[Adephylo-commits] r130 - in pkg: . inst/doc

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

Author: jombart
Date: 2009-11-05 13:51:26 +0100 (Thu, 05 Nov 2009)
New Revision: 130

Modified:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/inst/doc/adephylo.Rnw
Log:
fixes tdata in vignette


Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2009-11-05 12:43:40 UTC (rev 129)
+++ pkg/ChangeLog	2009-11-05 12:51:26 UTC (rev 130)
@@ -3,5 +3,12 @@
 
 NEW FEATURES
 
-	o 
+	o first release of the package with unstable status. Compatible
+	with phylobase (in	development) and ape packages; package
+	only released on R-Forge, not CRAN.
 
+	o re-implements all phylogenetic methods and datasets available in ade4
+
+	o add new features to compute phylogenetic distances/proximities,
+	pPCA, tree walks, ... 
+

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2009-11-05 12:43:40 UTC (rev 129)
+++ pkg/DESCRIPTION	2009-11-05 12:51:26 UTC (rev 130)
@@ -1,10 +1,10 @@
 Package: adephylo
-Version: 1.0-0
-Date: 2008/11/20
+Version: 1.0-1
+Date: 2009/11/5
 Title: adephylo: exploratory analyses for the phylogenetic comparative method.
-Author: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>, Stephane Dray <dray at biomserv.univ-lyon1.fr>
-Maintainer: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>
-Suggests: 
+Author: Thibaut Jombart <t.jombart at imperial.ac.uk>, Stephane Dray <dray at biomserv.univ-lyon1.fr>
+Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
+Suggests:
 Depends: methods, phylobase, ape, ade4
 Description: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
 License: GPL (>=2)

Modified: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw	2009-11-05 12:43:40 UTC (rev 129)
+++ pkg/inst/doc/adephylo.Rnw	2009-11-05 12:51:26 UTC (rev 130)
@@ -326,15 +326,15 @@
 
 <<moranI>>=
 W <- proxTips(myTree, met="Abouheif")
-moran.idx(tdata(ung)$afbw, W)
-moran.idx(ung at tip.data[,1], W, addInfo=TRUE)
+moran.idx(tdata(ung, type="tip")$afbw, W)
+moran.idx(tdata(ung, type="tip")[,1], W, addInfo=TRUE)
 @
 
 From here, it is quite straightforward to build a non-parametric test
 based on Moran's $I$.
 For instance (taken from \code{?moran.idx}):
 <<fig=TRUE>>=
-afbw <- tdata(ung)$afbw
+afbw <- tdata(ung, type="tip")$afbw
 sim <- replicate(499, moran.idx(sample(afbw), W)) # permutations
 sim <- c(moran.idx(afbw, W), sim)