[Picante-commits] r169 - branches/gsoc/man branches/phylosor/man pkg pkg/man tags/0.1-2/man tags/0.2-0/man tags/0.3-0/man tags/0.4-0/man www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 23 20:44:51 CET 2009
Author: skembel
Date: 2009-01-23 20:44:50 +0100 (Fri, 23 Jan 2009)
New Revision: 169
Modified:
branches/gsoc/man/comm.phylo.cor.Rd
branches/gsoc/man/cor.table.Rd
branches/gsoc/man/evolve.brownian.Rd
branches/gsoc/man/matrix2sample.Rd
branches/gsoc/man/mnnd.Rd
branches/gsoc/man/mpd.Rd
branches/gsoc/man/multiPhylosignal.Rd
branches/gsoc/man/phylosignal.Rd
branches/gsoc/man/picante-package.Rd
branches/gsoc/man/pruning.Rd
branches/gsoc/man/randomizeSample.Rd
branches/gsoc/man/readsample.Rd
branches/gsoc/man/sample2matrix.Rd
branches/gsoc/man/ses.mnnd.Rd
branches/gsoc/man/ses.mpd.Rd
branches/gsoc/man/species.dist.Rd
branches/gsoc/man/utility.Rd
branches/gsoc/man/writesample.Rd
branches/gsoc/man/writetraits.Rd
branches/phylosor/man/comm.phylo.cor.Rd
branches/phylosor/man/cor.table.Rd
branches/phylosor/man/evolve.brownian.Rd
branches/phylosor/man/matrix2sample.Rd
branches/phylosor/man/mnnd.Rd
branches/phylosor/man/mpd.Rd
branches/phylosor/man/multiPhylosignal.Rd
branches/phylosor/man/phylosignal.Rd
branches/phylosor/man/picante-package.Rd
branches/phylosor/man/pruning.Rd
branches/phylosor/man/randomizeSample.Rd
branches/phylosor/man/readsample.Rd
branches/phylosor/man/sample2matrix.Rd
branches/phylosor/man/ses.mnnd.Rd
branches/phylosor/man/ses.mpd.Rd
branches/phylosor/man/species.dist.Rd
branches/phylosor/man/utility.Rd
branches/phylosor/man/writesample.Rd
branches/phylosor/man/writetraits.Rd
pkg/DESCRIPTION
pkg/man/comm.phylo.cor.Rd
pkg/man/cor.table.Rd
pkg/man/evolve.brownian.Rd
pkg/man/matrix2sample.Rd
pkg/man/mnnd.Rd
pkg/man/mpd.Rd
pkg/man/multiPhylosignal.Rd
pkg/man/phylosignal.Rd
pkg/man/picante-package.Rd
pkg/man/pruning.Rd
pkg/man/randomizeSample.Rd
pkg/man/readsample.Rd
pkg/man/sample2matrix.Rd
pkg/man/ses.mnnd.Rd
pkg/man/ses.mpd.Rd
pkg/man/species.dist.Rd
pkg/man/utility.Rd
pkg/man/writesample.Rd
pkg/man/writetraits.Rd
tags/0.1-2/man/comm.phylo.cor.Rd
tags/0.1-2/man/cor.table.Rd
tags/0.1-2/man/evolve.brownian.Rd
tags/0.1-2/man/matrix2sample.Rd
tags/0.1-2/man/mnnd.Rd
tags/0.1-2/man/mpd.Rd
tags/0.1-2/man/multiPhylosignal.Rd
tags/0.1-2/man/phylosignal.Rd
tags/0.1-2/man/picante-package.Rd
tags/0.1-2/man/pruning.Rd
tags/0.1-2/man/randomizeSample.Rd
tags/0.1-2/man/readsample.Rd
tags/0.1-2/man/sample2matrix.Rd
tags/0.1-2/man/ses.mnnd.Rd
tags/0.1-2/man/ses.mpd.Rd
tags/0.1-2/man/species.dist.Rd
tags/0.1-2/man/utility.Rd
tags/0.1-2/man/writesample.Rd
tags/0.1-2/man/writetraits.Rd
tags/0.2-0/man/comm.phylo.cor.Rd
tags/0.2-0/man/cor.table.Rd
tags/0.2-0/man/evolve.brownian.Rd
tags/0.2-0/man/matrix2sample.Rd
tags/0.2-0/man/mnnd.Rd
tags/0.2-0/man/mpd.Rd
tags/0.2-0/man/multiPhylosignal.Rd
tags/0.2-0/man/phylosignal.Rd
tags/0.2-0/man/picante-package.Rd
tags/0.2-0/man/pruning.Rd
tags/0.2-0/man/randomizeSample.Rd
tags/0.2-0/man/readsample.Rd
tags/0.2-0/man/sample2matrix.Rd
tags/0.2-0/man/ses.mnnd.Rd
tags/0.2-0/man/ses.mpd.Rd
tags/0.2-0/man/species.dist.Rd
tags/0.2-0/man/utility.Rd
tags/0.2-0/man/writesample.Rd
tags/0.2-0/man/writetraits.Rd
tags/0.3-0/man/comm.phylo.cor.Rd
tags/0.3-0/man/cor.table.Rd
tags/0.3-0/man/evolve.brownian.Rd
tags/0.3-0/man/matrix2sample.Rd
tags/0.3-0/man/mnnd.Rd
tags/0.3-0/man/mpd.Rd
tags/0.3-0/man/multiPhylosignal.Rd
tags/0.3-0/man/phylosignal.Rd
tags/0.3-0/man/picante-package.Rd
tags/0.3-0/man/pruning.Rd
tags/0.3-0/man/randomizeSample.Rd
tags/0.3-0/man/readsample.Rd
tags/0.3-0/man/sample2matrix.Rd
tags/0.3-0/man/ses.mnnd.Rd
tags/0.3-0/man/ses.mpd.Rd
tags/0.3-0/man/species.dist.Rd
tags/0.3-0/man/utility.Rd
tags/0.3-0/man/writesample.Rd
tags/0.3-0/man/writetraits.Rd
tags/0.4-0/man/comm.phylo.cor.Rd
tags/0.4-0/man/cor.table.Rd
tags/0.4-0/man/evolve.brownian.Rd
tags/0.4-0/man/matrix2sample.Rd
tags/0.4-0/man/mnnd.Rd
tags/0.4-0/man/mpd.Rd
tags/0.4-0/man/multiPhylosignal.Rd
tags/0.4-0/man/phylosignal.Rd
tags/0.4-0/man/picante-package.Rd
tags/0.4-0/man/pruning.Rd
tags/0.4-0/man/randomizeSample.Rd
tags/0.4-0/man/readsample.Rd
tags/0.4-0/man/sample2matrix.Rd
tags/0.4-0/man/ses.mnnd.Rd
tags/0.4-0/man/ses.mpd.Rd
tags/0.4-0/man/species.dist.Rd
tags/0.4-0/man/utility.Rd
tags/0.4-0/man/writesample.Rd
tags/0.4-0/man/writetraits.Rd
www/index.php
Log:
Added nlme as dependency to pass check with new ape version, added phylosor functions by Helene, change DESCRIPTION and contact information for release 0.5, update website
Modified: branches/gsoc/man/comm.phylo.cor.Rd
===================================================================
--- branches/gsoc/man/comm.phylo.cor.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/comm.phylo.cor.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -35,7 +35,7 @@
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\section{Warning }{ Weighted null model currently only works with presence-absence data. Convert your data to presence-absence before using this null model (e.g. \code{decostand(x,method="pa")})}
\examples{
data(phylocom)
Modified: branches/gsoc/man/cor.table.Rd
===================================================================
--- branches/gsoc/man/cor.table.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/cor.table.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -22,5 +22,5 @@
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{univar}
Modified: branches/gsoc/man/evolve.brownian.Rd
===================================================================
--- branches/gsoc/man/evolve.brownian.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/evolve.brownian.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,5 +16,5 @@
\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> }
+\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <skembel at uoregon.edu> }
\keyword{datagen}
Modified: branches/gsoc/man/matrix2sample.Rd
===================================================================
--- branches/gsoc/man/matrix2sample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/matrix2sample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,7 +17,7 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
\examples{
data(phylocom)
matrix2sample(phylocom$sample)
Modified: branches/gsoc/man/mnnd.Rd
===================================================================
--- branches/gsoc/man/mnnd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/mnnd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,6 +16,6 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{ses.mnnd}} }
\keyword{univar}
Modified: branches/gsoc/man/mpd.Rd
===================================================================
--- branches/gsoc/man/mpd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/mpd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,6 +17,6 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{ses.mpd}}}
\keyword{univar}
Modified: branches/gsoc/man/multiPhylosignal.Rd
===================================================================
--- branches/gsoc/man/multiPhylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/multiPhylosignal.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,5 +16,5 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{univar}
Modified: branches/gsoc/man/phylosignal.Rd
===================================================================
--- branches/gsoc/man/phylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/phylosignal.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -26,7 +26,7 @@
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> }
+\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{
Modified: branches/gsoc/man/picante-package.Rd
===================================================================
--- branches/gsoc/man/picante-package.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/picante-package.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -18,8 +18,8 @@
}
}
\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>
+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>, Cam Webb <cwebb at oeb.harvard.edu>
-Maintainer: Steve Kembel <skembel at berkeley.edu>
+Maintainer: Steven Kembel <skembel at uoregon.edu>
}
\keyword{package}
Modified: branches/gsoc/man/pruning.Rd
===================================================================
--- branches/gsoc/man/pruning.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/pruning.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -19,5 +19,5 @@
\value{
Returns a pruned phylo object
}
-\author{ Steve Kembel <skembel at berkeley.edu> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{manip}
Modified: branches/gsoc/man/randomizeSample.Rd
===================================================================
--- branches/gsoc/man/randomizeSample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/randomizeSample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -28,7 +28,7 @@
\cr
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\examples{
data(phylocom)
randomizeSample(phylocom$sample, null.model="richness")}
Modified: branches/gsoc/man/readsample.Rd
===================================================================
--- branches/gsoc/man/readsample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/readsample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,5 +17,5 @@
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> }
+\author{ Steven Kembel <skembel> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{IO}
Modified: branches/gsoc/man/sample2matrix.Rd
===================================================================
--- branches/gsoc/man/sample2matrix.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/sample2matrix.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -20,5 +20,5 @@
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{IO}
Modified: branches/gsoc/man/ses.mnnd.Rd
===================================================================
--- branches/gsoc/man/ses.mnnd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/ses.mnnd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -34,7 +34,7 @@
\item{runs}{Number of randomizations}
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\section{Warning }{ Weighted null model currently only works with presence-absence data. Convert your data to presence-absence before using this null model (e.g. \code{decostand(x,method="pa")})}
\seealso{ \code{\link{mnnd}} }
\examples{
Modified: branches/gsoc/man/ses.mpd.Rd
===================================================================
--- branches/gsoc/man/ses.mpd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/ses.mpd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -34,7 +34,7 @@
\item{runs}{Number of randomizations}
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\section{Warning }{ Weighted null model currently only works with presence-absence data. Convert your data to presence-absence before using this null model (e.g. \code{decostand(x,method="pa")})}
\seealso{ \code{\link{mpd}} }
\examples{
Modified: branches/gsoc/man/species.dist.Rd
===================================================================
--- branches/gsoc/man/species.dist.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/species.dist.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -24,7 +24,7 @@
A \code{dist} object with co-occurrences among all species pairs
}
-\author{ Steve Kembel <skembel at berkeley.edu> }
+\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.
Modified: branches/gsoc/man/utility.Rd
===================================================================
--- branches/gsoc/man/utility.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/utility.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -44,5 +44,5 @@
Various utility functions for manipulating trees, data, etc.
}
-\author{ Steven Kembel <skembel at berkeley.edu>, Peter Cowan <pdc at berkeley.edu>, David Ackerly <dackerly at berkeley.edu> }
+\author{ Steven Kembel <skembel at uoregon.edu>, Peter Cowan <pdc at berkeley.edu>, David Ackerly <dackerly at berkeley.edu> }
\keyword{manip}
Modified: branches/gsoc/man/writesample.Rd
===================================================================
--- branches/gsoc/man/writesample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/writesample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -14,5 +14,5 @@
\item{filename}{ Filename path }
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{file}
Modified: branches/gsoc/man/writetraits.Rd
===================================================================
--- branches/gsoc/man/writetraits.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/gsoc/man/writetraits.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,5 +17,5 @@
}
\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{ David Ackerly <dackerly at berkeley.edu> and Steve Kembel <skembel at berkeley.edu> }
+\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <skembel at uoregon.edu> }
\keyword{file}
Modified: branches/phylosor/man/comm.phylo.cor.Rd
===================================================================
--- branches/phylosor/man/comm.phylo.cor.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/comm.phylo.cor.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -35,7 +35,7 @@
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{randomizeSample}} }
\examples{
data(phylocom)
Modified: branches/phylosor/man/cor.table.Rd
===================================================================
--- branches/phylosor/man/cor.table.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/cor.table.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -22,5 +22,5 @@
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{univar}
Modified: branches/phylosor/man/evolve.brownian.Rd
===================================================================
--- branches/phylosor/man/evolve.brownian.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/evolve.brownian.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,5 +16,5 @@
\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> }
+\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <skembel at uoregon.edu> }
\keyword{datagen}
Modified: branches/phylosor/man/matrix2sample.Rd
===================================================================
--- branches/phylosor/man/matrix2sample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/matrix2sample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,7 +17,7 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
\examples{
data(phylocom)
matrix2sample(phylocom$sample)
Modified: branches/phylosor/man/mnnd.Rd
===================================================================
--- branches/phylosor/man/mnnd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/mnnd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,6 +16,6 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{ses.mnnd}} }
\keyword{univar}
Modified: branches/phylosor/man/mpd.Rd
===================================================================
--- branches/phylosor/man/mpd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/mpd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,6 +17,6 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{ses.mpd}}}
\keyword{univar}
Modified: branches/phylosor/man/multiPhylosignal.Rd
===================================================================
--- branches/phylosor/man/multiPhylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/multiPhylosignal.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,5 +16,5 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{univar}
Modified: branches/phylosor/man/phylosignal.Rd
===================================================================
--- branches/phylosor/man/phylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/phylosignal.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -26,7 +26,7 @@
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> }
+\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{
Modified: branches/phylosor/man/picante-package.Rd
===================================================================
--- branches/phylosor/man/picante-package.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/picante-package.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -18,8 +18,8 @@
}
}
\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>
+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>, Cam Webb <cwebb at oeb.harvard.edu>
-Maintainer: Steve Kembel <skembel at berkeley.edu>
+Maintainer: Steven Kembel <skembel at uoregon.edu>
}
\keyword{package}
Modified: branches/phylosor/man/pruning.Rd
===================================================================
--- branches/phylosor/man/pruning.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/pruning.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -19,5 +19,5 @@
\value{
Returns a pruned phylo object
}
-\author{ Steve Kembel <skembel at berkeley.edu> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{manip}
Modified: branches/phylosor/man/randomizeSample.Rd
===================================================================
--- branches/phylosor/man/randomizeSample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/randomizeSample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -28,7 +28,7 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\examples{
data(phylocom)
randomizeSample(phylocom$sample, null.model="richness")}
Modified: branches/phylosor/man/readsample.Rd
===================================================================
--- branches/phylosor/man/readsample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/readsample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,5 +17,5 @@
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> }
+\author{ Steven Kembel <skembel> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{IO}
Modified: branches/phylosor/man/sample2matrix.Rd
===================================================================
--- branches/phylosor/man/sample2matrix.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/sample2matrix.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -20,5 +20,5 @@
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{IO}
Modified: branches/phylosor/man/ses.mnnd.Rd
===================================================================
--- branches/phylosor/man/ses.mnnd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/ses.mnnd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -38,7 +38,7 @@
\item{runs}{Number of randomizations}
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{mnnd}}, \code{\link{randomizeSample}} }
\examples{
data(phylocom)
Modified: branches/phylosor/man/ses.mpd.Rd
===================================================================
--- branches/phylosor/man/ses.mpd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/ses.mpd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -38,7 +38,7 @@
\item{runs}{Number of randomizations}
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{mpd}}, \code{\link{randomizeSample}} }
\examples{
data(phylocom)
Modified: branches/phylosor/man/species.dist.Rd
===================================================================
--- branches/phylosor/man/species.dist.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/species.dist.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -24,7 +24,7 @@
A \code{dist} object with co-occurrences among all species pairs
}
-\author{ Steve Kembel <skembel at berkeley.edu> }
+\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.
Modified: branches/phylosor/man/utility.Rd
===================================================================
--- branches/phylosor/man/utility.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/utility.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -44,5 +44,5 @@
Various utility functions for manipulating trees, data, etc.
}
-\author{ Steven Kembel <skembel at berkeley.edu>, Peter Cowan <pdc at berkeley.edu>, David Ackerly <dackerly at berkeley.edu> }
+\author{ Steven Kembel <skembel at uoregon.edu>, Peter Cowan <pdc at berkeley.edu>, David Ackerly <dackerly at berkeley.edu> }
\keyword{manip}
Modified: branches/phylosor/man/writesample.Rd
===================================================================
--- branches/phylosor/man/writesample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/writesample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -14,5 +14,5 @@
\item{filename}{ Filename path }
}
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
\keyword{file}
Modified: branches/phylosor/man/writetraits.Rd
===================================================================
--- branches/phylosor/man/writetraits.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ branches/phylosor/man/writetraits.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,5 +17,5 @@
}
\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{ David Ackerly <dackerly at berkeley.edu> and Steve Kembel <skembel at berkeley.edu> }
+\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <skembel at uoregon.edu> }
\keyword{file}
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/DESCRIPTION 2009-01-23 19:44:50 UTC (rev 169)
@@ -1,11 +1,11 @@
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
+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
Modified: pkg/man/comm.phylo.cor.Rd
===================================================================
--- pkg/man/comm.phylo.cor.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/comm.phylo.cor.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -35,7 +35,7 @@
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{randomizeSample}} }
\examples{
data(phylocom)
Modified: pkg/man/cor.table.Rd
===================================================================
--- pkg/man/cor.table.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/cor.table.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -22,5 +22,5 @@
\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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{univar}
Modified: pkg/man/evolve.brownian.Rd
===================================================================
--- pkg/man/evolve.brownian.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/evolve.brownian.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,5 +16,5 @@
\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> }
+\author{ David Ackerly <dackerly at berkeley.edu> and Steven Kembel <skembel at uoregon.edu> }
\keyword{datagen}
Modified: pkg/man/matrix2sample.Rd
===================================================================
--- pkg/man/matrix2sample.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/matrix2sample.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,7 +17,7 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> and Cam Webb <cwebb at oeb.harvard.edu> }
\examples{
data(phylocom)
matrix2sample(phylocom$sample)
Modified: pkg/man/mnnd.Rd
===================================================================
--- pkg/man/mnnd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/mnnd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,6 +16,6 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{ses.mnnd}} }
\keyword{univar}
Modified: pkg/man/mpd.Rd
===================================================================
--- pkg/man/mpd.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/mpd.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -17,6 +17,6 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\seealso{ \code{\link{ses.mpd}}}
\keyword{univar}
Modified: pkg/man/multiPhylosignal.Rd
===================================================================
--- pkg/man/multiPhylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/multiPhylosignal.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -16,5 +16,5 @@
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> }
+\author{ Steven Kembel <skembel at uoregon.edu> }
\keyword{univar}
Modified: pkg/man/phylosignal.Rd
===================================================================
--- pkg/man/phylosignal.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/phylosignal.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -26,7 +26,7 @@
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> }
+\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{
Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/picante-package.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -12,14 +12,14 @@
\tabular{ll}{
Package: \tab picante\cr
Type: \tab Package\cr
-Version: \tab 0.4-0\cr
-Date: \tab 2008-8-22\cr
+Version: \tab 0.5-0\cr
+Date: \tab 2009-1-22\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>
+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: Steve Kembel <skembel at berkeley.edu>
+Maintainer: Steven Kembel <skembel at uoregon.edu>
}
\keyword{package}
Modified: pkg/man/pruning.Rd
===================================================================
--- pkg/man/pruning.Rd 2008-11-06 18:29:44 UTC (rev 168)
+++ pkg/man/pruning.Rd 2009-01-23 19:44:50 UTC (rev 169)
@@ -19,5 +19,5 @@
\value{
Returns a pruned phylo object
}
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/picante -r 169
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