ape 0.2 is on CRAN

[Emmanuel Paradis]

A new version of ape (Analysis of Phylogenetics and Evolution) is on CRAN.

>From the Changes file:


		CHANGES IN APE VERSION 0.2


NEW FEATURES

    o The function write.tree() writes phylogenetic trees (objects of class
      "phylo") in an ASCII file using the Newick parenthetic format.

    o The function birthdeath() fits a birth-death model to branching times
      by maximum likelihood, and estimates the corresponding speciation and
      extinction rates.

    o The function scale.bar() adds a scale bar to a plot of a phylogenetic
      tree.

    o The function is.binary.tree() tests whether a phylogeny is binary.

    o Two generic functions, coalescent.intervals() and collapsed.intervals(),
      as well as some methods are introduced.

    o Several functions, including some generics and methods, for computing
      skyline plot estimates (classic and generalized) of effective
      population size through time are introduced and replace the function
      skyline.plot() in version 0.1.

    o Two data sets are now included: the phylogenetic relationships among
      the families of birds from Sibley and Ahlquist (1990), and an
      estimated clock-like phylogeny of HIV sequences sampled in the
      Democratic Republic of Congo.


DEPRECATED & DEFUNCT

    o The function skyline.plot() in ape 0.1 has been deprecated and
      replaced by more elaborate functions (see above).


BUG FIXES

    o Two important bugs were fixed in plot.phylo(): phylogenies with
      multichotomies not at the root or not with only terminal branches,
      and phylogenies with a single node (i.e. only terminal branches)
      did not plot. These trees should be plotted correctly now.

    o Several bugs were fixed in diversi.time() in the computation of
      AICs and LRTs.

    o Various errors were corrected in the help pages.

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