faster nj()!!!

[ape.git] / ChangeLog

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+               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