[Picante-commits] r242 - in pkg: . R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 29 22:28:40 CEST 2013
Author: skembel
Date: 2013-05-29 22:28:39 +0200 (Wed, 29 May 2013)
New Revision: 242
Added:
pkg/R/phyEstimate.R
pkg/man/phyEstimate.Rd
Modified:
pkg/
pkg/DESCRIPTION
pkg/R/randomizeSample.R
pkg/inst/doc/picante-intro.Rnw
pkg/man/comdist.Rd
pkg/man/comdistnt.Rd
pkg/man/comm.phylo.cor.Rd
pkg/man/comm.phylo.qr.Rd
pkg/man/cor.table.Rd
pkg/man/data.checking.Rd
pkg/man/expected.pd.Rd
pkg/man/matrix2sample.Rd
pkg/man/mntd.Rd
pkg/man/mpd.Rd
pkg/man/multiPhylosignal.Rd
pkg/man/pd.Rd
pkg/man/phylosignal.Rd
pkg/man/phylosor.Rd
pkg/man/phylosor.rnd.Rd
pkg/man/picante-package.Rd
pkg/man/pruning.Rd
pkg/man/randomizeSample.Rd
pkg/man/raoD.Rd
pkg/man/sample2matrix.Rd
pkg/man/ses.mntd.Rd
pkg/man/ses.mpd.Rd
pkg/man/ses.pd.Rd
pkg/man/species.dist.Rd
pkg/man/unifrac.Rd
pkg/man/utility.Rd
pkg/man/writesample.Rd
pkg/man/writetraits.Rd
Log:
Adding phyEstimate functions, updating maintainer email address for 1.6-0
Property changes on: pkg
___________________________________________________________________
Added: svn:ignore
+ .Rproj.user
.Rhistory
.RData
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/DESCRIPTION 2013-05-29 20:28:39 UTC (rev 242)
@@ -1,10 +1,10 @@
Package: picante
Type: Package
Title: R tools for integrating phylogenies and ecology
-Version: 1.5-2
-Date: 2012-10-9
-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>
+Version: 1.6-0
+Date: 2013-5-29
+Author: Steven W. Kembel <steve.kembel at gmail.com>, 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 <steve.kembel at gmail.com>
Depends: ape, vegan, nlme
Suggests: brglm, circular, corpcor, quantreg, plotrix
Description: Phylocom integration, community analyses, null-models, traits and evolution in R
Added: pkg/R/phyEstimate.R
===================================================================
--- pkg/R/phyEstimate.R (rev 0)
+++ pkg/R/phyEstimate.R 2013-05-29 20:28:39 UTC (rev 242)
@@ -0,0 +1,122 @@
+#phyEstimate.R
+#use phylogeny to predict trait values for new species
+phyEstimate <- function(phy, trait, method="pic", ...) {
+
+ #trait should be a data.frame or vector with (row)names matching phylogeny
+ if (is.vector(trait)) {
+ trait <- data.frame(trait)
+ }
+
+ trait.orig <- trait
+
+ #given a tree with a novel species on it
+ sppObs <- row.names(trait)
+ #(novel spp. are in tree but have no trait value)
+ sppUnobs <- phy$tip.label[!(phy$tip.label %in% sppObs)]
+
+ res <- as.data.frame(matrix(nrow=length(sppUnobs), ncol=2, dimnames=list(sppUnobs, c("estimate","se"))))
+
+ for (i in sppUnobs) {
+
+ #for each novel species, prune all but measured + that species
+ tree <- drop.tip(phy, subset(sppUnobs, sppUnobs != i))
+
+ #root the tree at the novel species (leave root as trichotomy)
+ tree <- root(tree, i, resolve.root=FALSE)
+
+ #record branch length leading to novel species in rerooted tree
+ edge <- Nnode(tree) - 1 + which(tree$tip.label==i)
+ bl <- tree$edge.length[edge]
+
+ #prune novel species and match new pruned tree <-> trait data
+ tree <- drop.tip(tree, i)
+ trait <- trait.orig[tree$tip.label,]
+
+ #use PIC framework to estimate trait value at root node + error
+ est <- ace(trait, tree, method=method, ...)
+ val <- est$ace[1]
+ cimax <- est$CI95[1,2]
+ se <- abs(cimax-val)/1.96
+
+ se.adj <- sqrt(bl)+se
+
+ res[i,] <- data.frame(estimate=val, se=se.adj)
+
+ }
+
+ return(res)
+
+}
+
+
+# for discrete traits
+phyEstimateDisc <- function(phy, trait, best.state=TRUE, cutoff=0.5, ...) {
+
+ #trait should be a data.frame or vector with names matching phylogeny
+ if (is.vector(trait)|is.factor(trait)) {
+ trait <- data.frame(trait)
+ }
+
+ trait[,1] <- factor(trait[,1])
+ trait.orig <- trait
+
+ #given a tree with a novel taxa on it (taxa with no trait value)
+ sppObs <- row.names(trait)
+ sppUnobs <- phy$tip.label[!(phy$tip.label %in% sppObs)]
+ trtlevels <- levels(trait[,1])
+ res <- as.data.frame(matrix(nrow=length(sppUnobs), ncol=length(trtlevels), dimnames=list(sppUnobs, trtlevels)))
+
+ #estimate support for different states for each novel taxon
+ for (i in sppUnobs) {
+
+ #for each novel species, prune all but measured + that species
+ tree <- drop.tip(phy, subset(sppUnobs, sppUnobs != i))
+
+ #root the tree at the novel species (leave root as trichotomy)
+ tree <- root(tree, i, resolve.root=FALSE)
+
+ #record branch length leading to novel species in rerooted tree
+ edge <- Nnode(tree) - 1 + which(tree$tip.label==i)
+ bl <- tree$edge.length[edge]
+
+ #prune novel species and match new pruned tree <-> trait data
+ tree <- drop.tip(tree, i)
+ trait <- trait.orig[tree$tip.label,]
+
+ #calculate value at root node and impute to novel species
+ est <- ace(trait, tree, type="discrete", ...)
+ val <- est$lik.anc[1,]
+
+ res[i,] <- val
+
+ }
+
+ #estimate the best-supported state for each taxon
+ if (best.state) {
+ beststate <- as.data.frame(matrix(nrow=dim(res)[1], ncol=2))
+ colnames(beststate) <- c("estimated.state","estimated.state.support")
+ rownames(beststate) <- rownames(res)
+
+ for (i in 1:dim(res)[1]) {
+ #if >=cutoff % taxa have same label assign a consensus taxon to node
+ best <- -sort(-(res[i,]))[1]
+ if (best >= cutoff) {
+ beststate[i,1] <- names(best)
+ beststate[i,2] <- best
+ }
+ else
+ {
+ beststate[i,1] <- NA
+ beststate[i,2] <- NA
+ }
+ }
+ }
+
+ #return the output
+ if (best.state) {
+ return(cbind(as.matrix(res),beststate))
+ } else {
+ return(as.matrix(res))
+ }
+
+}
Modified: pkg/R/randomizeSample.R
===================================================================
--- pkg/R/randomizeSample.R 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/R/randomizeSample.R 2013-05-29 20:28:39 UTC (rev 242)
@@ -1,7 +1,3 @@
-.First.lib <- function(lib,pkg) {
- library.dynam("picante",pkg,lib)
-}
-
`randomizeMatrix` <-
function(samp, null.model=c("frequency","richness","independentswap","trialswap"),
iterations=1000)
Modified: pkg/inst/doc/picante-intro.Rnw
===================================================================
--- pkg/inst/doc/picante-intro.Rnw 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/inst/doc/picante-intro.Rnw 2013-05-29 20:28:39 UTC (rev 242)
@@ -8,7 +8,7 @@
\usepackage{url}
\title{An introduction to the picante package}
-\author{Steven Kembel (skembel at uoregon.edu)}
+\author{Steven Kembel (steve.kembel at gmail.com)}
\date{April 2010}
\begin{document}
Modified: pkg/man/comdist.Rd
===================================================================
--- pkg/man/comdist.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/comdist.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -21,7 +21,7 @@
This function calculates a measure of phylogenetic beta diversity: the expected phylogenetic distance separating two individuals or taxa drawn randomly from different communities.
}
\references{ C.O. Webb, D.D. Ackerly, and S.W. Kembel. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 18:2098-2100. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{mpd}}, \code{\link{ses.mpd}} }
\examples{
data(phylocom)
Modified: pkg/man/comdistnt.Rd
===================================================================
--- pkg/man/comdistnt.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/comdistnt.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -24,7 +24,7 @@
This function calculates a measure of phylogenetic beta diversity: the average phylogenetic distance to the most similar taxon or individual in the other community for taxa or individuals in two communities.
}
\references{ C.O. Webb, D.D. Ackerly, and S.W. Kembel. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 18:2098-2100. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{mntd}}, \code{\link{ses.mntd}} }
\examples{
data(phylocom)
Modified: pkg/man/comm.phylo.cor.Rd
===================================================================
--- pkg/man/comm.phylo.cor.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/comm.phylo.cor.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -39,7 +39,7 @@
}
}
\references{ Cavender-Bares J., D.A. Ackerly, D. Baum and F.A. Bazzaz. 2004. Phylogenetic overdispersion in Floridian oak communities, American Naturalist, 163(6):823-843. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{randomizeMatrix}} }
\examples{
data(phylocom)
Modified: pkg/man/comm.phylo.qr.Rd
===================================================================
--- pkg/man/comm.phylo.qr.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/comm.phylo.qr.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -47,7 +47,7 @@
Cavender-Bares J., D.A. Ackerly, D. Baum and F.A. Bazzaz. 2004. Phylogenetic overdispersion in Floridian oak communities, American Naturalist, 163(6):823-843.
Slingsby, J. A. and G. A. Verboom. 2006. Phylogenetic relatedness limits coexistence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa. The American Naturalist 168:14-27.
}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{randomizeMatrix}} }
\examples{
data(phylocom)
Modified: pkg/man/cor.table.Rd
===================================================================
--- pkg/man/cor.table.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/cor.table.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -23,5 +23,5 @@
\references{ Garland, T., Jr., P. H. Harvey, and A. R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41:18-32. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\keyword{univar}
Modified: pkg/man/data.checking.Rd
===================================================================
--- pkg/man/data.checking.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/data.checking.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -38,7 +38,7 @@
These utility functions are used by several functions that assume taxa labels in phylogeny and data match, including \code{\link{Kcalc}}, \code{\link{phylosignal}}, and \code{\link{raoD}}.
}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{\code{\link{prune.missing}}, \code{\link{prune.sample}}}
\examples{
data(phylocom)
Modified: pkg/man/expected.pd.Rd
===================================================================
--- pkg/man/expected.pd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/expected.pd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -29,7 +29,7 @@
\references{ O'Dwyer, Kembel, and Green. 2012. Phylogenetic diversity theory sheds light on the structure of microbial communities. }
-\author{ Steven Kembel <skembel at uoregon.edu> and James O'Dwyer <jodwyer at santafe.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> and James O'Dwyer <jodwyer at santafe.edu> }
\seealso{ \code{\link{pd}} }
Modified: pkg/man/matrix2sample.Rd
===================================================================
--- pkg/man/matrix2sample.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/matrix2sample.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -17,7 +17,7 @@
Phylocom database-format community sample
}
\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}.}
-\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> and Cam Webb <cwebb at oeb.harvard.edu> }
\examples{
data(phylocom)
matrix2sample(phylocom$sample)
Modified: pkg/man/mntd.Rd
===================================================================
--- pkg/man/mntd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/mntd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -21,7 +21,7 @@
This metric has also been referred to as MNND (mean nearest neighbour distance), and the function was named \code{mnnd} in picante versions < 0.7.
}
\references{ Webb, C., D. Ackerly, M. McPeek, and M. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33:475-505. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{ses.mntd}} }
\examples{
data(phylocom)
Modified: pkg/man/mpd.Rd
===================================================================
--- pkg/man/mpd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/mpd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -18,7 +18,7 @@
Vector of MPD values for each community
}
\references{ Webb, C., D. Ackerly, M. McPeek, and M. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33:475-505. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{ses.mpd}}}
\examples{
data(phylocom)
Modified: pkg/man/multiPhylosignal.Rd
===================================================================
--- pkg/man/multiPhylosignal.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/multiPhylosignal.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -16,5 +16,5 @@
\value{
Returns a data frame with phylogenetic signal results for each trait
}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\keyword{univar}
Modified: pkg/man/pd.Rd
===================================================================
--- pkg/man/pd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/pd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -33,7 +33,7 @@
\code{prunedTree <- prune.sample(sample,tree)}
}
\references{ Faith D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10. }
-\author{ Matthew Helmus \email{mrhelmus at gmail.com}, Jonathan Davies \email{davies at nceas.ucsb.edu}, Steven Kembel \email{skembel at uoregon.edu}}
+\author{ Matthew Helmus \email{mrhelmus at gmail.com}, Jonathan Davies \email{davies at nceas.ucsb.edu}, Steven Kembel \email{steve.kembel at gmail.com}}
\seealso{ \code{\link{psr}}, \code{\link{ses.pd}} }
\examples{
data(phylocom)
Added: pkg/man/phyEstimate.Rd
===================================================================
--- pkg/man/phyEstimate.Rd (rev 0)
+++ pkg/man/phyEstimate.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -0,0 +1,56 @@
+\name{phyEstimate}
+\alias{phyEstimate}
+\alias{phyEstimateDisc}
+
+\title{ Phylogenetic estimation of traits for unobserved taxa }
+\description{
+ Uses phylogenetic ancestral state reconstruction to estimate trait values for unobserved taxa.
+}
+\usage{
+phyEstimate(phy, trait, method="pic", ...)
+phyEstimateDisc(phy, trait, best.state=TRUE, cutoff=0.5, ...)
+}
+
+\arguments{
+ \item{phy }{ phylo object }
+ \item{trait }{ vector or data.frame containing trait values }
+ \item{method }{ ancestral state estimation method used by \code{ace} (default="pic")}
+ \item{best.state }{ estimate best-supported trait state for discrete variables? (default=TRUE)}
+ \item{cutoff }{ support cutoff required to declare a best.state }
+ \item{...}{ Additional arguments passed to \code{ace} }
+}
+\value{
+ phyEstimate produces a data frame with columns:
+ \item{est}{ Estimated trait value }
+ \item{se}{ Standard error of estimated trait value }
+ phyEstimateDisc produces a data frame with columns:
+ \item{states 1..N}{ A column with statistical support is produced for each discrete trait state }
+ \item{estimated.state}{ If best.state=TRUE, a column with the state with the highest support }
+ \item{estimated.state.support}{ Statistical support for the state with the highest support }
+}
+
+\details{
+These functions use phylogenetic ancestral state estimation to infer trait values for novel taxa on a phylogenetic tree, for continuous (\code{phyEstimate}) and discrete (\code{phyEstimateDisc}) traits.
+
+The required input is a phylogenetic tree object plus a vector or data.frame containing estimated trait values for a subset of the taxa in the phylogenetic tree. Trait values for taxa that are present in the tree but not the trait data will be estimated using ancestral state estimation (Garland and Ives 2000). Briefly, for each taxon present in the tree but not the trait data, the phylogeny is rerooted at the most recent common ancestor of the novel taxon and the rest of the phylogeny, and the trait value of the novel taxon is estimated from the reconstructed trait value at the root of the rerooted phylogeny.
+
+For \code{phyEstimateDisc}, the state with the highest support will be reported if argument \code{best.state=TRUE}. If the best-supported state's support is less than the specified \code{cutoff}, no best state is reported and a \code{NA} value will be returned.
+}
+
+\references{
+T. Garland Jr., and A.R. Ives. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155:346364.
+
+S.W. Kembel, M. Wu, J.A. Eisen, and J.L. Green. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Computational Biology 8(10):e1002743.
+
+}
+\author{ Steven Kembel <steve.kembel at gmail.com> }
+
+\examples{
+#generate random phylogeny
+randtree <- rcoal(50)
+#simulate trait evolution for a subset of taxa on phylogeny
+randtraits <- sample(rTraitCont(randtree, sigma=10, root.value=100), 40)
+#estimate trait values for "missing" taxa using PIC method
+phyEstimate(randtree, randtraits, method="pic")
+}
+\keyword{univar}
\ No newline at end of file
Modified: pkg/man/phylosignal.Rd
===================================================================
--- pkg/man/phylosignal.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/phylosignal.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -27,7 +27,7 @@
Blomberg, S. P., and T. Garland, Jr. 2002. Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology 15:899-910.
Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{Kcalc}} }
\examples{
randtree <- rcoal(20)
Modified: pkg/man/phylosor.Rd
===================================================================
--- pkg/man/phylosor.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/phylosor.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -13,7 +13,7 @@
}
\value{A distance object of the PhyloSor index of similarity between communities, the fraction of PD (branch-length) shared between two samples}
\references{Bryant, J.B., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J., Green, J.L. 2008. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105 Supplement 1: 11505-11511}
-\author{ Helene Morlon <morlon.helene at gmail.com> and Steven Kembel <skembel at uoregon.edu> }
+\author{ Helene Morlon <morlon.helene at gmail.com> and Steven Kembel <steve.kembel at gmail.com> }
\seealso{\code{\link{phylosor.rnd}}, \code{\link{pd}}}
\note{
The root of the supplied tree is included in calculations of PhyloSor. The supplied tree must be rooted. Single-species samples will be assigned a PD value equal to the distance from the root to the present.
Modified: pkg/man/phylosor.rnd.Rd
===================================================================
--- pkg/man/phylosor.rnd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/phylosor.rnd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -35,7 +35,7 @@
}
}
\references{Bryant, J.B., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J., Green, J.L. 2008. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105 Supplement 1: 11505-11511}
-\author{ Helene Morlon <morlon.helene at gmail.com> and Steven Kembel <skembel at uoregon.edu> }
+\author{ Helene Morlon <morlon.helene at gmail.com> and Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{phylosor}}, \code{\link{randomizeMatrix}} }
\examples{
data(phylocom)
Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/picante-package.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -12,13 +12,13 @@
\tabular{ll}{
Package: \tab picante\cr
Type: \tab Package\cr
-Version: \tab 1.5-2\cr
-Date: \tab 2012-10-9\cr
+Version: \tab 1.6-0\cr
+Date: \tab 2013-5-29\cr
License: \tab GPL-2\cr
}
}
\author{
-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>
+Author: Steven W. Kembel <steve.kembel at gmail.com>, 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 <steve.kembel at gmail.com>
}
\keyword{package}
Modified: pkg/man/pruning.Rd
===================================================================
--- pkg/man/pruning.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/pruning.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -19,5 +19,5 @@
\value{
Returns a pruned phylo object
}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\keyword{manip}
Modified: pkg/man/randomizeSample.Rd
===================================================================
--- pkg/man/randomizeSample.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/randomizeSample.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -32,7 +32,7 @@
Miklos I. & Podani J. 2004. Randomization of presence-absence matrices: Comments and new algorithms. Ecology 85: 86-92.
}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\examples{
data(phylocom)
randomizeMatrix(phylocom$sample, null.model="richness")}
Modified: pkg/man/raoD.Rd
===================================================================
--- pkg/man/raoD.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/raoD.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -56,7 +56,7 @@
Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}.
}
\seealso{ \code{\link{mpd}}, \code{\link{comdist}} }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\examples{
data(phylocom)
raoD(phylocom$sample)
Modified: pkg/man/sample2matrix.Rd
===================================================================
--- pkg/man/sample2matrix.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/sample2matrix.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -20,5 +20,5 @@
}
\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}.}
-\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{IO}
Modified: pkg/man/ses.mntd.Rd
===================================================================
--- pkg/man/ses.mntd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/ses.mntd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -46,7 +46,7 @@
}
}
\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{mntd}}, \code{\link{randomizeMatrix}} }
\examples{
data(phylocom)
Modified: pkg/man/ses.mpd.Rd
===================================================================
--- pkg/man/ses.mpd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/ses.mpd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -45,7 +45,7 @@
}
\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}. }
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{mpd}}, \code{\link{randomizeMatrix}} }
\examples{
data(phylocom)
Modified: pkg/man/ses.pd.Rd
===================================================================
--- pkg/man/ses.pd.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/ses.pd.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -47,7 +47,7 @@
\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}.
Proches, S., Wilson, J.R.U. and Cowling, R.M. 2006. How much evolutionary history in a 10 x 10m plot? Proceedings of Royal Society of London B, Biological Sciences 273:1143-1148.}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{ \code{\link{pd}}, \code{\link{randomizeMatrix}} }
\examples{
data(phylocom)
Modified: pkg/man/species.dist.Rd
===================================================================
--- pkg/man/species.dist.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/species.dist.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -27,7 +27,7 @@
\item{doij}{ DOij index of co-occurrence }
}
}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\references{
Hardy, O.J. 2008. Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community. Journal of Ecology 96:914-926.
}
Modified: pkg/man/unifrac.Rd
===================================================================
--- pkg/man/unifrac.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/unifrac.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -15,7 +15,7 @@
\references{
Lozupone, C., Hamady, M., and Knight, R. 2006. UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371.
}
-\author{ Steven Kembel <skembel at uoregon.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> }
\seealso{\code{\link{pd}}}
\note{
The supplied tree must be rooted. Single-species samples will be assigned a PD value equal to the distance from the root to the present.
Modified: pkg/man/utility.Rd
===================================================================
--- pkg/man/utility.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/utility.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -47,5 +47,5 @@
Various utility functions for manipulating trees, data, etc.
}
-\author{ Steven Kembel <skembel at uoregon.edu>, Peter Cowan <pdc at berkeley.edu>, David Ackerly <dackerly at berkeley.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com>, Peter Cowan <pdc at berkeley.edu>, David Ackerly <dackerly at berkeley.edu> }
\keyword{manip}
Modified: pkg/man/writesample.Rd
===================================================================
--- pkg/man/writesample.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/writesample.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -14,5 +14,5 @@
\item{filename}{ Filename path }
}
\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}. }
-\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
+\author{ Steven Kembel <steve.kembel at gmail.com> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{file}
Modified: pkg/man/writetraits.Rd
===================================================================
--- pkg/man/writetraits.Rd 2012-10-09 13:12:23 UTC (rev 241)
+++ pkg/man/writetraits.Rd 2013-05-29 20:28:39 UTC (rev 242)
@@ -17,5 +17,5 @@
}
\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}. }
-\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <skembel at uoregon.edu> }
+\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <steve.kembel at gmail.com> }
\keyword{file}
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