[Picante-commits] r40 - in pkg: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 3 08:50:05 CET 2008
Author: skembel
Date: 2008-03-03 08:50:05 +0100 (Mon, 03 Mar 2008)
New Revision: 40
Added:
pkg/man/corr.table.Rd
pkg/man/ses.mnnd.Rd
pkg/man/ses.mpd.Rd
Removed:
pkg/man/corr.table.R
pkg/man/ses.mnnd.R
pkg/man/ses.mpd.R
Modified:
pkg/DESCRIPTION
Log:
Docs still need some cleaning but getting there. Updated TODO.
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2008-03-03 07:39:31 UTC (rev 39)
+++ pkg/DESCRIPTION 2008-03-03 07:50:05 UTC (rev 40)
@@ -5,7 +5,7 @@
Date: 2008-2-22
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>, Cam Webb <cwebb at oeb.harvard.edu>
Maintainer: Steve Kembel <skembel at berkeley.edu>
-Depends: ape, geiger, vegan
+Depends: ape, vegan
Suggests: circular, ade4
Description: Phylocom integration, community analyses, null-models, traits and evolution in R
License: GPL v2
Deleted: pkg/man/corr.table.R
===================================================================
--- pkg/man/corr.table.R 2008-03-03 07:39:31 UTC (rev 39)
+++ pkg/man/corr.table.R 2008-03-03 07:50:05 UTC (rev 40)
@@ -1,17 +0,0 @@
-\name{contrast.cor.table}
-\alias{contrast.cor.table}
-\title{ Table of PIC correlations }
-\description{
- Table of PIC correlations with corrected P-values and df
-}
-\usage{
-contrast.cor.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}
Copied: pkg/man/corr.table.Rd (from rev 38, pkg/man/corr.table.R)
===================================================================
--- pkg/man/corr.table.Rd (rev 0)
+++ pkg/man/corr.table.Rd 2008-03-03 07:50:05 UTC (rev 40)
@@ -0,0 +1,17 @@
+\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}
Deleted: pkg/man/ses.mnnd.R
===================================================================
--- pkg/man/ses.mnnd.R 2008-03-03 07:39:31 UTC (rev 39)
+++ pkg/man/ses.mnnd.R 2008-03-03 07:50:05 UTC (rev 40)
@@ -1,27 +0,0 @@
-\name{ses.mnnd}
-\alias{nti}
-\alias{ses.mnnd}
-
-\title{ Nearest Taxon Index }
-\description{
- Nearest Taxon Index of community phylogenetic structure
-}
-\usage{
-nti(samp, phylo.dist, 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{null.model}{ Choice of null models }
- \item{runs}{ Number of randomizations }
-}
-
-\value{
- Data frame of results
-}
-\references{ Webb et al. 2002, 2007 }
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\section{Warning }{Weighted sample pool null ONLY works with presence-absence data}
-\seealso{ \code{\link{mnnd}} }
-\keyword{univar}
Copied: pkg/man/ses.mnnd.Rd (from rev 39, pkg/man/ses.mnnd.R)
===================================================================
--- pkg/man/ses.mnnd.Rd (rev 0)
+++ pkg/man/ses.mnnd.Rd 2008-03-03 07:50:05 UTC (rev 40)
@@ -0,0 +1,27 @@
+\name{ses.mnnd}
+\alias{nti}
+\alias{ses.mnnd}
+
+\title{ Nearest Taxon Index }
+\description{
+ Nearest Taxon Index of community phylogenetic structure
+}
+\usage{
+nti(samp, phylo.dist, 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{null.model}{ Choice of null models }
+ \item{runs}{ Number of randomizations }
+}
+
+\value{
+ Data frame of results
+}
+\references{ Webb et al. 2002, 2007 }
+\author{ Steve Kembel <skembel at berkeley.edu> }
+\section{Warning }{Weighted sample pool null ONLY works with presence-absence data}
+\seealso{ \code{\link{mnnd}} }
+\keyword{univar}
Deleted: pkg/man/ses.mpd.R
===================================================================
--- pkg/man/ses.mpd.R 2008-03-03 07:39:31 UTC (rev 39)
+++ pkg/man/ses.mpd.R 2008-03-03 07:50:05 UTC (rev 40)
@@ -1,27 +0,0 @@
-\name{ses.mpd}
-\alias{nri}
-\alias{ses.mpd}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ Net Relatedness Index }
-\description{
- Net Relatedness Index of community phylogenetic structure
-}
-\usage{
-nri(samp, phylo.dist, 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{null.model}{ Choice of null models }
- \item{runs}{ Number of randomizations }
-}
-
-\value{
- Data frame of results
-}
-\references{ Webb et al. 2002, 2007 }
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\section{Warning }{Weighted sample pool null ONLY works with presence-absence data}
-\seealso{ \code{\link{mpd}} }
-\keyword{univar}
Copied: pkg/man/ses.mpd.Rd (from rev 39, pkg/man/ses.mpd.R)
===================================================================
--- pkg/man/ses.mpd.Rd (rev 0)
+++ pkg/man/ses.mpd.Rd 2008-03-03 07:50:05 UTC (rev 40)
@@ -0,0 +1,27 @@
+\name{ses.mpd}
+\alias{nri}
+\alias{ses.mpd}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Net Relatedness Index }
+\description{
+ Net Relatedness Index of community phylogenetic structure
+}
+\usage{
+nri(samp, phylo.dist, 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{null.model}{ Choice of null models }
+ \item{runs}{ Number of randomizations }
+}
+
+\value{
+ Data frame of results
+}
+\references{ Webb et al. 2002, 2007 }
+\author{ Steve Kembel <skembel at berkeley.edu> }
+\section{Warning }{Weighted sample pool null ONLY works with presence-absence data}
+\seealso{ \code{\link{mpd}} }
+\keyword{univar}
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