[Picante-commits] r53 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Apr 13 08:30:41 CEST 2008
Author: skembel
Date: 2008-04-13 08:30:41 +0200 (Sun, 13 Apr 2008)
New Revision: 53
Added:
pkg/R/cor.table.R
pkg/man/cor.table.Rd
Removed:
pkg/R/corr.table.R
pkg/man/corr.table.Rd
Modified:
pkg/R/utility.R
pkg/man/mnnd.Rd
pkg/man/mpd.Rd
pkg/man/phylocom.Rd
pkg/man/randomizeSample.Rd
pkg/man/ses.mnnd.Rd
pkg/man/ses.mpd.Rd
pkg/man/species.dist.Rd
pkg/man/utility.Rd
Log:
Documentation and minor code bugfixes to pass check cleanly
Added: pkg/R/cor.table.R
===================================================================
--- pkg/R/cor.table.R (rev 0)
+++ pkg/R/cor.table.R 2008-04-13 06:30:41 UTC (rev 53)
@@ -0,0 +1,20 @@
+cor.table <- function (x, cor.method = "pearson", cor.type=c("standard","contrast"))
+{
+ cor.type <- match.arg(cor.type)
+ if (identical(cor.type,"standard")) {
+ concorr <- list()
+ concorr$r <- cor(x, method = cor.method)
+ concorr$df <- dim(x)[1] - 2
+ t <- concorr$r * sqrt(concorr$df/(1 - concorr$r^2))
+ concorr$P <- dt(t, concorr$df)
+ concorr
+ }
+ else {
+ concorr <- list()
+ concorr$r <- cor(rbind(x,x*-1),method=cor.method)
+ concorr$df <- length(x[,1])-1
+ t <- concorr$r * sqrt(concorr$df/(1-concorr$r^2))
+ concorr$P <- dt(t,concorr$df)
+ concorr
+ }
+}
Deleted: pkg/R/corr.table.R
===================================================================
--- pkg/R/corr.table.R 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/R/corr.table.R 2008-04-13 06:30:41 UTC (rev 53)
@@ -1,20 +0,0 @@
-corr.table <- function (x, cor.method = "pearson", cor.type=c("standard","contrast"))
-{
- cor.type <- match.arg(cor.type)
- if (identical(cor.type,"standard")) {
- concorr <- list()
- concorr$r <- cor(x, method = cor.method)
- concorr$df <- dim(x)[1] - 2
- t <- concorr$r * sqrt(concorr$df/(1 - concorr$r^2))
- concorr$P <- dt(t, concorr$df)
- concorr
- }
- else {
- concorr <- list()
- concorr$r <- cor(rbind(x,x*-1),method=cor.method)
- concorr$df <- length(x[,1])-1
- t <- concorr$r * sqrt(concorr$df/(1-concorr$r^2))
- concorr$P <- dt(t,concorr$df)
- concorr
- }
-}
Modified: pkg/R/utility.R
===================================================================
--- pkg/R/utility.R 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/R/utility.R 2008-04-13 06:30:41 UTC (rev 53)
@@ -2,8 +2,8 @@
# some data input error checking, all taxa in tree and x
# no missing data values
stopifnot(traitcol %in% names(x), taxacol %in% names(x),
- class(x) == "data.frame", class(phylo) == "phylo")
- len.tips <- length(phylo$tip.label)
+ class(x) == "data.frame", class(phy) == "phylo")
+ len.tips <- length(phy$tip.label)
len.taxa <- length(x[,taxacol])
if (any(missing <- !(phy$tip.label %in% x[, taxacol]))) {
stop("ERROR. phylogeny tip(s): ", phy$tip.label[missing],
Added: pkg/man/cor.table.Rd
===================================================================
--- pkg/man/cor.table.Rd (rev 0)
+++ pkg/man/cor.table.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -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"))
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{x}{ Data frame of data points or contrasts at nodes }
+ \item{cor.method}{ Correlation method (as \code{\link{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 et al. 1992 }
+
+\author{ Steve Kembel <skembel at berkeley.edu> }
+\keyword{univar}
Deleted: pkg/man/corr.table.Rd
===================================================================
--- pkg/man/corr.table.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/corr.table.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -1,17 +0,0 @@
-\name{corr.table}
-\alias{corr.table}
-\title{ Table of PIC correlations }
-\description{
- Table of PIC correlations with corrected P-values and df
-}
-\usage{
-corr.table(nodes, cor.method = "pearson")
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{nodes}{ Data frame of standardized contrasts at nodes }
- \item{cor.method}{ Correlation method (as \code{\link{cor}}) }
-}
-
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\keyword{univar}
Modified: pkg/man/mnnd.Rd
===================================================================
--- pkg/man/mnnd.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/mnnd.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -1,17 +1,17 @@
\name{mnnd}
\alias{mnnd}
%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ Mean nearest relative phylogenetic distance }
+\title{ Mean nearest neighbour distance }
\description{
- Calculates MNND (mean nearest neighbour or relative phylogenetic distance) for a community
+ Calculates MNND (mean nearest neighbour distance) for a community
}
\usage{
-mnnd(samp, phy.dist)
+mnnd(samp, dis)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{samp}{ Phylocom sample file }
- \item{phy.dist}{ Cophenetic phylogenetic distance matrix }
+ \item{dis}{ Interspecific (e.g. phylogenetic) distance matrix }
}
\value{
Vector of MNND values for each community
Modified: pkg/man/mpd.Rd
===================================================================
--- pkg/man/mpd.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/mpd.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -1,16 +1,16 @@
\name{mpd}
\alias{mpd}
-\title{ Mean pairwise phylogenetic distance }
+\title{ Mean pairwise distance }
\description{
- Calculates mean pairwise phylogenetic distance for a community
+ Calculates mean pairwise distance for a community
}
\usage{
-mpd(samp, phy.dist)
+mpd(samp, dis)
}
\arguments{
\item{samp}{ Community data matrix }
- \item{phy.dist}{ Cophenetic phylogenetic distance matrix }
+ \item{dis}{ Interspecific (e.g. phylogenetic) distance matrix }
}
\value{
Modified: pkg/man/phylocom.Rd
===================================================================
--- pkg/man/phylocom.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/phylocom.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -8,9 +8,9 @@
\usage{data(phylocom)}
\format{
A list with three elements
- \item{phylocom$phylo}{Phylogenetic tree}
- \item{phylocom$sample}{Community data}
- \item{phylocom$traits}{Trait data}
+ \item{phylocom\$phylo}{Phylogenetic tree}
+ \item{phylocom\$sample}{Community data}
+ \item{phylocom\$traits}{Trait data}
}
\source{
Modified: pkg/man/randomizeSample.Rd
===================================================================
--- pkg/man/randomizeSample.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/randomizeSample.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -6,7 +6,7 @@
Various null models for randomizing community data matrices
}
\usage{
-randomizeSample(samp, null.model = c("keepFreq", "keepRichness", "keepBoth"))
+randomizeSample(samp, null.model = c("frequency", "richness", "both"))
}
%- maybe also 'usage' for other objects documented here.
\arguments{
Modified: pkg/man/ses.mnnd.Rd
===================================================================
--- pkg/man/ses.mnnd.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/ses.mnnd.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -7,12 +7,12 @@
Nearest Taxon Index of community phylogenetic structure
}
\usage{
-ses.mnnd(samp, phylo.dist, null.model = c("taxa.labels", "sample.pool", "phylogeny.pool", "weighted.sample.pool"), runs = 99)
+ses.mnnd(samp, dis, null.model = c("taxa.labels", "sample.pool", "phylogeny.pool", "weighted.sample.pool"), runs = 99)
}
\arguments{
\item{samp}{ Community data matrix }
- \item{phylo.dist}{ Cophenetic phylogenetic distance matrix }
+ \item{dis}{ Cophenetic phylogenetic distance matrix }
\item{null.model}{ Choice of null models }
\item{runs}{ Number of randomizations }
}
Modified: pkg/man/ses.mpd.Rd
===================================================================
--- pkg/man/ses.mpd.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/ses.mpd.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -7,12 +7,12 @@
Net Relatedness Index of community phylogenetic structure
}
\usage{
-ses.mpd(samp, phylo.dist, null.model = c("taxa.labels", "sample.pool", "phylogeny.pool", "weighted.sample.pool"), runs = 99)
+ses.mpd(samp, dis, null.model = c("taxa.labels", "sample.pool", "phylogeny.pool", "weighted.sample.pool"), runs = 99)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{samp}{ Community data matrix }
- \item{phylo.dist}{ Cophenetic phylogenetic distance matrix }
+ \item{dis}{ Cophenetic phylogenetic distance matrix }
\item{null.model}{ Choice of null models }
\item{runs}{ Number of randomizations }
}
Modified: pkg/man/species.dist.Rd
===================================================================
--- pkg/man/species.dist.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/species.dist.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -5,12 +5,13 @@
\description{
Compute various indices of species co-occurrence
}
+
\usage{
-species.dist(samp, metric = c("cij", "jaccard", "roij"))
+species.dist(x, metric = c("cij", "jaccard", "checkerboard", "roij"))
}
\arguments{
- \item{samp}{ Community data matrix }
+ \item{x}{ Community data matrix }
\item{metric}{ Distance metric to use (COij, Jaccard, ROij) }
}
Modified: pkg/man/utility.Rd
===================================================================
--- pkg/man/utility.Rd 2008-04-13 02:50:56 UTC (rev 52)
+++ pkg/man/utility.Rd 2008-04-13 06:30:41 UTC (rev 53)
@@ -3,6 +3,7 @@
\alias{internal2tips}
\alias{node.age}
\alias{phylo2phylog}
+\alias{pic.variance}
\alias{sortColumns}
\alias{sortRows}
\alias{taxaShuffle}
@@ -16,6 +17,7 @@
internal2tips(phy, int.node, return.names = FALSE)
node.age(phy)
phylo2phylog(phy, ...)
+pic.variance(x, phy, scaled = TRUE)
sortColumns(x)
sortRows(x)
taxaShuffle(x)
@@ -24,12 +26,11 @@
\arguments{
\item{phy}{ phylo object }
- \item{species}{ Vector of species names }
\item{x}{ A data.frame, matrix or dist object }
\item{colID}{ Numeric or character ID of column to include }
\item{int.node}{ internal node number }
\item{return.names}{ TRUE or FALSE }
- \item{strata}{ Strata for randomization }
+ \item{scaled}{ Scale contrasts by branch length }
\item{taxacol} {column with taxa names}
\item{traitcol} {column with trait values}
\item{strict} {logical indicating whether matching should be strict or not}
@@ -42,6 +43,7 @@
\item{internal2tips}{Vector of tips descended from a node}
\item{node.age}{Phylo object with phylo\$ages vector of node ages corresponding to phylo\$edge}
\item{phylo2phylog}{An ade4 phylog}
+ \item{pic.variance}{Variance of independent contrasts}
\item{sortColumns}{A data.frame or matrix with columns sorted by name}
\item{sortRows}{A data.frame or matrix with rows sorted by name}
\item{taxaShuffle}{Matrix with taxa names shuffled}
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