X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=057cf583a570dd78448d2e318059d3aaadd33e53;hb=081bbd65bc9bbf19658c1dfc0724d17bf925626e;hp=8df6cc8b7aa06925ce5d54d8928a1742363128c8;hpb=269a1dbc3927260e5fc96f535f752fc09596e96e;p=ape.git

diff --git a/ChangeLog b/ChangeLog
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@@ -1,3 +1,126 @@
+		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
+      with the option model = "Ts" or model = "Tv", respectively.
+
+    o [node|tip|edge]labels() gain three options with default values to
+      control the aspect of thermometers: horiz = TRUE, width = NULL,
+      and height = NULL.
+
+    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 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