fix rTraitDisc

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@111 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/ChangeLog b/ChangeLog
index b8d7c8479bbaa2611b7af40c07b621653dba4ede..b1246e0e96a7e3be82c0fa2d4511cbbf36d8cd82 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,14 @@
-               CHANGES IN APE VERSION 2.5
+               CHANGES IN APE VERSION 2.5-1
+
+
+BUG FIXES
+
+    o rTraitDisc() did not use its 'freq' argument correctly (it was
+      multiplied with the rate matrix column-wise instead of row-wise).
+
+
+
+       CHANGES IN APE VERSION 2.5
 
 
 NEW FEATURES
@@ -27,6 +37,11 @@ NEW FEATURES
 
     o The branch length score replaces the geodesic distance in dist.topo.
 
+    o Three new data sets are included: the gopher-lice data (gopher.D),
+      SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
+      Rohlf 1995), and some host-parasite specificity data
+      (lmorigin.ex2, from Legendre & Desdevises 2009).
+
 
 BUG FIXES
 
@@ -37,6 +52,12 @@ BUG FIXES
       to Otto Cordero for the fix).
 
 
+OTHER CHANGES
+
+    o The geodesic distance has been replaced by the branch length score
+      in dist.topo().
+
+
 
                CHANGES IN APE VERSION 2.4-1
 

diff --git a/DESCRIPTION b/DESCRIPTION
index 0b756c136bf205fd2231e1ac8cf1bfd3eda5010f..a71fe22397b12e8b049c7b809cc4c7a393f398f3 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
-Version: 2.5
-Date: 2010-02-01
+Version: 2.5-1
+Date: 2010-02-03
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>

diff --git a/R/ace.R b/R/ace.R
index c9a45110ca7eb926c0ca406494b30cf9cb9e9553..f728ee7c6045f9478e21fa0edd1e12fafa5aa4fa 100644 (file)
--- a/R/ace.R
+++ b/R/ace.R
@@ -1,8 +1,8 @@
-## ace.R (2009-11-12)
+## ace.R (2010-02-03)
 
 ##   Ancestral Character Estimation
 
-## Copyright 2005-2009 Emmanuel Paradis and Ben Bolker
+## Copyright 2005-2010 Emmanuel Paradis and Ben Bolker
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -224,7 +224,7 @@ anova.ace <- function(object, ...)
     table <- data.frame(ll, df, ddf, dev,
                         pchisq(dev, ddf, lower.tail = FALSE))
     dimnames(table) <- list(1:length(X), c("Log lik.", "Df",
-                                           "Df change", "Deviance",
+                                           "Df change", "Resid. Dev",
                                            "Pr(>|Chi|)"))
     structure(table, heading = "Likelihood Ratio Test Table",
               class = c("anova", "data.frame"))

diff --git a/R/rTrait.R b/R/rTrait.R
index 3359df6f71da40c3b8a5d7a254844bafb50b79e3..642591e6e2523d2ac0da057b861f1831546f6621 100644 (file)
--- a/R/rTrait.R
+++ b/R/rTrait.R
@@ -1,4 +1,4 @@
-## rTrait.R (2010-01-11)
+## rTrait.R (2010-02-03)
 
 ##   Trait Evolution
 
@@ -59,6 +59,7 @@ rTraitDisc <-
         for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i])
     } else {
         diag(Q) <- -rowSums(Q)
+        freq <- rep(freq, each = k)
         for (i in N:1) {
             p <- matexpo(Q * freq * el[i])[x[anc[i]], ]
             x[des[i]] <- .Internal(sample(k, size = 1, FALSE, prob = p))