[Picante-commits] r243 - / www

[noreply at r-forge.r-project.org]

Author: skembel
Date: 2013-05-29 22:33:11 +0200 (Wed, 29 May 2013)
New Revision: 243

Modified:
   /
   www/index.php
Log:
Modify webpage for 1.6-0 release


Property changes on: 
___________________________________________________________________
Added: svn:ignore
   + .Rproj.user
.Rhistory
.RData


Modified: www/index.php
===================================================================
--- www/index.php	2013-05-29 20:28:39 UTC (rev 242)
+++ www/index.php	2013-05-29 20:33:11 UTC (rev 243)
@@ -40,29 +40,19 @@
 
 <h2>News</h2>
 <ul>
-<li>A manuscript describing Picante has been published in Bioinformatics.</li>
-<li>Picante 1.5 has been released
+<li>Picante 1.6 has been released
 <ul>
-<li>The phylogenetic generalized linear mixed models of Ives and Helmus (2011) are now included in function <code>pglmm</code></li>
-<li>The functions <code>pic.circular</code> and <code>pic3</code> have been deprecated.</li>
-<li>Code for rapid estimation of expected phylogenetic diversity and the edge abundance distribution (O'Dwyer et al. 2012) is now included in functions <code>expected.pd</code> and <code>ead</code>.
+<li>Added methods for phylogenetic estimation of trait values for unobserved taxa (Kembel et al. 2012 PLOS Comp Biol).</li>
 </ul>
 </li>
-<li>Lots of changes and new features since version 1.0
-<ul>
-<li>Calculate Rao's quadratic entropy (alpha and beta diversity taking phylogenetic distinctiveness into account)</li>
-<li>Added more phylobeta diversity measures (UniFrac, Rao's quadratic entropy)</li>
-<li>Changed name of randomizeSample to randomizeMatrix for consistency with other functions</li>
-<li>Added automatic checks to ensure taxa labels in phylogeny and other data sets match</li>
 </ul>
-</li>
-</ul>
 
 <h2>Current features</h2>
 <ul>
 <li>Community phylogenetic and trait diversity</li>
     <ul>
     <li>Faith's PD (phylogenetic diversity), standardized effect size of PD, expected PD of subsets of a phylogenetic tree.</li>
+    <li>Rapid estimation of PD (O'Dwyer et al. 2012)</li>
     <li>Webb's NRI/NTI and related measures of standardized effect size of community phylogenetic structure.</li>
     <li>Mean pairwise distance and mean distance to nearest taxon among co-occurring species (can be used with any interspecific distance measure). Distances can be calculated based on presence or abundance in samples.</li>
     <li>Rao's quadratic entropy, a measure of diversity within and among communities optionally taking phylogenetic distinctiveness into account.</li>
@@ -73,7 +63,7 @@
     <li>Numerous phylogenetic beta diversity measures (PCD, phylosor, UniFrac, betaMPD, betaMNTD, Rao's quadratic entropy).</li>
     </ul>
 <li>Phylogenetic signal (Blomberg <em>et al.</em>'s K statistic and P-value based on randomization test)</li>
-<li>Independent contrasts for traits with circular distributions</li>
+<li>Estimtion of trait values for unobserved taxa (Kembel et al. 2012 PLOS Comp Biol)</li>
 <li>Null models for community and phylogeny randomization</li>
     <ul>
     <li>Shuffle taxa labels across tips of phylogeny</li>
@@ -110,6 +100,7 @@
 
 <h2>Release history</h2>
 <p><ul>
+<li>Version 1.6: Add phylogenetic trait estimation for unobserved taxa (Kembel et al. 2012).</li>
 <li>Version 1.5: Add expected.pd and ead functions to estimate expected phylogenetic diversity and edge abundance distribution (O'Dwyer et al. 2012).</li>
 <li>Version 1.4: Add pglmm methods from Ives & Helmus (2011). Correct typos in vignette and documentation. Remove pic.circular function until further testing can be performed.</li>
 <li>Version 1.3: Add function pcd. Fix single-community error in pse.</li>