CHANGES IN PEGAS VERSION 0.4-2


BUG FIXES

    o amova() did not randomize correctly at the highest level,
      resulting in P-values that were always equal to 1.



		CHANGES IN PEGAS VERSION 0.4-1


BUG FIXES

    o site.spectrum(, folded = FALSE) failed.

    o The variances returned by nuc.div() were inflated (thanks to
      Paulina Ossa for the report).



		CHANGES IN PEGAS VERSION 0.4


NEW FEATURES

    o The new function rr.test by Alastair Potts performs Tajima's test
      of a molecular clock (Genetics, 1993, 135:599).

    o haploNet() has a new argument 'd = NULL' to specify an
      alternative distance matrix among haplotypes.

    o There are two new functions, as.network.haploNet() and
      as.igraph.haploNet() for converting networks of class
      "haploNet" towards other packages.


BUG FIXES

    o plot.haploNet() has now by default asp = 1.



		CHANGES IN PEGAS VERSION 0.3-4


OTHER CHANGES

    o The help command ?loci now points to the man page of read.loci()
      where this class is described.



		CHANGES IN PEGAS VERSION 0.3-3


BUG FIXES

    o read.loci() failed with haploid data. It also failed in some
      situations with the population column. The default behaviour is now
      more flexible and more reliable.

    o Variance components were not correctly computed by amova() in the
      single-level case.

    o print.amova() did not work correctly when amova() was called with
      'nperm = 0'.



		CHANGES IN PEGAS VERSION 0.3-2


BUG FIXES

    o A bug was fixed in Fst().



		CHANGES IN PEGAS VERSION 0.3-1


OTHER CHANGES

    o The default of 'loci.sep' in read.loci() is now "".



		CHANGES IN PEGAS VERSION 0.3


NEW FEATURES

    o The new function edit.loci allows to edit allelic data frame while
      keeping the attributes correct (which edit.data.frame doesn't).

    o There are new rbind() and cbind() methods for objects of class
      "loci".

    o There is a print 'method' for the class "haplotype".

    o `[.loci` has now an option 'drop = TRUE'.

    o There is a vignette detailing how to read allelic data files of
      various formats into R: type vignette("ReadingFiles") in R.


BUG FIXES

    o amova() did not compute SSD correctly with a single level.

    o getAlleles() did not work correctly.

    o read.loci() did not work when 'col.pop' was used.

    o Checking for ordered alleles did not work (i.e, A/a and a/A were
      treated as different genotypes: they are now pooled).

    o The display of haplotype labels by plot.haploNet() was not
      effective.


OTHER CHANGES

    o read.loci() loses the 'skip' option which is replaced by '...'.



		CHANGES IN PEGAS VERSION 0.2


NEW FEATURES

    o The new function site.spectrum computes the (un)folded site
      frequency spectrum of a set of DNA sequences.

    o The new function theta.tree estimates THETA from a phylogenetic tree
      under a simple coalescent model by maximum likelihood.

    o There is now a "[" method for the class "loci".

    o haplotype() has now an option 'labels' to give as rownames of
      the returned object.

    o amova() has a new option 'is.squared' to specify whether the
      distance matrix has been squared beforefand (FALSE by default).

    o write.loci() has a new argument '...' passed to write.table().

    o The functions heterozygosity, nuc.div, theta.h, theta.k and
      theta.s have been moved from ape to pegas.


BUG FIXES

    o amova() did not compute SSD correctly.

    o summary.loci() failed in the presence of NA's.