Changes in version 1.1-0

read.POPDIST, write.POPDIST, and freq.to.genpop functions added.

read.Tetrasat function changed so that the comment line can't be accidentally
read as a "Pop" line if it contains the letters "pop".  The documentation for
this function now also instructs the user not to have any locus name contain
the letters "pop" adjacent to each other.

write.Tetrasat function changed so that if the 'samples' argument excludes
some populations, there won't be a "Pop" line for these populations.

Changes in version 1.0-1

Bug fixed in the 'editGenotypes' method for "genambig" objects.
stringsAsFactors=FALSE was added for the data frame that is sent to the
'edit' function, so that samples and loci are indexed correctly when genotypes
are written back to the object that is returned.  Version 1.0 would rearrange
the genotypes if the samples or loci were not in alphabetical order.

Changes in version 1.0

The S4 classes "gendata", "genambig", and "genbinary" and their accompanying
methods have been added.  This allows genotypes, population identities,
population names, ploidies, microsatellite repeat lengths, and a description
to all be stored in one object, while in version 0.1 they had to be stored in
separate objects.  Because of this, many of the functions require fewer
arguments, and user error should be reduced.

The functions 'viewGenotypes' and 'editGenotypes' have been added so that
genotypes can be more neatly printed to the console, and can be edited with
the Data Editor as an alternative to command-line genotype editing.

The 'isMissing' function is added to simplify the identification of missing
genotypes.

The function 'estimatePloidy' now directly opens the Data Editor and then
returns the ploidies to the appropriate slot in the "gendata" object.
Previously, the function produced an array from which ploidies had to be
manually extracted.

The function 'distance.matrix.1locus' no longer exists since it has been
consolidated into the 'meandistance.matrix' function.  'Lynch.distance' has a
'usatnt' argument added to it for the sake of simplifying the code for
'meandistance.matrix'; this argument is ignored by 'Lynch.distance'.

The new function 'deSilvaFreq' performs an iterative computation to estimate
allele freqencies in populations with uniform, even-numbered ploidy and a
known selfing rate.  The old function 'estimate.freq' is renamed 'simpleFreq'.

A function 'write.freq.SPAGeDi' is added to export allele frequencies to
SPAGeDi.