[Picante-commits] r223 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Apr 9 01:44:07 CEST 2010
Author: skembel
Date: 2010-04-09 01:44:07 +0200 (Fri, 09 Apr 2010)
New Revision: 223
Modified:
pkg/R/phylodiversity.R
pkg/man/ses.mntd.Rd
pkg/man/ses.mpd.Rd
pkg/man/ses.pd.Rd
Log:
Reinstating the richness and frequency null models
Modified: pkg/R/phylodiversity.R
===================================================================
--- pkg/R/phylodiversity.R 2010-04-08 23:19:43 UTC (rev 222)
+++ pkg/R/phylodiversity.R 2010-04-08 23:44:07 UTC (rev 223)
@@ -165,7 +165,7 @@
`ses.mpd` <-
-function (samp, dis, null.model = c("taxa.labels", "sample.pool",
+function (samp, dis, null.model = c("taxa.labels", "richness", "frequency", "sample.pool",
"phylogeny.pool", "independentswap", "trialswap"),
abundance.weighted = FALSE, runs = 999, iterations = 1000)
{
@@ -174,6 +174,8 @@
null.model <- match.arg(null.model)
mpd.rand <- switch(null.model,
taxa.labels = t(replicate(runs, mpd(samp, taxaShuffle(dis), abundance.weighted=abundance.weighted))),
+ richness = t(replicate(runs, mpd(randomizeMatrix(samp,null.model="richness"), dis, abundance.weighted))),
+ frequency = t(replicate(runs, mpd(randomizeMatrix(samp,null.model="frequency"), dis, abundance.weighted))),
sample.pool = t(replicate(runs, mpd(randomizeMatrix(samp,null.model="richness"), dis, abundance.weighted))),
phylogeny.pool = t(replicate(runs, mpd(randomizeMatrix(samp,null.model="richness"),
taxaShuffle(dis), abundance.weighted))),
@@ -192,7 +194,7 @@
`ses.mntd` <-
-function (samp, dis, null.model = c("taxa.labels", "sample.pool",
+function (samp, dis, null.model = c("taxa.labels", "richness", "frequency", "sample.pool",
"phylogeny.pool", "independentswap", "trialswap"),
abundance.weighted = FALSE, runs = 999, iterations = 1000)
{
@@ -201,6 +203,8 @@
null.model <- match.arg(null.model)
mntd.rand <- switch(null.model,
taxa.labels = t(replicate(runs, mntd(samp, taxaShuffle(dis), abundance.weighted))),
+ richness = t(replicate(runs, mntd(randomizeMatrix(samp,null.model="richness"), dis, abundance.weighted))),
+ frequency = t(replicate(runs, mntd(randomizeMatrix(samp,null.model="frequency"), dis, abundance.weighted))),
sample.pool = t(replicate(runs, mntd(randomizeMatrix(samp,null.model="richness"), dis, abundance.weighted))),
phylogeny.pool = t(replicate(runs, mntd(randomizeMatrix(samp,null.model="richness"),
taxaShuffle(dis), abundance.weighted))),
@@ -591,13 +595,15 @@
}
`ses.pd` <-
-function (samp, tree, null.model = c("taxa.labels", "sample.pool",
+function (samp, tree, null.model = c("taxa.labels", "richness", "frequency", "sample.pool",
"phylogeny.pool", "independentswap", "trialswap"), runs = 999, iterations = 1000, ...)
{
pd.obs <- as.vector(pd(samp, tree, ...)$PD)
null.model <- match.arg(null.model)
pd.rand <- switch(null.model,
taxa.labels = t(replicate(runs, as.vector(pd(samp, tipShuffle(tree), ...)$PD))),
+ richness = t(replicate(runs, as.vector(pd(randomizeMatrix(samp,null.model="richness"), tree, ...)$PD))),
+ frequency = t(replicate(runs, as.vector(pd(randomizeMatrix(samp,null.model="frequency"), tree, ...)$PD))),
sample.pool = t(replicate(runs, as.vector(pd(randomizeMatrix(samp,null.model="richness"), tree, ...)$PD))),
phylogeny.pool = t(replicate(runs, as.vector(pd(randomizeMatrix(samp,null.model="richness"),
tipShuffle(tree), ...)$PD))),
Modified: pkg/man/ses.mntd.Rd
===================================================================
--- pkg/man/ses.mntd.Rd 2010-04-08 23:19:43 UTC (rev 222)
+++ pkg/man/ses.mntd.Rd 2010-04-08 23:44:07 UTC (rev 223)
@@ -7,7 +7,7 @@
Standardized effect size of mean nearest taxon distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Taxon Index (NTI).
}
\usage{
-ses.mntd(samp, dis, null.model = c("taxa.labels","sample.pool", "phylogeny.pool", "independentswap", "trialswap"),
+ses.mntd(samp, dis, null.model = c("taxa.labels", "richness", "frequency", "sample.pool", "phylogeny.pool", "independentswap", "trialswap"),
abundance.weighted=FALSE, runs = 999, iterations = 1000)
}
@@ -37,10 +37,10 @@
Currently implemented null models (arguments to null.model):
\describe{
\item{taxa.labels}{ Shuffle distance matrix labels (across all taxa included in distance matrix)}
+ \item{richness}{ Randomize community data matrix abundances within samples (maintains sample species richness)}
+ \item{frequency}{ Randomize community data matrix abundances within species (maintains species occurence frequency)}
\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 }
}
Modified: pkg/man/ses.mpd.Rd
===================================================================
--- pkg/man/ses.mpd.Rd 2010-04-08 23:19:43 UTC (rev 222)
+++ pkg/man/ses.mpd.Rd 2010-04-08 23:44:07 UTC (rev 223)
@@ -6,7 +6,7 @@
Standardized effect size of mean pairwise distances in communities. When used with a phylogenetic distance matrix, equivalent to -1 times the Nearest Relative Index (NRI).
}
\usage{
-ses.mpd(samp, dis, null.model = c("taxa.labels", "sample.pool",
+ses.mpd(samp, dis, null.model = c("taxa.labels", "richness", "frequency", "sample.pool",
"phylogeny.pool", "independentswap", "trialswap"),
abundance.weighted = FALSE, runs = 999, iterations = 1000)
}
@@ -35,10 +35,10 @@
Currently implemented null models (arguments to null.model):
\describe{
\item{taxa.labels}{ Shuffle distance matrix labels (across all taxa included in distance matrix)}
+ \item{richness}{ Randomize community data matrix abundances within samples (maintains sample species richness)}
+ \item{frequency}{ Randomize community data matrix abundances within species (maintains species occurence frequency)}
\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 }
}
Modified: pkg/man/ses.pd.Rd
===================================================================
--- pkg/man/ses.pd.Rd 2010-04-08 23:19:43 UTC (rev 222)
+++ pkg/man/ses.pd.Rd 2010-04-08 23:44:07 UTC (rev 223)
@@ -6,9 +6,9 @@
Standardized effect size of phylogenetic diversity (Faith's PD) in communities.
}
\usage{
-ses.pd(samp, tree, null.model = c("taxa.labels", "sample.pool",
- "phylogeny.pool", "independentswap", "trialswap"),
- runs = 999, iterations = 1000, ...)
+ses.pd(samp, tree, null.model = c("taxa.labels", "richness", "frequency",
+ "sample.pool", "phylogeny.pool", "independentswap", "trialswap"),
+ runs = 999, iterations = 1000, ...)
}
\arguments{
@@ -35,10 +35,10 @@
Currently implemented null models (arguments to null.model):
\describe{
\item{taxa.labels}{ Shuffle taxa labels across tips of phylogeny (across all taxa included in phylogeny)}
+ \item{richness}{ Randomize community data matrix abundances within samples (maintains sample species richness)}
+ \item{frequency}{ Randomize community data matrix abundances within species (maintains species occurence frequency)}
\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 phylogeny (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 }
}
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