final fixes for ape 2.7-3

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index f9af94942c616c89d85011a2975df7e8bb322552..528e4083f58b3b12478e26dc3cd95ac82461b9b0 100644 (file)
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+               CHANGES IN APE VERSION 2.7-3
+
+
+NEW FEATURES
+
+    o The new function compute.brtime computes and sets branching times.
+
+    o mantel.test() has a new argument 'alternative' which is
+      "two-sided" by default. Previously, this test was one-tailed
+      with no possibility to change.
+
+    o ace() can now do REML estimation with continuous characters,
+      giving better estimates of the variance of the Brownian motion
+      process.
+
+
+BUG FIXES
+
+    o Branch lengths were wrongly updated with bind.tree(, where = <tip>,
+      position = 0). (Thanks to Liam Revell for digging this bug out.)
+
+    o Simulation of OU process with rTraitCont() did not work correctly.
+      This now uses formula from Gillespie (1996) reduced to a BM
+      process when alpha = 0 to avoid division by zero. The option
+      'linear' has been removed.
+
+    o Cross-validation in chronopl() did not work when 'age.max' was
+      used.
+
+    o consensus(, p = 0.5) could return an incorrect tree if some
+      incompatible splits occur in 50% of the trees (especially with
+      small number of trees).
+
+    o c() with "multiPhylo" did not work correctly (thanks to Klaus
+      Schliep for the fix).
+
+    o root() failed in some cases with an outgroup made of several tips.
+      The help page has been clarified a bit.
+
+
+
                CHANGES IN APE VERSION 2.7-2
 
 
 NEW FEATURES
 
-    o plot.phylo() has a new option 'draw = TRUE'. If FALSE, the tree
+    o There is a new class "evonet" to code evolutionary networks, with
+      a constructor function evonet(), a print() and a plot() methods,
+      and four conversion methods to the classes "phylo", "networx",
+      "network", and "igraph".
+
+    o The new function rTraitMult does multivariate traits simulation
+      with user-defined models.
+
+    o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree
       is not plotted but the graphical device is set and the
-      coordinates are saved as normal.
+      coordinates are saved as usual.
 
     o diversity.contrast.test() gains a fourth version of the test with
       method = "logratio"; the literature citations have been clarified.
 
+    o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify
+      the aspect of the bar.
+
+    o boot.phylo() now displays a progress bar by default (can be off
+      if 'quiet = TRUE').
+
+    o There is a new predict() method for compar.gee().
+
 
 BUG FIXES
 
-    o bionj() made R crash if distances were two large. It now returns
+    o bionj() made R crash if distances were too large. It now returns
       an error if at least one distance is greater than 100.
 
     o drop.tip() returned a wrong tree if 'tip' was of zero length.
 
+    o read.nexus.data() failed with URLs.
+
+    o boot.phylo() returned overestimated support values in the
+      presence of identical or nearly identical sequences.
+
+
+OTHER CHANGES
+
+    o The data bird.families, bird.orders, cynipids, and woodmouse are
+      now provided as .rda files.
+
 
 
                CHANGES IN APE VERSION 2.7-1