X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=678bba7b17c60151cf7e1dd0924e69c7ae72341e;hb=f512087dd94a7dc3462a9f31b48f61214cdc0f5e;hp=8891e33091e47f5e69e6c3dce93857bb91a74b69;hpb=de88c4801a78a3d1a8376c19be8c852727eeaf09;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index 8891e33..678bba7 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,6 +1,164 @@
+		CHANGES IN APE VERSION 2.3-3
+
+
+BUG FIXES
+
+    o 
+
+
+
+		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.
@@ -9,6 +167,17 @@ BUG FIXES
       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