[Picante-commits] r171 - pkg pkg/R pkg/man tags tags/0.5-1 tags/0.5-1/R tags/0.5-1/man www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 27 00:29:57 CET 2009
Author: skembel
Date: 2009-01-27 00:29:56 +0100 (Tue, 27 Jan 2009)
New Revision: 171
Added:
tags/0.5-1/
tags/0.5-1/DESCRIPTION
tags/0.5-1/man/comm.phylo.cor.Rd
tags/0.5-1/man/cor.table.Rd
tags/0.5-1/man/evolve.brownian.Rd
tags/0.5-1/man/matrix2sample.Rd
tags/0.5-1/man/mnnd.Rd
tags/0.5-1/man/mpd.Rd
tags/0.5-1/man/multiPhylosignal.Rd
tags/0.5-1/man/phylosignal.Rd
tags/0.5-1/man/picante-package.Rd
tags/0.5-1/man/pruning.Rd
tags/0.5-1/man/randomizeSample.Rd
tags/0.5-1/man/readsample.Rd
tags/0.5-1/man/sample2matrix.Rd
tags/0.5-1/man/ses.mnnd.Rd
tags/0.5-1/man/ses.mpd.Rd
tags/0.5-1/man/species.dist.Rd
tags/0.5-1/man/utility.Rd
tags/0.5-1/man/writesample.Rd
tags/0.5-1/man/writetraits.Rd
Removed:
tags/0.5-1/DESCRIPTION
tags/0.5-1/man/comm.phylo.cor.Rd
tags/0.5-1/man/cor.table.Rd
tags/0.5-1/man/evolve.brownian.Rd
tags/0.5-1/man/matrix2sample.Rd
tags/0.5-1/man/mnnd.Rd
tags/0.5-1/man/mpd.Rd
tags/0.5-1/man/multiPhylosignal.Rd
tags/0.5-1/man/phylosignal.Rd
tags/0.5-1/man/picante-package.Rd
tags/0.5-1/man/pruning.Rd
tags/0.5-1/man/randomizeSample.Rd
tags/0.5-1/man/readsample.Rd
tags/0.5-1/man/sample2matrix.Rd
tags/0.5-1/man/ses.mnnd.Rd
tags/0.5-1/man/ses.mpd.Rd
tags/0.5-1/man/species.dist.Rd
tags/0.5-1/man/utility.Rd
tags/0.5-1/man/writesample.Rd
tags/0.5-1/man/writetraits.Rd
Modified:
pkg/DESCRIPTION
pkg/R/species.dist.R
pkg/man/comm.phylo.cor.Rd
pkg/man/picante-package.Rd
pkg/man/randomizeSample.Rd
pkg/man/ses.mnnd.Rd
pkg/man/ses.mpd.Rd
pkg/man/species.dist.Rd
tags/0.5-1/R/species.dist.R
www/index.php
Log:
Update documentation to meet stricter CRAN .Rd checks, tagged 0.5-1 for release. Note for future reference - no more nested item-itemize allowed in .Rd
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/DESCRIPTION 2009-01-26 23:29:56 UTC (rev 171)
@@ -1,8 +1,8 @@
Package: picante
Type: Package
-Title: Tools for integrating phylogenies and ecology
-Version: 0.5-0
-Date: 2009-1-22
+Title: R tools for integrating phylogenies and ecology
+Version: 0.5-1
+Date: 2009-1-26
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
Modified: pkg/R/species.dist.R
===================================================================
--- pkg/R/species.dist.R 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/R/species.dist.R 2009-01-26 23:29:56 UTC (rev 171)
@@ -1,5 +1,5 @@
`species.dist` <-
-function (x, metric=c("cij","jaccard","checkerboard","roij")) {
+function (x, metric=c("cij","jaccard","checkerboard","doij")) {
metric <- match.arg(metric)
if (identical(metric,"checkerboard")) {
#Gotelli 2000: Checker = Sum (Si - Q)(Sk - Q) / ((R*(R-1))/2)
@@ -25,9 +25,9 @@
if (identical(metric,"jaccard")) {
return( 1 - vegdist(t(sortColumns(x)), method = "jaccard"))
}
- if (identical(metric,"roij")) {
+ if (identical(metric,"doij")) {
#Hardy's standardized version of checkerboard
- #roij = (Pij - Pi*Pj)/(Pi*Pj)
+ #doij = (Pij - Pi*Pj)/(Pi*Pj)
x <- as.matrix(decostand(x,method="pa"))
Nsites <- dim(x)[1]
P <- apply(x,2,sum) / Nsites
Modified: pkg/man/comm.phylo.cor.Rd
===================================================================
--- pkg/man/comm.phylo.cor.Rd 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/man/comm.phylo.cor.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -14,14 +14,7 @@
\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{null.model}{ Null model to use (see Details section for description) }
\item{runs}{ Number of runs (randomizations) }
\item{...}{ Additional arguments to \link{randomizeSample}}
}
@@ -34,6 +27,17 @@
\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}
}
+\details{
+Currently implemented null models (arguments to null.model):
+\describe{
+ \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}
+ }
+}
\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}} }
Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/man/picante-package.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -6,14 +6,14 @@
Picante: Phylocom Integration, Community Analyses, Null-models, Traits, and Evolution in R
}
\description{
-Collection of functions for integrating ecology and evolutionary biology
+R tools for integrating phylogenies and ecology
}
\details{
\tabular{ll}{
Package: \tab picante\cr
Type: \tab Package\cr
-Version: \tab 0.5-0\cr
-Date: \tab 2009-1-22\cr
+Version: \tab 0.5-1\cr
+Date: \tab 2009-1-26\cr
License: \tab GPL-2\cr
}
}
Modified: pkg/man/randomizeSample.Rd
===================================================================
--- pkg/man/randomizeSample.Rd 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/man/randomizeSample.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -11,16 +11,21 @@
\arguments{
\item{samp}{ Community data matrix }
- \item{null.model}{ Null model
+ \item{null.model}{ Null model to use (see Details section for description) }
+ \item{iterations}{ Number of independent or trial-swaps to perform }
+}
+\value{
+ Randomized community data matrix
+}
+
+\details{
+Currently implemented null models (arguments to null.model):
+\describe{
\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
Modified: pkg/man/ses.mnnd.Rd
===================================================================
--- pkg/man/ses.mnnd.Rd 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/man/ses.mnnd.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -13,15 +13,7 @@
\arguments{
\item{ samp }{ Community data matrix }
\item{ dis }{ Distance matrix (generally a phylogenetic distance matrix)}
- \item{ null.model }{ Null model to use
- \item{taxa.labels}{ Shuffle distance matrix labels (across all taxa included in distance matrix)}
- \item{sample.pool}{ Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability}
- \item{phylogeny.pool}{ Randomize community data matrix by drawing species from pool of species occurring in the distance matrix (phylogeny pool) with equal probability}
- \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{ null.model }{ Null model to use (see Details section for description) }
\item{ runs }{ Number of randomizations }
\item{ iterations }{ Number of iterations to use for each randomization (for independent swap and trial null models) }
}
@@ -37,6 +29,18 @@
\item{mpd.obs.p}{P-value (quantile) of observed MNND vs. null communities (= mpd.obs.rank / runs + 1)}
\item{runs}{Number of randomizations}
}
+\details{
+Currently implemented null models (arguments to null.model):
+\describe{
+ \item{taxa.labels}{ Shuffle distance matrix labels (across all taxa included in distance matrix)}
+ \item{sample.pool}{ Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability}
+ \item{phylogeny.pool}{ Randomize community data matrix by drawing species from pool of species occurring in the distance matrix (phylogeny pool) with equal probability}
+ \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 }
+}
+}
\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> }
\seealso{ \code{\link{mnnd}}, \code{\link{randomizeSample}} }
Modified: pkg/man/ses.mpd.Rd
===================================================================
--- pkg/man/ses.mpd.Rd 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/man/ses.mpd.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -13,15 +13,7 @@
\arguments{
\item{ samp }{ Community data matrix }
\item{ dis }{ Distance matrix (generally a phylogenetic distance matrix)}
- \item{ null.model }{ Null model to use
- \item{taxa.labels}{ Shuffle distance matrix labels (across all taxa included in distance matrix)}
- \item{sample.pool}{ Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability}
- \item{phylogeny.pool}{ Randomize community data matrix by drawing species from pool of species occurring in the distance matrix (phylogeny pool) with equal probability}
- \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{ null.model }{ Null model to use (see Details section for description) }
\item{ runs }{ Number of randomizations }
\item{ iterations }{ Number of iterations to use for each randomization (for independent swap and trial null models) }
}
@@ -37,6 +29,19 @@
\item{mpd.obs.p}{P-value (quantile) of observed mpd vs. null communities (= mpd.obs.rank / runs + 1)}
\item{runs}{Number of randomizations}
}
+\details{
+Currently implemented null models (arguments to null.model):
+\describe{
+ \item{taxa.labels}{ Shuffle distance matrix labels (across all taxa included in distance matrix)}
+ \item{sample.pool}{ Randomize community data matrix by drawing species from pool of species occurring in at least one community (sample pool) with equal probability}
+ \item{phylogeny.pool}{ Randomize community data matrix by drawing species from pool of species occurring in the distance matrix (phylogeny pool) with equal probability}
+ \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 }
+ }
+}
+
\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> }
\seealso{ \code{\link{mpd}}, \code{\link{randomizeSample}} }
Modified: pkg/man/species.dist.Rd
===================================================================
--- pkg/man/species.dist.Rd 2009-01-23 19:46:28 UTC (rev 170)
+++ pkg/man/species.dist.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -7,27 +7,29 @@
}
\usage{
-species.dist(x, metric = c("cij", "jaccard", "checkerboard", "roij"))
+species.dist(x, metric = c("cij", "jaccard", "checkerboard", "doij"))
}
\arguments{
\item{x}{ Community data matrix }
- \item{metric}{
- \item{cij}{ Schoener's index of co-occurrence }
- \item{jaccard}{ Jaccard index of co-occurrence }
- \item{checkerboard}{ Checkerboard index of co-occurrence }
- \item{roij}{ ROij index of co-occurrence }
- }
+ \item{metric}{ Co-occurrence metric to use (see Details section for description) }
}
\value{
A \code{dist} object with co-occurrences among all species pairs
}
-
+\details{
+Currently implemented co-occurrence measures (arguments to metric):
+\describe{
+ \item{cij}{ Schoener's index of co-occurrence }
+ \item{jaccard}{ Jaccard index of co-occurrence }
+ \item{checkerboard}{ Checkerboard index of co-occurrence }
+ \item{roij}{ DOij index of co-occurrence }
+ }
+}
\author{ Steven Kembel <skembel at uoregon.edu> }
\references{
-Hardy, O. In press. 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.
+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.
}
\seealso{ \code{\link[vegan]{vegdist}} }
\keyword{univar}
Copied: tags/0.5-1 (from rev 168, pkg)
Deleted: tags/0.5-1/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/DESCRIPTION 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/DESCRIPTION (from rev 169, pkg/DESCRIPTION)
===================================================================
--- tags/0.5-1/DESCRIPTION (rev 0)
+++ tags/0.5-1/DESCRIPTION 2009-01-26 23:29:56 UTC (rev 171)
@@ -0,0 +1,11 @@
+Package: picante
+Type: Package
+Title: R tools for integrating phylogenies and ecology
+Version: 0.5-1
+Date: 2009-1-26
+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
Modified: tags/0.5-1/R/species.dist.R
===================================================================
--- pkg/R/species.dist.R 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/R/species.dist.R 2009-01-26 23:29:56 UTC (rev 171)
@@ -1,5 +1,5 @@
`species.dist` <-
-function (x, metric=c("cij","jaccard","checkerboard","roij")) {
+function (x, metric=c("cij","jaccard","checkerboard","doij")) {
metric <- match.arg(metric)
if (identical(metric,"checkerboard")) {
#Gotelli 2000: Checker = Sum (Si - Q)(Sk - Q) / ((R*(R-1))/2)
@@ -25,9 +25,9 @@
if (identical(metric,"jaccard")) {
return( 1 - vegdist(t(sortColumns(x)), method = "jaccard"))
}
- if (identical(metric,"roij")) {
+ if (identical(metric,"doij")) {
#Hardy's standardized version of checkerboard
- #roij = (Pij - Pi*Pj)/(Pi*Pj)
+ #doij = (Pij - Pi*Pj)/(Pi*Pj)
x <- as.matrix(decostand(x,method="pa"))
Nsites <- dim(x)[1]
P <- apply(x,2,sum) / Nsites
Deleted: tags/0.5-1/man/comm.phylo.cor.Rd
===================================================================
--- pkg/man/comm.phylo.cor.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/man/comm.phylo.cor.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/comm.phylo.cor.Rd (from rev 169, pkg/man/comm.phylo.cor.Rd)
===================================================================
--- tags/0.5-1/man/comm.phylo.cor.Rd (rev 0)
+++ tags/0.5-1/man/comm.phylo.cor.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -0,0 +1,47 @@
+\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 (see Details section for description) }
+ \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}
+}
+\details{
+Currently implemented null models (arguments to null.model):
+\describe{
+ \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}
+ }
+}
+\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/0.5-1/man/cor.table.Rd
===================================================================
--- pkg/man/cor.table.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/man/cor.table.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/cor.table.Rd (from rev 169, pkg/man/cor.table.Rd)
===================================================================
--- tags/0.5-1/man/cor.table.Rd (rev 0)
+++ tags/0.5-1/man/cor.table.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/evolve.brownian.Rd
===================================================================
--- pkg/man/evolve.brownian.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/man/evolve.brownian.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/evolve.brownian.Rd (from rev 169, pkg/man/evolve.brownian.Rd)
===================================================================
--- tags/0.5-1/man/evolve.brownian.Rd (rev 0)
+++ tags/0.5-1/man/evolve.brownian.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/matrix2sample.Rd
===================================================================
--- pkg/man/matrix2sample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/man/matrix2sample.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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$sample)
-}
-\keyword{manip}
Copied: tags/0.5-1/man/matrix2sample.Rd (from rev 169, pkg/man/matrix2sample.Rd)
===================================================================
--- tags/0.5-1/man/matrix2sample.Rd (rev 0)
+++ tags/0.5-1/man/matrix2sample.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -0,0 +1,25 @@
+\name{matrix2sample}
+\alias{matrix2sample}
+
+\title{ Convert community data matrix to Phylocom sample }
+\description{
+ Converts a community data matrix to a Phylocom database-format community sample
+}
+\usage{
+matrix2sample(z)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{z}{ Community data matrix }
+}
+
+\value{
+ Phylocom database-format community sample
+}
+\references{ Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0.1. \url{http://www.phylodiversity.net/phylocom/}.}
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
+\examples{
+data(phylocom)
+matrix2sample(phylocom$sample)
+}
+\keyword{manip}
Deleted: tags/0.5-1/man/mnnd.Rd
===================================================================
--- pkg/man/mnnd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/man/mnnd.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/mnnd.Rd (from rev 169, pkg/man/mnnd.Rd)
===================================================================
--- tags/0.5-1/man/mnnd.Rd (rev 0)
+++ tags/0.5-1/man/mnnd.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/mpd.Rd
===================================================================
--- pkg/man/mpd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ tags/0.5-1/man/mpd.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/mpd.Rd (from rev 169, pkg/man/mpd.Rd)
===================================================================
--- tags/0.5-1/man/mpd.Rd (rev 0)
+++ tags/0.5-1/man/mpd.Rd 2009-01-26 23:29:56 UTC (rev 171)
@@ -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/0.5-1/man/multiPhylosignal.Rd
===================================================================
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/picante -r 171
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