[Adephylo-commits] r139 - in pkg: . man

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

Author: jombart
Date: 2010-01-11 12:30:19 +0100 (Mon, 11 Jan 2010)
New Revision: 139

Modified:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/TODO
   pkg/man/adephylo.package.Rd
Log:
Updated files for the new minor release (1.0-2).
Package passes the check with two negligible warnings.


Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2010-01-11 11:16:12 UTC (rev 138)
+++ pkg/ChangeLog	2010-01-11 11:30:19 UTC (rev 139)
@@ -1,11 +1,23 @@
-			CHANGES IN ADEPHYLO VERSION 1.0-1
+			CHANGES IN ADEPHYLO VERSION 1.0-2
 
 
 BUG FIXES
 
 	o ...
 
+
 	
+			CHANGES IN ADEPHYLO VERSION 1.0-1
+
+
+NEW FEATURES
+
+	o first release on CRAN, first stable version
+
+	o compatible with the first stable release of the phylobase package
+
+	
+
 			CHANGES IN ADEPHYLO VERSION 1.0-0
 
 

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-01-11 11:16:12 UTC (rev 138)
+++ pkg/DESCRIPTION	2010-01-11 11:30:19 UTC (rev 139)
@@ -1,6 +1,6 @@
 Package: adephylo
-Version: 1.0-1
-Date: 2009/11/5
+Version: 1.0-2
+Date: 2010/01/11
 Title: adephylo: exploratory analyses for the phylogenetic comparative method.
 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>

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2010-01-11 11:16:12 UTC (rev 138)
+++ pkg/TODO	2010-01-11 11:30:19 UTC (rev 139)
@@ -1,6 +1,6 @@
 #######################
 #
-# adegenet TODO list
+# adephylo TODO list
 #
 #######################
 #
@@ -27,43 +27,21 @@
 
 # CODE ISSUES:
 ==============
-o make a working package that passes the check -- done (TJ)
 
+
 # DOCUMENTATION ISSUES:
 =======================
-* make a vignette
 
 
+
 # NEW IMPLEMENTATIONS:
 =====================
-o plot methods from phylobase ('old' version) -- done (TJ)
-o implement a pathTwoTips method, which has to go fast to find shortest path between two tips - done (TJ): is now sp.tips.
-o basic stuff existing in phylog objects (while option=TRUE), e.g. distance to the root for tips, etc.
-o proximities between OTUs like Abouheif, etc. -- done (TJ)
-o distances between OTUs (like sum of branch lengths) -- done (TJ)
-o dummy vectors indicating class of related OTUs (like in orthogram) -- done (TJ)
-o add a orthobasis method for objects inheriting phylo4 or phylo. -- done(TJ)
-o orthogram and multivariate orthogram; use Stephane's version -- done (SD, TJ)
-o ppca -- done (TJ)
-o migrate datasets from ade4 to adephylo: -- done (TJ)
-- carni19.Rd -- done
-- carni70.Rd -- done
-- lizards.Rd -- done
-- maples.Rd -- done
-- mjrochet.Rd -- done
-- palm.Rd -- done
-- procella.Rd -- done
-- tithonia.Rd -- done
-- ungulates.Rd -- done
-o build an orthobasis from treePart dummy variables -- done (TJ)
-o move gearymoran inside adephylo -- done, is now abouheif.moran. (TJ)
 
 
 
+
 # TESTING:
 ==========
-o test distTips a little more (see Abouheif with an outgroup, otherwise seems ok) -- done (TJ)
-o test ppca: are results identical to those with previous implementation? -- done (TJ)
 
 
 
@@ -76,10 +54,5 @@
 # LONG TERM
 ==========================
 ==========================
-o re-implement all relevant phylogenetic methods from ade4 in adephylo -- done (TJ)
-o implement several phylogenetic proximities -- done (TJ)
-o implement an orthobasis for phylogenies -- done (TJ)
 * write a comprehensive tutorial, going through adephylo, ade4, ape, phylobase, etc.
-o new plotting / summary for ppca objects. Maybe move actual plot to a scatter method, and make a plot similar to other plots. -- done (TJ)
-o make a summary method for ppca. -- done (TJ)
 

Modified: pkg/man/adephylo.package.Rd
===================================================================
--- pkg/man/adephylo.package.Rd	2010-01-11 11:16:12 UTC (rev 138)
+++ pkg/man/adephylo.package.Rd	2010-01-11 11:30:19 UTC (rev 139)
@@ -130,8 +130,8 @@
   \tabular{ll}{
     Package: \tab adephylo\cr
     Type: \tab Package\cr
-    Version: \tab 1.0-0\cr
-    Date: \tab 2008-12-24 \cr
+    Version: \tab 1.0-2\cr
+    Date: \tab 2009-01-11 \cr
     License: \tab GPL (>=2)
   }  
 }