changed some data sets (made lighter) + clarified man page for rcoal()

[ape.git] / Changes

diff --git a/Changes b/Changes
index 9633e8879b5c4a612b876514efac18aa2b8b1e4d..988dd6f1956c1ff5ea4138980f73348327f6bd73 100644 (file)
--- a/Changes
+++ b/Changes
@@ -1,3 +1,77 @@
+               CHANGES IN APE VERSION 2.2-2
+
+
+NEW FEATURES
+
+    o dist.gene() has been substantially improved and gains an option
+      'pairwise.deletion'.
+
+
+BUG FIXES
+
+    o prop.part() failed with a single tree with the default option
+     'check.labels = TRUE'.
+
+
+OTHER CHANGES
+
+    o The data sets bird.orders and bird.families are now stored as
+      Newick strings; e.g., the command data(bird.orders) calls
+      read.tree().
+
+
+
+               CHANGES IN APE VERSION 2.2-1
+
+
+NEW FEATURES
+
+    o The new function makeLabel() helps to modify labels of trees,
+      lists of trees, or DNA sequences, with several utilities to
+      truncate and/or make them unique, substituting some
+      characters, and so on.
+
+    o The new function del.gaps() removes insertion gaps ("-") in a
+      set of DNA sequences.
+
+    o read.dna() can now read Clustal files (*.aln).
+
+
+BUG FIXES
+
+    o root() failed with 'resolve.root = TRUE' when the root was
+      already the specified root.
+
+    o Several bugs were fixed in mlphylo().
+
+    o collapsed.singles() did not propagate the 'Nnode' and
+      'node.labels' elements (thanks to Elizabeth Purdom for the fix).
+
+    o read.nexus() failed to remove correctly the comments within
+      trees.
+
+    o read.nexus() failed to read a file with a single tree and no
+      translation of tip labels.
+
+    o read.nexus() failed to place correctly tip labels when reading
+      a single tree with no edge lengths.
+
+    o A bug was fixed in sh.test().
+
+
+OTHER CHANGES
+
+    o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
+      Minin.
+
+    o The option 'check.labels' of consensus() and prop.part() is now
+      TRUE by default.
+
+    o write.dna() now does not truncate names to 10 characters with
+      the Phylip formats.
+
+
+
                CHANGES IN APE VERSION 2.2
 
 
@@ -8,12 +82,18 @@ NEW FEATURES
       subtreeplot), and to return the graphical coordinates of tree
       (without plotting).
 
-    o The new function corPagel() implements the Pagel's "lambda"
-      correlation structure.
+    o The new functions corPagel and corBlomberg implement the Pagel's
+      "lambda" and Blomberg et al.'s "ACDC" correlation structures.
 
     o chronopl() has been improved and gains several options: see its
       help page for details.
 
+    o boot.phylo() has now an option 'trees' to possibly return the
+      bootstraped trees (the default is FALSE).
+
+    o prop.part() has been improved and should now be faster in all
+      situations.
+
 
 BUG FIXES
 
@@ -29,10 +109,13 @@ BUG FIXES
     o zoom() failed when tip labels were used instead of their numbers
       (thanks to Yan Wong for the fix).
 
-    o drop.tip() failed with some trees  (fixed by Yan Wong).
+    o drop.tip() failed with some trees (fixed by Yan Wong).
 
     o seg.sites() failed with a list.
 
+    o consensus() failed in some cases. The function has been improved
+      as well and is faster.
+
 
 
                CHANGES IN APE VERSION 2.1-3
@@ -165,9 +248,9 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o The code of mlphylo() has almost entirely rewritten, and should
-      be much stabler. The options have been also greatly simplified
-      (see ?mlphylo and ?DNAmodel for details).
+    o The code of mlphylo() has been almost entirely rewritten, and
+      should be much stabler. The options have been also greatly
+      simplified (see ?mlphylo and ?DNAmodel for details).
 
     o The internal function nTips has been renamed klastorin_nTips.