- CHANGES IN APE VERSION 2.5-4
+ CHANGES IN APE VERSION 2.6
NEW FEATURES
+ o The new functions rlineage and rbdtree simulate phylogenies under
+ any user-defined time-dependent speciation-extinction model. They
+ use new continuous time algorithms.
+
+ o The new function drop.fossil removes the extinct species from a
+ phylogeny.
+
+ o The new function MPR does most parsimonious reconstruction of
+ discrete characters.
+
+ o The new function Ftab computes the contingency table of base
+ frequencies from a pair of sequences.
+
o There is now an 'as.list' method for the class "DNAbin".
o dist.dna() can compute the number of transitions or transversions
control the aspect of thermometers: horiz = TRUE, width = NULL,
and height = NULL.
+ o compar.gee() has been improved with the new option 'corStruct' as an
+ alternative to 'phy' to specify the correlation structure, and
+ calculation of the QIC (Pan 2001, Biometrics). The display of the
+ results has also been improved.
+
+ o read.GenBank() has a new option 'gene.names' to return the name of
+ the gene (FALSE by default).
+
+
+BUG FIXES
+
+ o extract.clade() sometimes shuffled the tip labels.
+
+ o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
+ Schliep for the fix)
+
+ o dist.dna(model = "logdet") used to divide distances by 4. The
+ documentation has been clarified on the formulae used.
+
+
+OTHER CHANGES
+
+ o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
+ change the parameterisation (see ?rTraitCont for details).
+
+ o pic() now returns a vector with the node labels of the tree (if
+ available) as names.
+
CHANGES IN APE VERSION 2.5-3
projects / ape.git / blobdiff