bug fix in read.dna + change the default of tol in drop.fossil

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 5a6817e06a65c287771809a14472393a88a7fe2c..a4985e5dfcc71b19f3d191007abe15da6ec9bbab 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,91 @@
+               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.
+
+
+OTHER CHANGES
+
+    o In drop.fossil() the default tol = 0 has been raised to 1e-8.
+
+
+
+               CHANGES IN APE VERSION 2.6-2
+
+
+NEW FEATURES
+
+    o Two new functions, pic.ortho and varCompPhylip, implements the
+      orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
+      second function requires Phylip to be installed on the computer.
+
+    o bd.ext() has a new option conditional = TRUE to use probabilities
+      conditioned on no extinction for the taxonomic data.
+
+
+BUG FIXES
+
+    o write.tree() failed to output correctly tree names.
+
+    o dist.nodes() returned duplicated column(s) with unrooted and/or
+      multichotomous trees.
+
+    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
+
+
+NEW FEATURES
+
+    o The new function speciesTree calculates the species tree from a set
+      of gene trees. Several methods are available including maximum tree
+      and shallowest divergence tree.
+
+
+BUG FIXES
+
+    o A bug introduced in write.tree() with ape 2.6 has been fixed.
+
+    o as.list.DNAbin() did not work correctly with vectors.
+
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Filipe Vieira for the fix).
+
+
+
                CHANGES IN APE VERSION 2.6
 
 
@@ -5,11 +93,15 @@ NEW FEATURES
 
     o The new functions rlineage and rbdtree simulate phylogenies under
       any user-defined time-dependent speciation-extinction model. They
-      use new continuous time algorithms.
+      use continuous time algorithms.
 
     o The new function drop.fossil removes the extinct species from a
       phylogeny.
 
+    o The new function bd.time fits a user-defined time-dependent
+      birth-death model. It is a generalization of yule.time() taking
+      extinction into account.
+
     o The new function MPR does most parsimonious reconstruction of
       discrete characters.
 
@@ -53,6 +145,9 @@ OTHER CHANGES
     o pic() now returns a vector with the node labels of the tree (if
       available) as names.
 
+    o write.tree() and read.tree() have been substantially improved thanks
+      to contributions by Klaus Schliep.
+
 
 
                CHANGES IN APE VERSION 2.5-3