From noreply at r-forge.r-project.org  Sat Oct 12 20:02:49 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 12 Oct 2013 20:02:49 +0200 (CEST)
Subject: [Picante-commits] r246 - pkg/R
Message-ID: <20131012180250.1021B185720@r-forge.r-project.org>

Author: jmaspons
Date: 2013-10-12 20:02:48 +0200 (Sat, 12 Oct 2013)
New Revision: 246

Modified:
   pkg/R/phylosignal.R
Log:
Correct a bug in multiPhylosignal when there are NAs in traits

Modified: pkg/R/phylosignal.R
===================================================================
--- pkg/R/phylosignal.R	2013-05-31 19:21:13 UTC (rev 245)
+++ pkg/R/phylosignal.R	2013-10-12 18:02:48 UTC (rev 246)
@@ -77,13 +77,14 @@
 	trait <- x[,1]
 	names(trait) <- row.names(x)
 	pruned <- prune.missing(trait,phy)
-	output <- data.frame(phylosignal(pruned$data,pruned$tree,...))
+	attributes(pruned$data)$na.action<- NULL
+	output <- data.frame(phylosignal(pruned$data, pruned$tree, ...))
 	if(length(colnames(x))>1) {
 		for (i in 2:length(colnames(x))) {
 			trait <- x[,i]
 			names(trait) <- row.names(x)
 			pruned <- prune.missing(trait, phy)
-			trait <- trait[phy$tip.label]
+                        attributes(pruned$data)$na.action<- NULL
 			output <- rbind(output, phylosignal(pruned$data, pruned$tree, checkdata=FALSE, ...))
 		}
 	}


From noreply at r-forge.r-project.org  Fri Oct 18 03:29:46 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 18 Oct 2013 03:29:46 +0200 (CEST)
Subject: [Picante-commits] r247 - in pkg: . man
Message-ID: <20131018012946.8CC46185A7B@r-forge.r-project.org>

Author: skembel
Date: 2013-10-18 03:29:45 +0200 (Fri, 18 Oct 2013)
New Revision: 247

Modified:
   pkg/DESCRIPTION
   pkg/man/picante-package.Rd
Log:
Updating for 1.6-1 release

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2013-10-12 18:02:48 UTC (rev 246)
+++ pkg/DESCRIPTION	2013-10-18 01:29:45 UTC (rev 247)
@@ -1,8 +1,8 @@
 Package: picante
 Type: Package
 Title: R tools for integrating phylogenies and ecology
-Version: 1.6-0
-Date: 2013-5-29
+Version: 1.6-1
+Date: 2013-10-17
 Author: Steven W. Kembel <steve.kembel at gmail.com>, 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 <steve.kembel at gmail.com>
 Depends: ape, vegan, nlme

Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd	2013-10-12 18:02:48 UTC (rev 246)
+++ pkg/man/picante-package.Rd	2013-10-18 01:29:45 UTC (rev 247)
@@ -12,8 +12,8 @@
 \tabular{ll}{
 Package: \tab picante\cr
 Type: \tab Package\cr
-Version: \tab 1.6-0\cr
-Date: \tab 2013-5-29\cr
+Version: \tab 1.6-1\cr
+Date: \tab 2013-10-17\cr
 License: \tab GPL-2\cr
 }
 }