X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=430c21093791aab51038f32d86ce4575df8f8698;hb=bd55cf71ae1a3d20d237d7fdd36af138c21769df;hp=402cf950ff587b3fb54fe40fb26c9f6e2e28f369;hpb=5de3d16fdc60bcbab2ae04933bca4ab931ed48f8;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index 402cf95..430c210 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,161 @@
+		CHANGES IN APE VERSION 2.5-2
+
+
+BUG FIXES
+
+    o as.phylo.hclust() used to multiply edge lengths by 2.
+
+
+DEPRECATED & DEFUNCT
+
+    o evolve.phylo() and plot.ancestral() have been removed.
+
+
+OTHER CHANGES
+
+    o nj() has been improved and is now about 30% faster.
+
+
+
+ 		CHANGES IN APE VERSION 2.5-1
+
+
+NEW FEATURES
+
+    o The new function stree generates trees with regular shapes.
+
+    o It is now possible to bind two trees with x + y (see ?bind.tree for
+      details).
+
+    o drop.tip(), extract.clade(), root(), and bind.tree() now have an
+      'interactive' option to make the operation on a plotted tree.
+
+    o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
+      association links; they are recycled like 'col' (which wasn't before).
+
+
+BUG FIXES
+
+    o rTraitDisc() did not use its 'freq' argument correctly (it was
+      multiplied with the rate matrix column-wise instead of row-wise).
+
+    o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
+      with NA values. Nothing is drawn now like with 'text' or 'pch'.
+      The same bug occurred with the 'pie' option.
+
+    o A bug was fixed in compar.ou() and the help page was clarified.
+
+    o bind.tree() has been rewritten fixing several bugs and making it
+      more efficient.
+
+    o plot.phylo(type = "p") sometimes failed to colour correctly the
+      vertical lines representing the nodes.
+
+    o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
+      in the correct direction though the tip labels were displayed
+      correctly.
+
+
+OTHER CHANGES
+
+    o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
+      the sequences are correctly stored (in a list for c, in a matrix
+      for the two other functions).
+
+
+
+	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 function lmorigin by Pierre Legendre performs multiple
+      regression through the origin with testing by permutation.
+
+    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 The new function edges draws additional branches between any nodes
+      and/or tips on a plotted tree.
+
+    o The new function fancyarrows enhances arrows from graphics with
+      triangle and harpoon heads; it can be called from edges().
+
+    o add.scale.bar() has a new option 'ask' to draw interactively.
+
+    o The branch length score replaces the geodesic distance in dist.topo.
+
+    o Three new data sets are included: the gopher-lice data (gopher.D),
+      SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal &
+      Rohlf 1995), and some host-parasite specificity data
+      (lmorigin.ex2, from Legendre & Desdevises 2009).
+
+
+BUG FIXES
+
+    o add.scale.bar() drew the bar outside the plotting region with the
+      default options with unrooted or radial trees.
+
+    o dist.topo() made R stuck when the trees had different sizes (thanks
+      to Otto Cordero for the fix).
+
+
+OTHER CHANGES
+
+    o The geodesic distance has been replaced by the branch length score
+      in dist.topo().
+
+
+
+		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
 
 
@@ -44,6 +202,8 @@ 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
@@ -204,7 +364,7 @@ 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'.
 
 
 
@@ -1157,6 +1317,8 @@ OTHER CHANGES
 
     o dist.taxo() has been renamed as weight.taxo().
 
+    o dist.phylo() has been replaced by the method cophenetic.phylo().
+
     o Various error and warning messages have been improved.