.Rd 2010-05-21 20:52:08 UTC (rev 229)
@@ -1,20 +0,0 @@
-\name{evolve.brownian}
-\alias{evolve.brownian}
-\title{ Trait evolution under Brownian motion }
-\description{
- Trait evolution under Brownian motion model
-}
-\usage{
-evolve.brownian(phy, value = 0, var = 1)
-}
-
-\arguments{
- \item{phy}{ phylo object }
- \item{value}{ mean }
- \item{var}{ variance }
-}
-\value{
- Vector of trait values with names corresponding to phylo$tip.label
-}
-\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <skembel at uoregon.edu> }
-\keyword{datagen}
Modified: pkg/man/phylosignal.Rd
===================================================================
--- pkg/man/phylosignal.Rd 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/man/phylosignal.Rd 2010-05-21 20:52:08 UTC (rev 229)
@@ -31,7 +31,7 @@
\seealso{ \code{\link{Kcalc}} }
\examples{
randtree <- rcoal(20)
-randtraits <- evolve.brownian(randtree)
+randtraits <- rTraitCont(randtree)
phylosignal(randtraits[randtree$tip.label],randtree)
}
\keyword{univar}
\ No newline at end of file
Modified: pkg/man/pic3.Rd
===================================================================
--- pkg/man/pic3.Rd 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/man/pic3.Rd 2010-05-21 20:52:08 UTC (rev 229)
@@ -32,7 +32,7 @@
\section{Warning }{ Assumes that trait data are sorted in the same order as phylo\$tip.label }
\examples{
randtree <- rcoal(20)
-randtraits <- evolve.brownian(randtree)
+randtraits <- rTraitCont(randtree)
pic3(randtraits,randtree)
}
\keyword{univar}
\ No newline at end of file
Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/man/picante-package.Rd 2010-05-21 20:52:08 UTC (rev 229)
@@ -12,8 +12,8 @@
\tabular{ll}{
Package: \tab picante\cr
Type: \tab Package\cr
-Version: \tab 1.1-0\cr
-Date: \tab 2010-4-9\cr
+Version: \tab 1.1-1\cr
+Date: \tab 2010-5-18\cr
License: \tab GPL-2\cr
}
}
Modified: pkg/man/traitgram.Rd
===================================================================
--- pkg/man/traitgram.Rd 2010-04-12 20:29:59 UTC (rev 228)
+++ pkg/man/traitgram.Rd 2010-05-21 20:52:08 UTC (rev 229)
@@ -27,7 +27,7 @@
\seealso{ \code{\link{pic3}} }
\examples{
randtree <- rcoal(20)
-randtraits <- evolve.brownian(randtree)
+randtraits <- rTraitCont(randtree)
traitgram(randtraits,randtree)
traitgram(randtraits,randtree,method='pic')
}
Modified: www/index.php
===================================================================
--- www/index.php 2010-04-12 20:29:59 UTC (rev 228)
+++ www/index.php 2010-05-21 20:52:08 UTC (rev 229)
@@ -91,7 +91,7 @@
<h2>Obtaining picante</h2>
<ul>
-<li>Version 1.1-0 is available on <a href="http://cran.r-project.org/">CRAN</a>. Simply type <strong><code>install.packages("picante")</code></strong> from within R.</li>
+<li>Version 1.1-1 is available on <a href="http://cran.r-project.org/">CRAN</a>. Simply type <strong><code>install.packages("picante")</code></strong> from within R.</li>
<li>You can grab the latest nightly build <a href="http://r-forge.r-project.org/R/?group_id=134">here</a>, or by typing <strong><code>install.packages("picante",repos="http://R-Forge.R-project.org")</code></strong> from within R.</li>
</ul>
@@ -108,6 +108,7 @@
<h2>Release history</h2>
<p><ul>
+<li>Version 1.1-1: Minor update to address deprecation of evolve.phylo function in ape package; deleted evolve.brownian function and changed example code.</li>
<li>Version 1.1: Added package vignette, new example data set from Ives & Godfray (2006), function example code. Reinstated "richness" and "frequency" null models for ses.* functions.</li>
<li>Version 1.0: Added raoD, unifrac, taxonomic and evolutionary distinctiveness functions. Modified phylosor to work with non-ultrametric phylogenies. Changed name of randomizeSample to randomizeMatrix. Added functions for checking taxa label matching between phylogenies and other data.</li>
<li>Version 0.7-1: Added ses.pd function</li>
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