[Picante-commits] r170 - in tags: . 0.5-0 0.5-0/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 23 20:46:29 CET 2009
Author: skembel
Date: 2009-01-23 20:46:28 +0100 (Fri, 23 Jan 2009)
New Revision: 170
Added:
tags/0.5-0/
tags/0.5-0/DESCRIPTION
tags/0.5-0/man/comm.phylo.cor.Rd
tags/0.5-0/man/cor.table.Rd
tags/0.5-0/man/evolve.brownian.Rd
tags/0.5-0/man/matrix2sample.Rd
tags/0.5-0/man/mnnd.Rd
tags/0.5-0/man/mpd.Rd
tags/0.5-0/man/multiPhylosignal.Rd
tags/0.5-0/man/phylosignal.Rd
tags/0.5-0/man/picante-package.Rd
tags/0.5-0/man/pruning.Rd
tags/0.5-0/man/randomizeSample.Rd
tags/0.5-0/man/readsample.Rd
tags/0.5-0/man/sample2matrix.Rd
tags/0.5-0/man/ses.mnnd.Rd
tags/0.5-0/man/ses.mpd.Rd
tags/0.5-0/man/species.dist.Rd
tags/0.5-0/man/utility.Rd
tags/0.5-0/man/writesample.Rd
tags/0.5-0/man/writetraits.Rd
Removed:
tags/0.5-0/DESCRIPTION
tags/0.5-0/man/comm.phylo.cor.Rd
tags/0.5-0/man/cor.table.Rd
tags/0.5-0/man/evolve.brownian.Rd
tags/0.5-0/man/matrix2sample.Rd
tags/0.5-0/man/mnnd.Rd
tags/0.5-0/man/mpd.Rd
tags/0.5-0/man/multiPhylosignal.Rd
tags/0.5-0/man/phylosignal.Rd
tags/0.5-0/man/picante-package.Rd
tags/0.5-0/man/pruning.Rd
tags/0.5-0/man/randomizeSample.Rd
tags/0.5-0/man/readsample.Rd
tags/0.5-0/man/sample2matrix.Rd
tags/0.5-0/man/ses.mnnd.Rd
tags/0.5-0/man/ses.mpd.Rd
tags/0.5-0/man/species.dist.Rd
tags/0.5-0/man/utility.Rd
tags/0.5-0/man/writesample.Rd
tags/0.5-0/man/writetraits.Rd
Log:
Tagging version 0.5-0 for release
Copied: tags/0.5-0 (from rev 168, pkg)
Deleted: tags/0.5-0/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/DESCRIPTION 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,11 +0,0 @@
-Package: picante
-Type: Package
-Title: Tools for integrating phylogenies and ecology
-Version: 0.4-0
-Date: 2008-8-22
-Author: Steve Kembel <skembel at berkeley.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>, Cam Webb <cwebb at oeb.harvard.edu>
-Maintainer: Steve Kembel <skembel at berkeley.edu>
-Depends: ape, vegan
-Suggests: brglm, circular
-Description: Phylocom integration, community analyses, null-models, traits and evolution in R
-License: GPL-2
Copied: tags/0.5-0/DESCRIPTION (from rev 169, pkg/DESCRIPTION)
===================================================================
--- tags/0.5-0/DESCRIPTION (rev 0)
+++ tags/0.5-0/DESCRIPTION 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,11 @@
+Package: picante
+Type: Package
+Title: Tools for integrating phylogenies and ecology
+Version: 0.5-0
+Date: 2009-1-22
+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>
+Maintainer: Steven Kembel <skembel at uoregon.edu>
+Depends: ape, vegan, nlme
+Suggests: brglm, circular
+Description: Phylocom integration, community analyses, null-models, traits and evolution in R
+License: GPL-2
Deleted: tags/0.5-0/man/comm.phylo.cor.Rd
===================================================================
--- pkg/man/comm.phylo.cor.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/comm.phylo.cor.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,43 +0,0 @@
-\name{comm.phylo.cor}
-\alias{comm.phylo.cor}
-
-\title{ Correlations between species co-occurrence and phylogenetic distances }
-\description{
- Calculates measures of community phylogenetic structure (correlation between co-occurrence and phylogenetic distance) to patterns expected under various null models
-}
-\usage{
-comm.phylo.cor(samp, phylo, metric = c("cij", "checkerboard", "jaccard", "roij"),
- null.model = c("sample.taxa.labels", "pool.taxa.labels",
- "frequency", "richness", "independentswap","trialswap"), runs = 999, ...)
-}
-\arguments{
- \item{samp}{ Community data matrix }
- \item{phylo}{ Phylogenetic tree }
- \item{metric}{ Metric of co-occurrence to use (see \code{\link{species.dist}})}
- \item{null.model}{ Null model to use:
- \item{sample.taxa.labels}{Shuffle phylogeny tip labels (only within set of taxa present in community data)}
- \item{pool.taxa.labels}{Shuffle phylogeny tip labels (across all taxa included in phylogenetic tree)}
- \item{frequency}{Randomize community data matrix abundances within species (maintains species occurence frequency)}
- \item{richness}{Randomize community data matrix abundances within samples (maintains sample species richness)}
- \item{independentswap}{Randomize community data matrix maintaining species occurrence frequency and site richnessing using independent swap}
- \item{trialswap}{Randomize community data matrix maintaining species occurrence frequency and site richnessing using trial swap}
- }
- \item{runs}{ Number of runs (randomizations) }
- \item{...}{ Additional arguments to \link{randomizeSample}}
-}
-\value{
- A list with elements:
- \item{obs.corr }{ Observed co-occurrence/phylogenetic distance correlation}
- \item{obs.corr.p}{ P-value of observed correlation (standard P-value for correlation coefficient, not based on comparison with randomizations)}
- \item{obs.rank}{ Rank of observed correlation vs. random}
- \item{runs}{ Number of runs (randomizations) }
- \item{obs.rand.p}{ P-value of observed correlation vs. randomizations (= obs.rank / (runs + 1))}
- \item{random.corrs}{A vector of random correlation calculated for each run}
-}
-\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{ Steve Kembel <skembel at berkeley.edu> }
-\seealso{ \code{\link{randomizeSample}} }
-\examples{
-data(phylocom)
-comm.phylo.cor(phylocom$sample, phylocom$phylo, metric="cij",null.model="sample.taxa.labels")}
-\keyword{univar}
Copied: tags/0.5-0/man/comm.phylo.cor.Rd (from rev 169, pkg/man/comm.phylo.cor.Rd)
===================================================================
--- tags/0.5-0/man/comm.phylo.cor.Rd (rev 0)
+++ tags/0.5-0/man/comm.phylo.cor.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,43 @@
+\name{comm.phylo.cor}
+\alias{comm.phylo.cor}
+
+\title{ Correlations between species co-occurrence and phylogenetic distances }
+\description{
+ Calculates measures of community phylogenetic structure (correlation between co-occurrence and phylogenetic distance) to patterns expected under various null models
+}
+\usage{
+comm.phylo.cor(samp, phylo, metric = c("cij", "checkerboard", "jaccard", "roij"),
+ null.model = c("sample.taxa.labels", "pool.taxa.labels",
+ "frequency", "richness", "independentswap","trialswap"), runs = 999, ...)
+}
+\arguments{
+ \item{samp}{ Community data matrix }
+ \item{phylo}{ Phylogenetic tree }
+ \item{metric}{ Metric of co-occurrence to use (see \code{\link{species.dist}})}
+ \item{null.model}{ Null model to use:
+ \item{sample.taxa.labels}{Shuffle phylogeny tip labels (only within set of taxa present in community data)}
+ \item{pool.taxa.labels}{Shuffle phylogeny tip labels (across all taxa included in phylogenetic tree)}
+ \item{frequency}{Randomize community data matrix abundances within species (maintains species occurence frequency)}
+ \item{richness}{Randomize community data matrix abundances within samples (maintains sample species richness)}
+ \item{independentswap}{Randomize community data matrix maintaining species occurrence frequency and site richnessing using independent swap}
+ \item{trialswap}{Randomize community data matrix maintaining species occurrence frequency and site richnessing using trial swap}
+ }
+ \item{runs}{ Number of runs (randomizations) }
+ \item{...}{ Additional arguments to \link{randomizeSample}}
+}
+\value{
+ A list with elements:
+ \item{obs.corr }{ Observed co-occurrence/phylogenetic distance correlation}
+ \item{obs.corr.p}{ P-value of observed correlation (standard P-value for correlation coefficient, not based on comparison with randomizations)}
+ \item{obs.rank}{ Rank of observed correlation vs. random}
+ \item{runs}{ Number of runs (randomizations) }
+ \item{obs.rand.p}{ P-value of observed correlation vs. randomizations (= obs.rank / (runs + 1))}
+ \item{random.corrs}{A vector of random correlation calculated for each run}
+}
+\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> }
+\seealso{ \code{\link{randomizeSample}} }
+\examples{
+data(phylocom)
+comm.phylo.cor(phylocom$sample, phylocom$phylo, metric="cij",null.model="sample.taxa.labels")}
+\keyword{univar}
Deleted: tags/0.5-0/man/cor.table.Rd
===================================================================
--- pkg/man/cor.table.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/cor.table.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,26 +0,0 @@
-\name{cor.table}
-\alias{cor.table}
-\title{ Table of correlations and P-values }
-\description{
- Table of correlations with associated P-values and df, can be used with regular or independent contrast data
-}
-\usage{
-cor.table(x, cor.method = "pearson", cor.type=c("standard","contrast"))
-}
-
-\arguments{
- \item{x}{ Data frame of data points or contrasts at nodes }
- \item{cor.method}{ Correlation method (as \code{\link[stats]{cor}}) }
- \item{cor.type}{ Are data \code{standard} or independent \code{contrast} values?}
-}
-
-\value{
- \item{r}{Correlation values}
- \item{df}{Degrees of freedom}
- \item{P}{P-values}
-}
-
-\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{ Steve Kembel <skembel at berkeley.edu> }
-\keyword{univar}
Copied: tags/0.5-0/man/cor.table.Rd (from rev 169, pkg/man/cor.table.Rd)
===================================================================
--- tags/0.5-0/man/cor.table.Rd (rev 0)
+++ tags/0.5-0/man/cor.table.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,26 @@
+\name{cor.table}
+\alias{cor.table}
+\title{ Table of correlations and P-values }
+\description{
+ Table of correlations with associated P-values and df, can be used with regular or independent contrast data
+}
+\usage{
+cor.table(x, cor.method = "pearson", cor.type=c("standard","contrast"))
+}
+
+\arguments{
+ \item{x}{ Data frame of data points or contrasts at nodes }
+ \item{cor.method}{ Correlation method (as \code{\link[stats]{cor}}) }
+ \item{cor.type}{ Are data \code{standard} or independent \code{contrast} values?}
+}
+
+\value{
+ \item{r}{Correlation values}
+ \item{df}{Degrees of freedom}
+ \item{P}{P-values}
+}
+
+\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> }
+\keyword{univar}
Deleted: tags/0.5-0/man/evolve.brownian.Rd
===================================================================
--- pkg/man/evolve.brownian.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/evolve.brownian.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -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 Steve Kembel <skembel at berkeley.edu> }
-\keyword{datagen}
Copied: tags/0.5-0/man/evolve.brownian.Rd (from rev 169, pkg/man/evolve.brownian.Rd)
===================================================================
--- tags/0.5-0/man/evolve.brownian.Rd (rev 0)
+++ tags/0.5-0/man/evolve.brownian.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,20 @@
+\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}
Deleted: tags/0.5-0/man/matrix2sample.Rd
===================================================================
--- pkg/man/matrix2sample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/matrix2sample.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,25 +0,0 @@
-\name{matrix2sample}
-\alias{matrix2sample}
-
-\title{ Convert community data matrix to Phylocom sample }
-\description{
- Converts a community data matrix to a Phylocom database-format community sample
-}
-\usage{
-matrix2sample(z)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{z}{ Community data matrix }
-}
-
-\value{
- 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{ Steve Kembel <skembel at berkeley.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
-\examples{
-data(phylocom)
-matrix2sample(phylocom$sample)
-}
-\keyword{manip}
Copied: tags/0.5-0/man/matrix2sample.Rd (from rev 169, pkg/man/matrix2sample.Rd)
===================================================================
--- tags/0.5-0/man/matrix2sample.Rd (rev 0)
+++ tags/0.5-0/man/matrix2sample.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,25 @@
+\name{matrix2sample}
+\alias{matrix2sample}
+
+\title{ Convert community data matrix to Phylocom sample }
+\description{
+ Converts a community data matrix to a Phylocom database-format community sample
+}
+\usage{
+matrix2sample(z)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{z}{ Community data matrix }
+}
+
+\value{
+ Phylocom database-format community sample
+}
+\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}.}
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
+\examples{
+data(phylocom)
+matrix2sample(phylocom$sample)
+}
+\keyword{manip}
Deleted: tags/0.5-0/man/mnnd.Rd
===================================================================
--- pkg/man/mnnd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/mnnd.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,21 +0,0 @@
-\name{mnnd}
-\alias{mnnd}
-\title{ Mean nearest neighbour distance }
-\description{
- Calculates MNND (mean nearest neighbour distance) for taxa in a community
-}
-\usage{
-mnnd(samp, dis)
-}
-
-\arguments{
- \item{samp}{ Community data matrix }
- \item{dis}{ Interspecific distance matrix }
-}
-\value{
- Vector of MNND 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{ Steve Kembel <skembel at berkeley.edu> }
-\seealso{ \code{\link{ses.mnnd}} }
-\keyword{univar}
Copied: tags/0.5-0/man/mnnd.Rd (from rev 169, pkg/man/mnnd.Rd)
===================================================================
--- tags/0.5-0/man/mnnd.Rd (rev 0)
+++ tags/0.5-0/man/mnnd.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,21 @@
+\name{mnnd}
+\alias{mnnd}
+\title{ Mean nearest neighbour distance }
+\description{
+ Calculates MNND (mean nearest neighbour distance) for taxa in a community
+}
+\usage{
+mnnd(samp, dis)
+}
+
+\arguments{
+ \item{samp}{ Community data matrix }
+ \item{dis}{ Interspecific distance matrix }
+}
+\value{
+ Vector of MNND 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> }
+\seealso{ \code{\link{ses.mnnd}} }
+\keyword{univar}
Deleted: tags/0.5-0/man/mpd.Rd
===================================================================
--- pkg/man/mpd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/mpd.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,22 +0,0 @@
-\name{mpd}
-\alias{mpd}
-\title{ Mean pairwise distance }
-\description{
- Calculates mean pairwise distance for a community
-}
-\usage{
-mpd(samp, dis)
-}
-
-\arguments{
- \item{samp}{ Community data matrix }
- \item{dis}{ Interspecific distance matrix }
-}
-
-\value{
- 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{ Steve Kembel <skembel at berkeley.edu> }
-\seealso{ \code{\link{ses.mpd}}}
-\keyword{univar}
Copied: tags/0.5-0/man/mpd.Rd (from rev 169, pkg/man/mpd.Rd)
===================================================================
--- tags/0.5-0/man/mpd.Rd (rev 0)
+++ tags/0.5-0/man/mpd.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,22 @@
+\name{mpd}
+\alias{mpd}
+\title{ Mean pairwise distance }
+\description{
+ Calculates mean pairwise distance for a community
+}
+\usage{
+mpd(samp, dis)
+}
+
+\arguments{
+ \item{samp}{ Community data matrix }
+ \item{dis}{ Interspecific distance matrix }
+}
+
+\value{
+ 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> }
+\seealso{ \code{\link{ses.mpd}}}
+\keyword{univar}
Deleted: tags/0.5-0/man/multiPhylosignal.Rd
===================================================================
--- pkg/man/multiPhylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/multiPhylosignal.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,20 +0,0 @@
-\name{multiPhylosignal}
-\alias{multiPhylosignal}
-\title{ Calculates phylogenetic signal for data.frame of traits }
-\description{
- Calculates phylogenetic signal for data.frame of traits. Traits may have missing values in which case the tree will be pruned prior to calculating phylogenetic signal for each trait.
-}
-\usage{
-multiPhylosignal(x, phy, ...)
-}
-\arguments{
- \item{x}{ Data frame of trait data (traits in columns) with row names corresponding to tip.labels}
- \item{phy}{ phylo object }
- \item{...}{ Additional arguments to \link{phylosignal} }
-}
-\value{
- Returns a data frame with phylogenetic signal results for each trait
-}
-\section{Warning }{ Assumes that trait data are sorted in the same order as phylo tip.label }
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\keyword{univar}
Copied: tags/0.5-0/man/multiPhylosignal.Rd (from rev 169, pkg/man/multiPhylosignal.Rd)
===================================================================
--- tags/0.5-0/man/multiPhylosignal.Rd (rev 0)
+++ tags/0.5-0/man/multiPhylosignal.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,20 @@
+\name{multiPhylosignal}
+\alias{multiPhylosignal}
+\title{ Calculates phylogenetic signal for data.frame of traits }
+\description{
+ Calculates phylogenetic signal for data.frame of traits. Traits may have missing values in which case the tree will be pruned prior to calculating phylogenetic signal for each trait.
+}
+\usage{
+multiPhylosignal(x, phy, ...)
+}
+\arguments{
+ \item{x}{ Data frame of trait data (traits in columns) with row names corresponding to tip.labels}
+ \item{phy}{ phylo object }
+ \item{...}{ Additional arguments to \link{phylosignal} }
+}
+\value{
+ Returns a data frame with phylogenetic signal results for each trait
+}
+\section{Warning }{ Assumes that trait data are sorted in the same order as phylo tip.label }
+\author{ Steven Kembel <skembel at uoregon.edu> }
+\keyword{univar}
Deleted: tags/0.5-0/man/phylosignal.Rd
===================================================================
--- pkg/man/phylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/phylosignal.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,37 +0,0 @@
-\name{phylosignal}
-\alias{phylosignal}
-
-\title{ Measure phylogenetic signal }
-\description{
- Calculates K statistic of phylogenetic signal as well as P-value based on variance of phylogenetically independent contrasts relative to tip shuffling randomization.
-}
-\usage{
-phylosignal(x, phy, reps = 999, ...)
-}
-
-\arguments{
- \item{x}{ Trait vector (same order as phy\$tip.label) }
- \item{phy}{ phylo object }
- \item{reps}{ Number of randomizations }
- \item{...}{ Additional arguments passed to pic }
-}
-\value{
- Data frame with columns:
- \item{K }{K statistic}
- \item{PIC.variance }{Mean observed PIC variance}
- \item{PIC.variance.P }{P-value of observed vs. random variance of PICs}
- \item{PIC.variance.z }{Z-score of observed vs. random variance of PICs}
-}
-\references{
-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{ Steve Kembel <skembel at berkeley.edu> }
-\seealso{ \code{\link{Kcalc}} }
-\section{Warning }{ Assumes that trait data are sorted in the same order as phylo\$tip.label }
-\examples{
-randtree <- rcoal(20)
-randtraits <- evolve.brownian(randtree)
-phylosignal(randtraits[randtree$tip.label],randtree)
-}
-\keyword{univar}
\ No newline at end of file
Copied: tags/0.5-0/man/phylosignal.Rd (from rev 169, pkg/man/phylosignal.Rd)
===================================================================
--- tags/0.5-0/man/phylosignal.Rd (rev 0)
+++ tags/0.5-0/man/phylosignal.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,37 @@
+\name{phylosignal}
+\alias{phylosignal}
+
+\title{ Measure phylogenetic signal }
+\description{
+ Calculates K statistic of phylogenetic signal as well as P-value based on variance of phylogenetically independent contrasts relative to tip shuffling randomization.
+}
+\usage{
+phylosignal(x, phy, reps = 999, ...)
+}
+
+\arguments{
+ \item{x}{ Trait vector (same order as phy\$tip.label) }
+ \item{phy}{ phylo object }
+ \item{reps}{ Number of randomizations }
+ \item{...}{ Additional arguments passed to pic }
+}
+\value{
+ Data frame with columns:
+ \item{K }{K statistic}
+ \item{PIC.variance }{Mean observed PIC variance}
+ \item{PIC.variance.P }{P-value of observed vs. random variance of PICs}
+ \item{PIC.variance.z }{Z-score of observed vs. random variance of PICs}
+}
+\references{
+Blomberg, S. P., and T. Garland, Jr. 2002. Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology 15:899-910.
+
+Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. }
+\author{ Steven Kembel <skembel at uoregon.edu> }
+\seealso{ \code{\link{Kcalc}} }
+\section{Warning }{ Assumes that trait data are sorted in the same order as phylo\$tip.label }
+\examples{
+randtree <- rcoal(20)
+randtraits <- evolve.brownian(randtree)
+phylosignal(randtraits[randtree$tip.label],randtree)
+}
+\keyword{univar}
\ No newline at end of file
Deleted: tags/0.5-0/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/picante-package.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,25 +0,0 @@
-\name{picante-package}
-\alias{picante-package}
-\alias{picante}
-\docType{package}
-\title{
-Picante: Phylocom Integration, Community Analyses, Null-models, Traits, and Evolution in R
-}
-\description{
-Collection of functions for integrating ecology and evolutionary biology
-}
-\details{
-\tabular{ll}{
-Package: \tab picante\cr
-Type: \tab Package\cr
-Version: \tab 0.4-0\cr
-Date: \tab 2008-8-22\cr
-License: \tab GPL-2\cr
-}
-}
-\author{
-Steve Kembel <skembel at berkeley.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>, Cam Webb <cwebb at oeb.harvard.edu>
-
-Maintainer: Steve Kembel <skembel at berkeley.edu>
-}
-\keyword{package}
Copied: tags/0.5-0/man/picante-package.Rd (from rev 169, pkg/man/picante-package.Rd)
===================================================================
--- tags/0.5-0/man/picante-package.Rd (rev 0)
+++ tags/0.5-0/man/picante-package.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,25 @@
+\name{picante-package}
+\alias{picante-package}
+\alias{picante}
+\docType{package}
+\title{
+Picante: Phylocom Integration, Community Analyses, Null-models, Traits, and Evolution in R
+}
+\description{
+Collection of functions for integrating ecology and evolutionary biology
+}
+\details{
+\tabular{ll}{
+Package: \tab picante\cr
+Type: \tab Package\cr
+Version: \tab 0.5-0\cr
+Date: \tab 2009-1-22\cr
+License: \tab GPL-2\cr
+}
+}
+\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>
+
+Maintainer: Steven Kembel <skembel at uoregon.edu>
+}
+\keyword{package}
Deleted: tags/0.5-0/man/pruning.Rd
===================================================================
--- pkg/man/pruning.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/pruning.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,23 +0,0 @@
-\name{prune.sample}
-\alias{prune.sample}
-\alias{prune.missing}
-
-\title{ Prune tree to match community data or trait data }
-\description{
- Prune a phylogenetic tree to include only species present in a community data set or with non-missing trait data}
-\usage{
-prune.sample(samp, phylo)
-prune.missing(x, phylo)
-}
-
-\arguments{
- \item{phylo}{ phylo object }
- \item{samp}{ Community data matrix }
- \item{x}{ Vector of trait data }
-}
-
-\value{
- Returns a pruned phylo object
-}
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\keyword{manip}
Copied: tags/0.5-0/man/pruning.Rd (from rev 169, pkg/man/pruning.Rd)
===================================================================
--- tags/0.5-0/man/pruning.Rd (rev 0)
+++ tags/0.5-0/man/pruning.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,23 @@
+\name{prune.sample}
+\alias{prune.sample}
+\alias{prune.missing}
+
+\title{ Prune tree to match community data or trait data }
+\description{
+ Prune a phylogenetic tree to include only species present in a community data set or with non-missing trait data}
+\usage{
+prune.sample(samp, phylo)
+prune.missing(x, phylo)
+}
+
+\arguments{
+ \item{phylo}{ phylo object }
+ \item{samp}{ Community data matrix }
+ \item{x}{ Vector of trait data }
+}
+
+\value{
+ Returns a pruned phylo object
+}
+\author{ Steven Kembel <skembel at uoregon.edu> }
+\keyword{manip}
Deleted: tags/0.5-0/man/randomizeSample.Rd
===================================================================
--- pkg/man/randomizeSample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/randomizeSample.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,35 +0,0 @@
-\name{randomizeSample}
-\alias{randomizeSample}
-
-\title{ Null models for community data matrix randomization}
-\description{
- Various null models for randomizing community data matrices
-}
-\usage{
-randomizeSample(samp, null.model = c("frequency", "richness", "independentswap", "trialswap"),
- iterations = 1000)
-}
-
-\arguments{
- \item{samp}{ Community data matrix }
- \item{null.model}{ Null model
- \item{frequency}{ Randomize community data matrix abundances within species (maintains species occurence frequency)}
- \item{richness}{ Randomize community data matrix abundances within samples (maintains sample species richness)}
- \item{independentswap}{ Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness }
- \item{trialswap}{ Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness }
- }
- \item{iterations}{ Number of independent or trial-swaps to perform }
-}
-\value{
- Randomized community data matrix
-}
-\references{
-Gotelli, N.J. 2000. Null model analysis of species co-occurrence patterns. Ecology 81: 2606-2621
-
-Miklos I. & Podani J. 2004. Randomization of presence-absence matrices: Comments and new algorithms. Ecology 85: 86-92.
-}
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\examples{
-data(phylocom)
-randomizeSample(phylocom$sample, null.model="richness")}
-\keyword{manip}
Copied: tags/0.5-0/man/randomizeSample.Rd (from rev 169, pkg/man/randomizeSample.Rd)
===================================================================
--- tags/0.5-0/man/randomizeSample.Rd (rev 0)
+++ tags/0.5-0/man/randomizeSample.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,34 @@
+\name{randomizeSample}
+\alias{randomizeSample}
+
+\title{ Null models for community data matrix randomization}
+\description{
+ Various null models for randomizing community data matrices
+}
+\usage{
+randomizeSample(samp, null.model = c("frequency", "richness", "independentswap", "trialswap"),iterations = 1000)
+}
+
+\arguments{
+ \item{samp}{ Community data matrix }
+ \item{null.model}{ Null model
+ \item{frequency}{ Randomize community data matrix abundances within species (maintains species occurence frequency)}
+ \item{richness}{ Randomize community data matrix abundances within samples (maintains sample species richness)}
+ \item{independentswap}{ Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness }
+ \item{trialswap}{ Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness }
+ }
+ \item{iterations}{ Number of independent or trial-swaps to perform }
+}
+\value{
+ Randomized community data matrix
+}
+\references{
+Gotelli, N.J. 2000. Null model analysis of species co-occurrence patterns. Ecology 81: 2606-2621
+
+Miklos I. & Podani J. 2004. Randomization of presence-absence matrices: Comments and new algorithms. Ecology 85: 86-92.
+}
+\author{ Steven Kembel <skembel at uoregon.edu> }
+\examples{
+data(phylocom)
+randomizeSample(phylocom$sample, null.model="richness")}
+\keyword{manip}
Deleted: tags/0.5-0/man/readsample.Rd
===================================================================
--- pkg/man/readsample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/readsample.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,21 +0,0 @@
-\name{readsample}
-\alias{readsample}
-
-\title{ Read Phylocom sample }
-\description{
- Reads a Phylocom sample file and converts to a community data matrix
-}
-\usage{
-readsample(filename = "")
-}
-
-\arguments{
- \item{filename}{ Phylocom sample file path }
-}
-
-\value{
- Community data matrix
-}
-\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{ Steve Kembel <skembel> and Cam Webb <cwebb at oeb.harvard.edu> }
-\keyword{IO}
Copied: tags/0.5-0/man/readsample.Rd (from rev 169, pkg/man/readsample.Rd)
===================================================================
--- tags/0.5-0/man/readsample.Rd (rev 0)
+++ tags/0.5-0/man/readsample.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,21 @@
+\name{readsample}
+\alias{readsample}
+
+\title{ Read Phylocom sample }
+\description{
+ Reads a Phylocom sample file and converts to a community data matrix
+}
+\usage{
+readsample(filename = "")
+}
+
+\arguments{
+ \item{filename}{ Phylocom sample file path }
+}
+
+\value{
+ Community data matrix
+}
+\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> and Cam Webb <cwebb at oeb.harvard.edu> }
+\keyword{IO}
Deleted: tags/0.5-0/man/sample2matrix.Rd
===================================================================
--- pkg/man/sample2matrix.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-0/man/sample2matrix.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -1,24 +0,0 @@
-\name{sample2matrix}
-\alias{sample2matrix}
-
-\title{ Convert Phylocom sample to community data matrix }
-\description{
- Convert a Phylocom database-format sample to community data matrix.
-}
-\usage{
-sample2matrix(x)
-}
-
-\arguments{
- \item{x}{ Phylocom sample formatted data frame, a data frame with three columns:
- \itemize{
- \item{Column 1}{ Community name}
- \item{Column 2}{ Species abundance}
- \item{Column 3}{ Species name}
- }
- }
-}
-
-\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{ Steve Kembel <skembel at berkeley.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
-\keyword{IO}
Copied: tags/0.5-0/man/sample2matrix.Rd (from rev 169, pkg/man/sample2matrix.Rd)
===================================================================
--- tags/0.5-0/man/sample2matrix.Rd (rev 0)
+++ tags/0.5-0/man/sample2matrix.Rd 2009-01-23 19:46:28 UTC (rev 170)
@@ -0,0 +1,24 @@
+\name{sample2matrix}
+\alias{sample2matrix}
+
+\title{ Convert Phylocom sample to community data matrix }
+\description{
+ Convert a Phylocom database-format sample to community data matrix.
+}
+\usage{
+sample2matrix(x)
+}
+
+\arguments{
[TRUNCATED]
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svnlook diff /svnroot/picante -r 170
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