bug fix in write.tree()

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index f92c51c79ab6a4b03291edf8ebd528884cd2884d..057cf583a570dd78448d2e318059d3aaadd33e53 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,8 +1,84 @@
-               CHANGES IN APE VERSION 2.5-4
+               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 for the fix).
+
+
+
+               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
+
+
+NEW FEATURES
+
+    o The new functions rlineage and rbdtree simulate phylogenies under
+      any user-defined time-dependent speciation-extinction model. They
+      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.
+
+    o The new function Ftab computes the contingency table of base
+      frequencies from a pair of sequences.
+
     o There is now an 'as.list' method for the class "DNAbin".
 
     o dist.dna() can compute the number of transitions or transversions
@@ -15,13 +91,34 @@ NEW FEATURES
     o compar.gee() has been improved with the new option 'corStruct' as an
       alternative to 'phy' to specify the correlation structure, and
       calculation of the QIC (Pan 2001, Biometrics). The display of the
-      results have also been improved.
+      results has also been improved.
+
+    o read.GenBank() has a new option 'gene.names' to return the name of
+      the gene (FALSE by default).
 
 
 BUG FIXES
 
     o extract.clade() sometimes shuffled the tip labels.
 
+    o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
+      Schliep for the fix)
+
+    o dist.dna(model = "logdet") used to divide distances by 4. The
+      documentation has been clarified on the formulae used.
+
+
+OTHER CHANGES
+
+    o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
+      change the parameterisation (see ?rTraitCont for details).
+
+    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