X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=c3a2a844a0e098a57e65e6d93e27e1ce3439377b;hb=01fef1c23b7a8c96d003f14d82ba8a3d61d2a079;hp=a3923a68c8dbcc4856a24e6622e1a5076cdba634;hpb=285d0e6700c8381d66b5c671aacd9494fa8ad444;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index a3923a6..c3a2a84 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,176 @@
+		CHANGES IN APE VERSION 2.3-2
+
+
+BUG FIXES
+
+    o all.equal.phylo() did not compare unrooted trees correctly.
+
+    o dist.topo(... method = "PH85") did not treat unrooted trees
+      correctly (thanks to Tim Wallstrom for the fix).
+
+    o root() sometimes failed to test for the monophyly of the
+      outgroup correctly.
+
+    o extract.clade() sometimes included too many edges.
+
+    o vcv.phylo() did not work correctly when the tree is in
+      "pruningwise" order.
+
+    o nj() did not handle correctly distance matrices with many 0's.
+      The code has also been significantly improved: 7, 70, 160 times
+      faster with n = 100, 500, 1000, respectively.
+
+
+
+		CHANGES IN APE VERSION 2.3-1
+
+
+NEW FEATURES
+
+    o The new function is.monophyletic tests the monophyly of a group.
+
+    o There is now a c() method for lists of class "DNAbin".
+
+    o yule.cov() now fits the null model, and its help page has been
+      corrected with respect to this change.
+
+    o drop.tip() has a new option 'rooted' to force (or not) a tree
+      to be treated as (un)rooted.
+
+
+BUG FIXES
+
+    o dist.gene() failed on most occasions with the default
+      pairwise.deletion = FALSE.
+
+    o read.tree() failed to read correctly the tree name(s).
+
+    o boot.phylo() now treats correctly data frames.
+
+    o del.gaps() did not copy the rownames of a matrix.
+
+    o A small bug was fixed in CDAM.global().
+
+    o ace() failed with large data sets. Thanks to Rich FitzJohn for
+      the fix. With other improvements, this function is now about 6
+      times faster.
+
+    o write.tree() failed with objects of class "multiPhylo".
+
+    o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
+
+
+OTHER CHANGES
+
+    o [.multiPhylo and [.DNAbin now respect the original class.
+
+    o Instances of the form class(phy) == "phylo" have been replaced
+      by inherits(phy, "phylo").
+
+    o rcoal() is now faster.
+
+
+DEPRECATED & DEFUNCT
+
+    o klastorin() has been removed.
+
+
+
+		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
 
 
@@ -6,6 +179,9 @@ NEW FEATURES
     o dist.gene() has been substantially improved and gains an option
       'pairwise.deletion'.
 
+    o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
+      more flexible.
+
 
 BUG FIXES
 
@@ -28,8 +204,8 @@ OTHER CHANGES
     o phymltest() has been updated for PhyML 3.0 and gains an option
       'append', whereas the option 'path2exec' has been removed.
 
-    o rbind.DNAbin() now accepts a single matrix which is returned
-      unchanged instead of an error.
+    o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
+      which is returned unchanged (instead of an error).
 
     o The data sets bird.orders and bird.families are now stored as
       Newick strings; i.e., the command data(bird.orders) calls