a few bug fixes especially in plot.phylo()

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 2858cd498b2c2f10943e0200468b45528a04bb1e..8480ce8d82dec01af58e8f2dba26fcf09b40c9b7 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,36 @@
+               CHANGES IN APE VERSION 2.6-3
+
+
+NEW FEATURES
+
+    o rTraitCont() and rTraitDisc() gains a '...' argument used with
+      user-defined models (suggestion by Gene Hunt).
+
+
+BUG FIXES
+
+    o as.hclust.phylo() now returns an error with unrooted trees.
+
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Jinlong Zhang for pointing this bug out).
+
+    o read.dna(, "fasta") failed if sequences were not all of the same
+      length.
+
+    o plot.phylo() did not recycle values of 'font', 'cex' and
+      'tip.color' correctly when type = "fan" or "radial".
+
+
+OTHER CHANGES
+
+    o In drop.fossil() the default tol = 0 has been raised to 1e-8.
+
+    o The help command ?phylo now points to the man page of read.tree()
+      where this class is described. Similarly, ?matching points to the
+      man page of as.matching().
+
+
+
                CHANGES IN APE VERSION 2.6-2
 
 
@@ -21,6 +54,22 @@ BUG FIXES
     o mcmc.popsize() terminated unexpectedly if the progress bar was
       turned off.
 
+    o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
+
+    o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
+
+    o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
+      = FALSE.
+
+    o Objects returned by as.hclust.phylo() failed when analysed with
+      cutree() or rect.hclust().
+
+    o write.tree() did not output correctly node labels (thanks to Naim
+      Matasci and Jeremy Beaulieu for the fix).
+
+    o ace(type = "discrete") has been improved thanks to Naim Marasci and
+      Jeremy Beaulieu.
+
 
 
                CHANGES IN APE VERSION 2.6-1