From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Tue, 20 Jan 2009 09:16:20 +0000 (+0000)
Subject: fix to avoid uncessary warning in ace(method = "GLS")
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=6527122e02cccd1449de4ea9c2498075ad405e69;p=ape.git

fix to avoid uncessary warning in ace(method = "GLS")

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@61 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/ChangeLog b/ChangeLog
index 6e2f4f1..2f05200 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -3,7 +3,9 @@
 BUG FIXES
 
     o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
-      now fixed. (thanks to Peter Wragg for the fix!)
+      now fixed. (Thanks to Peter Wragg for the fix!)
+
+    o A warning message occurred for no reason with ace(method="GLS").
 
 
 OTHER CHANGES
diff --git a/R/ace.R b/R/ace.R
index a67e6cf..c38faeb 100644
--- a/R/ace.R
+++ b/R/ace.R
@@ -1,8 +1,8 @@
-## ace.R (2008-03-10)
+## ace.R (2009-01-19)
 
 ##     Ancestral Character Estimation
 
-## Copyright 2005-2008 Emmanuel Paradis and Ben Bolker
+## Copyright 2005-2009 Emmanuel Paradis and Ben Bolker
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -102,7 +102,7 @@ did not match: the former were ignored in the analysis.')
             V <- corMatrix(Initialize(corStruct, data.frame(x)),
                            corr = FALSE)
             invV <- solve(V)
-            o <- gls(x ~ 1, correlation = Initialize(corStruct, data.frame(x)))
+            o <- gls(x ~ 1, data.frame(x), correlation = corStruct)
             GM <- o$coefficients
             obj$ace <- drop(varAY %*% invV %*% (x - GM) + GM)
             names(obj$ace) <- (nb.tip + 1):(nb.tip + nb.node)