[Picante-commits] r180 - pkg pkg/man www

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Feb 24 23:18:55 CET 2009 

Author: skembel
Date: 2009-02-24 23:18:55 +0100 (Tue, 24 Feb 2009)
New Revision: 180

Modified:
   pkg/DESCRIPTION
   pkg/man/pd.Rd
   pkg/man/phylosor.Rd
   pkg/man/picante-package.Rd
   www/index.php
Log:
Update webpage and documentation for 0.6 release

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2009-02-24 20:17:02 UTC (rev 179)
+++ pkg/DESCRIPTION	2009-02-24 22:18:55 UTC (rev 180)
@@ -1,8 +1,8 @@
 Package: picante
 Type: Package
 Title: R tools for integrating phylogenies and ecology
-Version: 0.5-3
-Date: 2009-1-27
+Version: 0.6-0
+Date: 2009-2-24
 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/man/pd.Rd
===================================================================
--- pkg/man/pd.Rd	2009-02-24 20:17:02 UTC (rev 179)
+++ pkg/man/pd.Rd	2009-02-24 22:18:55 UTC (rev 180)
@@ -3,30 +3,37 @@
 
 \title{ Calculate Faith's Phylogenetic Diversity }
 \description{
-  Calculate the sum of the total branch lengths for one or multiple samples.
+  Calculate the sum of the total phylogenetic branch length for one or multiple samples.
 }
 \usage{
-pd(samp, tree)
+pd(samp, tree, include.root=TRUE)
 }
 
 \arguments{
   \item{samp}{ Community data matrix }
   \item{tree}{ A phylo tree object }
+  \item{include.root}{ Should the root node be included in all PD calculations (default = TRUE)}
 }
 
 \value{
-	Returns a dataframe of the PD and species richness values for all samples
+	Returns a dataframe of the PD and species richness (SR) values for all samples
 }
 
-\note{This function does not calculate PD for samples with one or zero species. The data sets need not be species-community data sets but may be any sample
-  data set with an associated phylogeny. PD is not statistically independent of species richness, it positively correlates with species richness across samples.
+\note{
+The data sets need not be species-community data sets but may be any sample data set with an associated phylogeny. PD is not statistically independent of species richness, it positively correlates with species richness across samples.
+
+If the root is to be included in all calculations of PD (\code{include.root=TRUE}), the tree must be rooted and ultrametric. Single-species samples will be assigned a PD value equal to the distance from the root to the present.
+
+If the root is not included in all calculations by default (\code{include.root=FALSE}), the tree need not be ultrametric or rooted, but in the case of single-species samples the PD will be equal to NA and a warning will be issued.
+
 }
+\section{Warning }{
+If the root is to be included in all calculations (\code{include.root=TRUE}), the PD of all samples will include the branch length connecting taxa in those samples and the root of the supplied tree. The root of the supplied tree may not be spanned by any taxa in the sample. If you want the root of your tree to correspond to the most recent ancestor of the taxa actually present in your sample, you should prune the tree before running \code{pd}:
 
-
-\references{ Faith D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10 }
-\author{ Matthew Helmus \email{mrhelmus at gmail.com}\cr
-         Jonathan Davies \email{davies at nceas.ucsb.edu}
- }
+\code{prunedTree <- prune.sample(sample,tree)}
+}
+\references{ Faith D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10. }
+\author{ Matthew Helmus \email{mrhelmus at gmail.com}, Jonathan Davies \email{davies at nceas.ucsb.edu}, Steven Kembel \email{skembel at uoregon.edu}}
 \seealso{ \code{\link{psr}} }
 
 \keyword{univar}

Modified: pkg/man/phylosor.Rd
===================================================================
--- pkg/man/phylosor.Rd	2009-02-24 20:17:02 UTC (rev 179)
+++ pkg/man/phylosor.Rd	2009-02-24 22:18:55 UTC (rev 180)
@@ -11,10 +11,18 @@
   \item{samp}{ Community data matrix }
   \item{tree}{ Object of class phylo}
 }
-\value{Distance matrix reporting the PhyloSor index of similarity between communities: fraction of branch-length shared}
+\value{A distance object of the PhyloSor index of similarity between communities, the fraction of PD (branch-length) shared between two samples}
 \references{Bryant, J.B., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J., Green, J.L. 2008. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105 Supplement 1: 1505-11511}
 \author{ Helene Morlon <morlon.helene at gmail.com> and Steven Kembel <skembel at uoregon.edu> }
-\seealso{ \code{\link{phylosor.rnd}}}
+\seealso{\code{\link{phylosor.rnd}}, \code{\link{pd}}}
+\note{
+The root of the supplied tree is included in calculations of PhyloSor. The supplied tree must be rooted and ultrametric. Single-species samples will be assigned a PD value equal to the distance from the root to the present.
+}
+\section{Warning }{
+The phylosor of all samples will include the branch length connecting taxa in those samples and the root of the supplied tree. The root of the supplied tree may not be spanned by any taxa in the sample. If you want the root of your tree to correspond to the most recent ancestor of the taxa actually present in your sample, you should prune the tree before running \code{phylosor}:
+
+\code{prunedTree <- prune.sample(sample,tree)}
+}
 \examples{
 data(phylocom)
 phylosor(phylocom$sample, phylocom$phylo)}

Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd	2009-02-24 20:17:02 UTC (rev 179)
+++ pkg/man/picante-package.Rd	2009-02-24 22:18:55 UTC (rev 180)
@@ -12,8 +12,8 @@
 \tabular{ll}{
 Package: \tab picante\cr
 Type: \tab Package\cr
-Version: \tab 0.5-3\cr
-Date: \tab 2009-1-27\cr
+Version: \tab 0.6-0\cr
+Date: \tab 2009-2-24\cr
 License: \tab GPL-2\cr
 }
 }

Modified: www/index.php
===================================================================
--- www/index.php	2009-02-24 20:17:02 UTC (rev 179)
+++ www/index.php	2009-02-24 22:18:55 UTC (rev 180)
@@ -23,28 +23,25 @@
 
 <body>
 
-<! --- R-Forge Logo --- >
-<table border="0" width="100%" cellspacing="0" cellpadding="0">
-<tr><td>
-<a href="/"><img src="<?php echo $themeroot; ?>/images/logo.png" border="0" alt="R-Forge Logo" /> </a> </td>
-</tr>
-</table>
-
-
-<!-- get project title  -->
 <!-- own website starts here, the following may be changed as you like -->
 <h1>picante</h1>
 <h2><strong>P</strong>hylocom <strong>i</strong>ntegration, <strong>c</strong>ommunity <strong>a</strong>nalyses, <strong>n</strong>ull-models, <strong>t</strong>raits and <strong>e</strong>volution in R</h2>
 
 <!-- end of project description -->
 <h2>About picante</h2>
-<p>The picante package aims to provide a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities in R, along with a set of tools for other comparative analyses and manipulations of phenotypic and phylogenetic data.</p>
+<p>The picante package aims to provide a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities in R, along with other comparative analyses and manipulations of phenotypic and phylogenetic data.</p>
 <p><strong>Package maintainer:</strong> Steven Kembel</p>
 <p><strong>Developers:</strong> Peter Cowan, Matthew Helmus, Steven Kembel</p>
 <p><strong>Contributors:</strong> David Ackerly, Simon Blomberg, Peter Cowan,
     Matthew Helmus, Steven Kembel, Helene Morlon, Cam Webb<p>
-<p>Development of picante has been supported by <a href="http://nserc.ca">NSERC</a>, <a href="http://www.nescent.org/index.php">NESCent</a>, and the <a href="http://code.google.com/soc/2008/">Google Summer of Code</a>.
+<p>Development of picante has been supported by <a href="http://nserc.ca">NSERC</a>, <a href="http://www.nescent.org/index.php">NESCent</a>, and the <a href="http://code.google.com/soc/2008/">Google Summer of Code</a>.</p>
 
+<h2>News</h2>
+<ul>
+<li>The pd and phylosor functions in version 0.5 of picante could result in incorrect calculation of phylosor in cases where the supplied phylogeny included taxa not present in any sample, or when pairs of samples collectively contained all taxa in the phylogeny. These functions have been updated in version 0.6, please see the documentation for more information about how PD and phylosor are calculated. Thanks to Catherine Graham, Nick Matzke, Juan Parra, and Marten Winter for feedback and bug reports on this issue.
+</li>
+</ul>
+
 <h2>Current features</h2>
 <ul>
 <li>Community phylogenetic and trait similarity measures</li>
@@ -76,7 +73,7 @@
 
 <h2>Obtaining picante</h2>
 <ul>
-<li>Version 0.5-3 (stable) is available on <a href="http://cran.r-project.org/">CRAN</a>. Simply type <strong><code>install.packages("picante")</code></strong> from within R.</li>
+<li>Version 0.6 is available on <a href="http://cran.r-project.org/">CRAN</a>. Simply type <strong><code>install.packages("picante")</code></strong> from within R.</li>
 <li>You can grab the latest nightly build <a href="http://r-forge.r-project.org/R/?group_id=134">here</a>, or by typing <strong><code>install.packages("picante",repos="http://R-Forge.R-project.org")</code></strong> from within R.</li>
 </ul>
 
@@ -85,21 +82,23 @@
 
 <h2>Release history</h2>
 <p><ul>
-<li>Version 0.5-3:
-    <ul><li>Phylogenetic beta diversity measures (phylosor) with randomization testing</li>
-    <li>Minor bugfixes</li>
-    </ul>
-</li>
-<li>Version 0.4-0: New features and greatly improved speed of community randomizations (randomizeSample). New phylogenetic bipartite linear models functionality added.</li>
-<li>Version 0.3-0: Bugfixes. Added phylogenetic bipartite linear models, phylogenetic community-environment regressions.</li>
-<li>Version 0.2-0: Added new community phylogenetic structure metrics (PSR/PSV/PSC methods of Helmus et al.) and phylogenetic species richness accumulation curves</li>
-<li>Version 0.1-2: Initial public release</li>
+<li>Veresion 0.6: Bugfix release. Changes to pd and phylosor functions.</li>
+<li>Version 0.5: Phylogenetic beta diversity measures (phylosor) with randomization testing.</li>
+<li>Version 0.4: New features and greatly improved speed of community randomizations (randomizeSample). New phylogenetic bipartite linear models functionality added.</li>
+<li>Version 0.3: Bugfixes. Added phylogenetic bipartite linear models, phylogenetic community-environment regressions.</li>
+<li>Version 0.2: Added new community phylogenetic structure metrics (PSR/PSV/PSC methods of Helmus et al.) and phylogenetic species richness accumulation curves</li>
+<li>Version 0.1: Initial public release</li>
 </ul>
 </p>
 
-<p><a href="http://www4.clustrmaps.com/counter/maps.php?url=http://picante.r-forge.r-project.org/" id="clustrMapsLink"><img src="http://www4.clustrmaps.com/counter/index2.php?url=http://picante.r-forge.r-project.org/" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onerror="this.onerror=null; this.src='http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://www2.clustrmaps.com';" />
-</a>
-</p>
+<! --- R-Forge Logo --- >
+<table border="0" width="100%" cellspacing="0" cellpadding="0">
+<tr><td ALIGN="center">
+<a href="/"><img src="<?php echo $themeroot; ?>/images/logo.png" border="0" alt="R-Forge Logo" /> </a> </td>
+<td ALIGN="center"><a href="http://www4.clustrmaps.com/counter/maps.php?url=http://picante.r-forge.r-project.org/" id="clustrMapsLink"><img src="http://www4.clustrmaps.com/counter/index2.php?url=http://picante.r-forge.r-project.org/" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onerror="this.onerror=null; this.src='http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://www2.clustrmaps.com';" />
+</a></td>
+</tr>
+</table>
 
 </body>
 </html>

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