[Picante-commits] r241 - pkg pkg/R pkg/man www

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

Author: skembel
Date: 2012-10-09 15:12:23 +0200 (Tue, 09 Oct 2012)
New Revision: 241

Modified:
   pkg/DESCRIPTION
   pkg/R/traitgram.R
   pkg/man/picante-package.Rd
   pkg/man/traitgram.Rd
   www/index.php
Log:
Update website and traitgram documentation for version 1.5-2

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-10-09 12:10:48 UTC (rev 240)
+++ pkg/DESCRIPTION	2012-10-09 13:12:23 UTC (rev 241)
@@ -1,8 +1,8 @@
 Package: picante
 Type: Package
 Title: R tools for integrating phylogenies and ecology
-Version: 1.5-1
-Date: 2012-10-1
+Version: 1.5-2
+Date: 2012-10-9
 Author: Steven W. Kembel <skembel at uoregon.edu>, David D. Ackerly <dackerly at berkeley.edu>, Simon P. Blomberg <s.blomberg1 at uq.edu.au>, Will K. Cornwell <cornwell at zoology.ubc.ca>, Peter D. Cowan <pdc at berkeley.edu>, Matthew R. Helmus <mrhelmus at wisc.edu>, Helene Morlon <morlon.helene at gmail.com>, Campbell O. Webb <cwebb at oeb.harvard.edu>
 Maintainer: Steven W. Kembel <skembel at uoregon.edu>
 Depends: ape, vegan, nlme

Modified: pkg/R/traitgram.R
===================================================================
--- pkg/R/traitgram.R	2012-10-09 12:10:48 UTC (rev 240)
+++ pkg/R/traitgram.R	2012-10-09 13:12:23 UTC (rev 241)
@@ -36,8 +36,6 @@
 	lmar = 0.2
 	if (xaxt=='s') if (show.xaxis.values) lmar = 1 else lmar = 0.5
 	xanc <- ace(xx, phy, method=method)$ace
-	#if (method[1]=='ace') xanc = ace(xx,phy)$ace 
-	#	else xanc = pic3(xx,phy)[,3]
 	xall = c(xx,xanc)
 	
 	a0 = ages[phy$edge[,1]]

Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd	2012-10-09 12:10:48 UTC (rev 240)
+++ pkg/man/picante-package.Rd	2012-10-09 13:12:23 UTC (rev 241)
@@ -12,8 +12,8 @@
 \tabular{ll}{
 Package: \tab picante\cr
 Type: \tab Package\cr
-Version: \tab 1.5-1\cr
-Date: \tab 2012-10-1\cr
+Version: \tab 1.5-2\cr
+Date: \tab 2012-10-9\cr
 License: \tab GPL-2\cr
 }
 }

Modified: pkg/man/traitgram.Rd
===================================================================
--- pkg/man/traitgram.Rd	2012-10-09 12:10:48 UTC (rev 240)
+++ pkg/man/traitgram.Rd	2012-10-09 13:12:23 UTC (rev 241)
@@ -17,14 +17,13 @@
   \item{underscore}{ if FALSE remove underscore from taxonomic names }
   \item{show.names}{ if TRUE show taxon names across tips of phylogeny }
   \item{show.xaxis.values}{ if TRUE show values for trait on x=axis }
-  \item{method}{ method for calculation of internal trait values. 'ace' = ace maximum likelihood method from ape; 'pic' = independent contrasts method. pic option can be used when ace fails to converge or otherwise seems to fail to correctly reconstruct ancestral values}
+  \item{method}{ method for calculation of internal trait values. 'ML' = maximum likelihood method; 'pic' = independent contrasts method. pic option can be used when ML fails to converge or otherwise seems to fail to correctly reconstruct ancestral values}
   \item{...}{ Additional arguments passed to plot }
 }
 \value{
     Plots a traitgram, no values returned.
 }
 \author{ David Ackerly <dackerly at berkeley.edu> }
-\seealso{ \code{\link{pic3}} }
 \references{ 
 Ackerly, D. D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences USA 106:19699-19706. doi: 10.1073/pnas.0901635106. 
 

Modified: www/index.php
===================================================================
--- www/index.php	2012-10-09 12:10:48 UTC (rev 240)
+++ www/index.php	2012-10-09 13:12:23 UTC (rev 241)
@@ -44,7 +44,7 @@
 <li>Picante 1.5 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 function <code>pic.circular</code> has been deprecated until further testing can be performed.</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>.
 </ul>
 </li>