X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=3d55ac2e92a2c68f6d1a42692b7467d39eb3d740;hb=e85d89da7650e50517035d973798733d413af2aa;hp=e14ba74e0a6eb555f3ec04066d30911aed80ff96;hpb=100e0d086372a87bc2506873bdf86d3fcdda9922;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index e14ba74..3d55ac2 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,145 @@
+		CHANGES IN APE VERSION 2.5
+
+
+NEW FEATURES
+
+    o The new function parafit by Pierre Legendre tests for the
+      coevolution between hosts and parasites. It has a companion
+      function, pcoa, that does principal coordinate decomposition. The
+      latter has a biplot method.
+
+    o The new functions rTraitCont and rTraitDisc simulate continuous and
+      discrete traits under a wide range of evolutionary models.
+
+    o The new function delta.plot does a delta plot following Holland et
+      al. (2002, Mol. Biol. Evol. 12:2051).
+
+    o add.scale.bar() has a new option 'ask' to draw interactively.
+
+
+BUG FIXES
+
+    o add.scale.bar() drew the bar outside the plotting region with the
+      default options with unrooted or radial trees.
+
+
+
+		CHANGES IN APE VERSION 2.4-1
+
+
+NEW FEATURES
+
+    o rtree() and rcoal() now accept a numeric vector for the 'br'
+      argument.
+
+    o vcv() is a new generic function with methods for the classes "phylo"
+      and "corPhyl" so that it is possible to calculate the var-cov matrix
+      for "transformation models". vcv.phylo() can still be used for trees
+      of class "phylo"; its argument 'cor' has been renamed 'corr'.
+
+
+BUG FIXES
+
+    o bind.tree() failed when 'y' had no root edge.
+
+    o read.nexus() shuffled tip labels when the trees have no branch
+      lengths and there is a TRANSLATE block.
+
+    o read.nexus() does not try to translate node labels if there is a
+      translation table in the NEXUS file. See ?read.nexus for a
+      clarification on this behaviour.
+
+    o plot.multiPhylo() crashed R when plotting a list of trees with
+      compressed tip labels.
+
+    o write.nexus() did not translate the taxa names when asked for.
+
+    o plot.phylo(type = "fan") did not rotate the tip labels correctly
+      when the tree has branch lengths.
+
+    o ace(type = "continuous", method = "ML") now avoids sigma² being
+      negative (which resulted in an error).
+
+    o nj() crashed with NA/NaN in the distance matrix: an error in now
+      returned.
+
+
+
+		CHANGES IN APE VERSION 2.4
+
+
+NEW FEATURES
+
+    o base.freq() has a new option 'freq' to return the counts; the
+      default is still to return the proportions.
+
+
+BUG FIXES
+
+    o seg.sites() did not handle ambiguous nucleotides correctly: they
+      are now ignored.
+
+    o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
+      the tree: the argument is now ignored.
+
+    o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
+      Young for the fix).
+
+
+OTHER CHANGES
+
+    o Trying to plot a tree with a single tip now returns NULL with a
+      warning (it returned an error previously).
+
+    o The way lines representing nodes are coloured in phylograms has
+      been modified (as well as their widths and types) following some
+      users' request; this is only for dichotomous nodes.
+
+    o The argument 'adj' in [node][tip][edge]labels() now works when
+      using 'pie' or 'thermo'.
+
+    o A more informative message error is now returned by dist.dna() when
+      'model' is badly specified (partial matching of this argument is
+      done now).
+
+    o Deprecated functions are now listed in a help page: see
+      help("ape-defunct") with the quotes.
+
+
+DEPRECATED & DEFUNCT
+
+    o The functions heterozygosity, nuc.div, theta.h, theta.k and
+      theta.s have been moved from ape to pegas.
+
+    o The functions mlphylo, DNAmodel and sh.test have been removed.
+
+
+
+		CHANGES IN APE VERSION 2.3-3
+
+
+BUG FIXES
+
+    o add.scale.bar() always drew a horizontal bar.
+
+    o zoom() shuffled tips with unrooted trees.
+
+    o write.nexus() failed to write correctly trees with a "TipLabel"
+      attribute.
+
+    o rcoal() failed to compute branch lengths with very large n.
+
+    o A small bug was fixed in compar.cheverud() (thanks to Michael
+      Phelan for the fix).
+
+    o seg.sites() failed when passing a vector.
+
+    o drop.tip() sometimes shuffled tip labels.
+
+    o root() shuffled node labels with 'resolve.root = TRUE'.
+
+
+
 		CHANGES IN APE VERSION 2.3-2
 
 
@@ -17,6 +159,8 @@ BUG FIXES
       "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.
 
 
 
@@ -129,7 +273,7 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o There is now a general help page displayed with '?ape' 
+    o There is now a general help page displayed with '?ape'.
 
 
 
@@ -164,7 +308,7 @@ OTHER CHANGES
 
     o ape has now a namespace.
 
-    o drip.tip() has been improved: it should be much faster and work
+    o drop.tip() has been improved: it should be much faster and work
       better in some cases (e.g., see the example in ?zoom).