fix on dist.gene + a few man pages corrections

[ape.git] / ChangeLog

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+               CHANGES IN APE VERSION 2.3-1
+
+
+BUG FIXES
+
+    o dist.gene() failed on most occasions with the default
+      pairwise.deletion = FALSE.
+
+
+
+               CHANGES IN APE VERSION 2.3
+
+
+NEW FEATURES
+
+    o The new functions CADM.global and CADM.post, contributed by
+      Pierre Legendre, test the congruence among several distance
+      matrices.
+
+    o The new function yule.time fits a user-defined time-dependent
+      Yule model by maximum likelihood.
+
+    o The new function makeNodeLabel creates and/or modifies node
+      labels in a flexible way.
+
+    o read.tree() and write.tree() have been modified so that they can
+      handle individual tree names.
+
+    o plot.phylo() has a new argument 'edge.lty' that specifies the
+      types of lines used for the edges (plain, dotted, dashed, ...)
+
+    o phymltest() has been updated to work with PhyML 3.0.1.
+
+
+BUG FIXES
+
+    o drop.tip() shuffled tip labels in some cases.
+
+    o drop.tip() did not handle node.label correctly.
+
+    o is.ultrametric() now checks the ordering of the edge matrix.
+
+    o ace() sometimes returned negative values of likelihoods of
+      ancestral states (thanks to Dan Rabosky for solving this long
+      lasting bug).
+
+
+OTHER CHANGES
+
+    o The data set xenarthra has been removed.
+
+
+
+               CHANGES IN APE VERSION 2.2-4
+
+BUG FIXES
+
+    o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
+      now fixed. (Thanks to Peter Wragg for the fix!)
+
+    o A warning message occurred for no reason with ace(method="GLS").
+
+
+OTHER CHANGES
+
+    o There is now a general help page displayed with '?ape' 
+
+
+
                CHANGES IN APE VERSION 2.2-3
 
 
+NEW FEATURES
+
+    o The new function extract.clade extracts a clade from a tree by
+      specifying a node number or label.
+
+    o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
+      operations of the same names.
+
+    o dist.dna() can now return the number of site differences by
+      specifying model="N".
+
+
 BUG FIXES
 
     o chronopl() did not work with CV = TRUE.
 
+    o read.nexus() did not work correctly in some situations (trees on
+      multiple lines with different numbers of lines and/or with
+      comments inserted within the trees).
+
+    o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
+      the number of lineages with non-binary trees.
+
+
+OTHER CHANGES
+
+    o ape has now a namespace.
+
+    o drip.tip() has been improved: it should be much faster and work
+      better in some cases (e.g., see the example in ?zoom).
+
 
 
                CHANGES IN APE VERSION 2.2-2