From noreply at r-forge.r-project.org  Sat Nov  8 17:23:08 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  8 Nov 2014 17:23:08 +0100 (CET)
Subject: [Adephylo-commits] r202 - pkg/R
Message-ID: <20141108162308.8C35118629D@r-forge.r-project.org>

Author: aebilgrau
Date: 2014-11-08 17:23:08 +0100 (Sat, 08 Nov 2014)
New Revision: 202

Modified:
   pkg/R/utils.R
Log:
sp.tips should now return the internal nodes in the correct order for a walk along the tree

Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R	2013-11-29 15:46:01 UTC (rev 201)
+++ pkg/R/utils.R	2014-11-08 16:23:08 UTC (rev 202)
@@ -90,7 +90,7 @@
 
     ## function pathTwoTips (takes two path-to-root as args)
     pathTwoTips <- function(path1, path2){
-        cpath <- c(path1, path2)
+        cpath <- c(path1, rev(path2))
         temp <- factor(cpath, levels=unique(cpath))
         CA <- temp[table(temp)==2][1] # most recent common ancestor (MRCA)
         CA <- as.integer(as.character(CA)) # retrieve integer type
@@ -103,7 +103,7 @@
 
 
     pathTwoTips.no.mrca <- function(path1, path2){
-        cpath <- c(path1, path2)
+        cpath <- c(path1, rev(path2))
         temp <- intersect(path1, path2)
         res <- setdiff(cpath, temp)
         return(res)


From noreply at r-forge.r-project.org  Mon Nov 10 15:12:06 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 10 Nov 2014 15:12:06 +0100 (CET)
Subject: [Adephylo-commits] r203 - in pkg: . man
Message-ID: <20141110141206.6D375186D3D@r-forge.r-project.org>

Author: jombart
Date: 2014-11-10 15:12:05 +0100 (Mon, 10 Nov 2014)
New Revision: 203

Modified:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/man/adephylo.package.Rd
Log:
Updated contributors, dates and version number

Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2014-11-08 16:23:08 UTC (rev 202)
+++ pkg/ChangeLog	2014-11-10 14:12:05 UTC (rev 203)
@@ -1,6 +1,20 @@
+			CHANGES IN ADEPHYLO VERSION 1.1-7
+
+FIXES
+
+	o sp.tips now returns ordered paths between tips
+
+FRESH BLOOD
+
+	o Anders Ellern Bilgrau has joined the development team!
+
+
+
+
 			CHANGES IN ADEPHYLO VERSION 1.1-5
 
 FIXES
+
 	o the new NAMESPACE selectively imports procedures to avoid
 	conflicts between ape, phylobase, and ade4. Thes packages are no
 	longer attached when loading adephylo
@@ -10,6 +24,7 @@
 
 
 
+
 			CHANGES IN ADEPHYLO VERSION 1.1-4
 
 

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2014-11-08 16:23:08 UTC (rev 202)
+++ pkg/DESCRIPTION	2014-11-10 14:12:05 UTC (rev 203)
@@ -1,8 +1,8 @@
 Package: adephylo
-Version: 1.1-6
-Date: 2013/11/29
+Version: 1.1-7
+Date: 2014/11/10
 Title: adephylo: exploratory analyses for the phylogenetic comparative method.
-Author: Thibaut Jombart <t.jombart at imperial.ac.uk>, Stephane Dray <stephane.dray at univ-lyon1.fr>
+Author: Thibaut Jombart <t.jombart at imperial.ac.uk>, Stephane Dray <stephane.dray at univ-lyon1.fr>, Anders Ellern Bilgrau <abilgrau at math.aau.dk>
 Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
 Suggests:
 Depends: methods, ade4

Modified: pkg/man/adephylo.package.Rd
===================================================================
--- pkg/man/adephylo.package.Rd	2014-11-08 16:23:08 UTC (rev 202)
+++ pkg/man/adephylo.package.Rd	2014-11-10 14:12:05 UTC (rev 203)
@@ -136,14 +136,14 @@
   \tabular{ll}{
     Package: \tab adephylo\cr
     Type: \tab Package\cr
-    Version: \tab 1.1-4\cr
-    Date: \tab 2013-05-15 \cr
+    Version: \tab 1.1-7\cr
+    Date: \tab 2014-11-10 \cr
     License: \tab GPL (>=2)
   }  
 }
 \author{
   Thibaut Jombart <tjombart at imperial.ac.uk>\cr
-  with contributions St?phane Dray <dray at biomserv.univ-lyon1.fr>. \cr
+  with contributions St?phane Dray <dray at biomserv.univ-lyon1.fr> and Anders Ellern Bilgrau <abilgrau at math.aau.dk>. \cr
   Parts of former code from \code{ade4} by Daniel Chessel and S?bastien
   Ollier.
 }