o boot.phylo() and prop.clades() have a new option rooted =
FALSE. Note that the behaviour of prop.part() is unchanged.
+ o edgelabels() has a new option 'date' to place labels on edges of
+ chronograms using the time scale (suggestion by Rob Lanfear).
+
BUG FIXES
- o mantel.test() could return P-values > 1 with the default
+ o In chronopl(), the code setting the initial dates failed in
+ complicated settings (several dates known within intervals).
+ This has been generally improved and should result in faster
+ and more efficient convergence even in simple settings.
+
+ o mantel.test() sometimes returned P-values > 1 with the default
two-tailed test.
o extract.clade() sometimes shuffled some tip labels (thanks to
o The C code of base.freq() has been improved and is now nearly 8
times faster.
+ o The option 'original.data' of write.nexus() is now deprecated and
+ will be removed in a future release.
+
+ o The code of is.ultrametric() has been improved and is now 3 times
+ faster.
+
+ o The code of vcv.phylo() has been improved and is now 10 or 30
+ times faster for 100 or 1000 tips, respectively. Consequently,
+ fitting models with PGLS will be faster overall.
+
CHANGES IN APE VERSION 2.8
OTHER CHANGES
- o identify.phylo() now returns NULL if the user right-(instead of
- left-)clicks (an error was returned previously).
+ o identify.phylo() now returns NULL if the user right- (instead of
+ left-) clicks (an error was returned previously).
o read.nexus() should be robust to commands inserted in the TREES
block.