UPCOMING:
- [ADD] spatial autocorrelation using Smouse & Peakall (1999)
- [NEW] save.population() to text, STRUCTURE, and XXXX
- [NEW] added human data set to example data 
- [ADD] added congruence examples to PopulationGraph vignette.
- [ADD] Congruence of topologies for population graphs
- [ADD] Example of amova in genetic.structure
- [ADD] Fst (coalescent time) added to genetic.structure
- [ADD] add drop.one option to multivariate.loci option
- [ADD] stamova

2012-01-23 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.8
- [FIX] Added .Rinstignore to clean up inst/doc directory
- [NOFIX] tried compactPDF() but nothing.

2012-01-23 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.7
- [ADD] ability to create Locus() objects from SNP 0/1/2 minor allele encodings
- [ADD] flag in read.population() for snp 0/1/2 minor allele encodings
- [FIX] vignette problem (for some reason it is not being built in the previous versions) finally there now.

2012-01-11 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.6
- [CHANGE] Moved all the separate vignettes into a single document

2011-12-28 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.5
- [FIX] Vignette problem

2011-12-28 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.4
- [FIX] Fixed problem with subtracting alleles from NA data
- [FIX] Fixed issue when trying to subtract mother genotypes from family if mom is missing (see above)
- [FIX] Standardized individual and offspring indices for data columns for parent/offspring routines.
- [FIX] Reduced the size of the vignettes to below suggested limit.

2011-11-25 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.3
- [NEW] congruence.graph() function to create congruence topologies
- [NEW] congruence.graph.probability() determine the probability of the congruence graph given the size of the parental graphs
- [NEW] read.pgraph() to read in population graph files.
- [ADD] ability to load data from shared GoogleDocs Spreadsheet into read.population and updated vignette.
- [ADD] cornus_florida genotype dataset with parents and offspring
- [ADD] Vignette on Parent Offspring Data
- [ADD] column.class method added to Population to return indices of particular classes of variables in a population.
- [NEW] offspring.array() function added to parse out families of mom/offspring from large data set.
- [ADD] Comparison operators "==" and "!=" for Locus objects.
- [ADD] Arith operators "+" and "-" added for Locus objects for mating & pulling mother part (respectively).
- [NEW] minus.mom() added to pull maternal contributions to offspring arrays.
- [NEW] exclusion.probability()
- [ADD] "euclidean" distance option for stratum.distance()
- [NEW] paternity(pop, familyID) added, performs family-wise paternity and returns fractional assignment
- [ADD] option of pairwise to genetic.structure() function that returns a simple matrix of pairwise structure values
- [NEW] paternity.spiderplot(pop,paternity) Makes graphical output of paternity
- [FIX] fixed cGD estimation in genetic.distance function.

2011-08-26 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.2
- [FIX] Vignette names (popgraph was coming out as genetic structure) and new vignettes for the offspring analysis
- [ADD] option 'verbose' for genetic.structure to toggle printing of progress for longer jobs.
- [NEW] great.circle.distance() and stratum.distance() functions added to calculate physical separation amongst sites.
- [NEW] google.pie.chart() function to make pie icons for population plotting
- [NEW] pies.on.map() function to create KML file for examining allele frequencies of strata
- [CHANGE] population.graph() added routines to incorporate latitude, longitude, and grouping into the graph representation for spatial plotting.
- [NEW] popgraph.on.map() function to create KML file for population graphs
- [NEW] genetic.diversity() function to estimate diversity statistics using rarefaction.
- [NEW] Vignette on genetic.diversity
- [NEW] Vignette on mapping 'GStudio Mapping'
- [NEW] stratum.distance() function to get physical distances between populations.

2011-08-12 Rodney J. Dyer <rjdyer@vcu.edu> version = 0.1
- [NEW] S4 class for Locus
- [NEW] S4 class for Population
- [NEW] S4 class forAlleleFrequencies
- [NEW] genetic.distance() 
- [NEW] genetic.structure() 
- [NEW] read.population()
- [NEW] population.graph()