+ 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.
+
+
+
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 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.