fixing bug in chronopl(, CV = TRUE)

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@54 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/ChangeLog b/ChangeLog
index e2fc4cec9a3872f837ceb004644c41632ccec0ac..1a6a7ab27005480defebf00ab8ffda6ac9b5faf0 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,12 @@
+               CHANGES IN APE VERSION 2.2-3
+
+
+BUG FIXES
+
+    o chronopl() did not work with CV = TRUE.
+
+
+
                CHANGES IN APE VERSION 2.2-2
 
 

diff --git a/DESCRIPTION b/DESCRIPTION
index ba82d6cb3677a8c8d42f0ea912a17f85b44781a9..c2fab9ef69ee73eac7f6b09e6eae6c6fc86a2ac1 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
-Version: 2.2-2
-Date: 2008-10-08
+Version: 2.2-3
+Date: 2008-11-04
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
   Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,

diff --git a/R/chronopl.R b/R/chronopl.R
index 3139906c2e76af61601061bb9e4cceda99582f40..6a0bd89be6064680f5112f7e889b85156ab140ef 100644 (file)
--- a/R/chronopl.R
+++ b/R/chronopl.R
@@ -1,4 +1,4 @@
-## chronopl.R (2008-03-26)
+## chronopl.R (2008-11-04)
 
 ##   Molecular Dating With Penalized Likelihood
 
@@ -231,6 +231,8 @@ chronopl.cv <- function(ophy, lambda, age.min, age.max, nodes,
         if (length(node)) {
             chr <- chronopl(tr, lambda, age.min, age.max, node,
                             S, tol, FALSE, eval.max, iter.max, ...)
+            tmp <-
+                if (Nnode(chr) == Nnode(ophy)) BT else BT[-(ophy$edge[j, 1] - n)]
             D2[i] <- sum((tmp - branching.times(chr))^2 / tmp)
         } else D2[i] <- 0
     }