From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Tue, 4 Nov 2008 20:11:38 +0000 (+0000)
Subject: fixing bug in chronopl(, CV = TRUE)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=45da26e7c3c483aee0781f799da5ef336f14a028;p=ape.git

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 e2fc4ce..1a6a7ab 100644
--- 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 ba82d6c..c2fab9e 100644
--- 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 3139906..6a0bd89 100644
--- 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
     }