+ 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.
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
projects / ape.git / blobdiff