gstudio 1.2
-----------------
* [ADD] Added all the relatedness statistics to genetic_relatedness() function

* [ADD] Added spiderplot_data() function to take output from paternity() and plot it using geom_segment().
* [ADD] Added mixed ploidy for 2Gener analysis to dist_amova
* [ADD] Added cornus_florida data set for example parent/offspring data
* [FIX] Changed errors in minus_mom() to be more verbose.
* [ADD] Added option in ploidy() to return mean ploidy for data.frame of loci.
* [ADD] Added rel_ritland() to estimate Ritland (1996)
* [ADD] Added rel_lynch() to estimate Lynch & Ritland (1999)
* [ADD] Added rel_queller() to estimate Queller & Goodnight (1989)
* [ADD] Added rel_nason() as a function for allelic or locus-wide coancestry from Nasons fij 
* [ADD] Added kronecker_delta() function to return locus differences after Ritland 2000
* [FIX] Problem with pies_on_map() where one population was always a bit off.  This is really not a problem with the plotting, it is more of a problem with the ratio of h/w for the plot.  Make them the same and it will be fine.
* [ADD] Added option to sort strata in strata_coords (default=FALSE) in alphabetical order.
* [FIX] Inconsistance in case for arguments to strata_coordinates;  was longitude/latitude rather than Longitude/Latitude, also had to change stuff in pies_on_map and plot.data.frame
* [FIX] Two problems with strata_coordinates() for returning SpatialPoints.
* [FIX] Problems with bad_parent() and parent_finder()
* [ADD] Added ellipsis to read_population() function to allow optional values to be passed on to read.table()
* [ADD] Added Pe, locus specific polymorphic index sum(p_i(1-p_i)) for genetic_diversity()


gstudio 1.1 
-----------------
* [ADD] Added write_population() function to save textual output as text, GENEPOP, and STRUCTURE.
* [ADD] Added several functions to aid in export translations for other programs such as GENEPOP and STRUCTURE.  These functions include: to_fixed_locus(), to_STRUCTURE(), and to_GENEPOP().

* [FIX] Fixed the situation where you create a locus without a 'type' defined and it would not sort the alleles in ascending numeric order, rather it would sort them in ascii order, even if you had set the optional argment as 'phased=FALSE'.
* [ADD] Added ability to subtract vectors of loci instead of single locus estimates usiung the loc1 - loc2 operator.
* [ADD] Added bad_parents() to scan offspring, mother data.frames and determine if the mother could be the real mother.
* [ADD] Added parent_finder() to do fractional single parent identification.
* [ADD] Added ability to subtract vectors of loci instead of single locus estimates.
* [ADD] Added bad_parents() to scan offspring, mother data.frames and determine if the mother could be the real mother.
* [ADD] Added parent_finder() to do fractional maternal individual identification.
* [CHANGE] Dropped warming when subtracting loci when one is missing.  Used to result in a stop() but now only provides a warning and returns the left hand locus (the one the subtraction is being done from).
* [FIX] Changed mate() function for simplicity.
* [FIX] Made "Stratum" column from make_population() a factor and made the stratum of the resulting population not "Stratum" but "Population"
* [FIX] Gst(), Gst_prime(), and Dest() for when a data.frame is passed with only one locus, there is no need to do the multilocus response.  
* [FIX] Gst(), Gst_prime(), and Dest() for when subset of data is passed (e.g., stratum with zeros counts), the zeros are ignored.
* [FIX] transition_probability() had an issue with double hets.
* [FIX] Fixed problem when importing data from text file where you have only one external variable.  
* [ADD] Added paternity and other items to documentation.
* [ADD] Added ability to input GenePop files using read_population(file, type="genepop")
* [ADD] Added pairwise option to genetic_structure() function.
* [FIX] The function genetic_diversity() did not recognize the 'stratum' option 
* [ADD] Added Fis to genetic_diversity() for continuity.
* [FIX] A() was not accepting data.frames as it should have been.
* [FIX] Multilocus estimate of Gst_prime() was wrong if there was a single locus estimate that was negative, in which case the harmonic mean is not correct.
* [ADD] Added function strata_distance() to return distance matrix between stratum based upon either Euclidean distance or great-circle distance.
* [ADD] Added function genotype_frequencies() to return both observed and expected frequencies for a given locus.
* [ADD] Added ", space="free", scales="free_x" to plot_frequencies() for non-overlapping allele counts and better plots.
* [FIX] Fixed exclusion_probability() to return numeric values for various columns and added multilocus exclusion to result.
* [FIX] Dataframe column name on multilocus Ho was incorrect
* [ADD] Changed the transition_probability() function to handle multilocus estimates of both two parent and single parent situations when data are contained in data.frame elements.
* [FIX] Removed missing data from estimation of genotype_frequencies()
* [ADD] Added ability for mate() to do replacement random mating (e.g., take all individuals in data.frame and make equal size next generation using complete random mating).
* [ADD] Added ability to get SpatialPoints object from strata_coordinates() function as well as data.frame.
* [ADD] Added function optimal_sampling() to help estimate optimal sampling designs for methods requiring estimates of genetic differentiation.
* [ADD] Added multilocus_diversity() function to return proportion of sample size with unique multilocus genotypes.
* [ADD] Added geom_locus, geom_frequencies, geom_strata, and geom_surface to plotting functions 
* [ADD] Added function genetic_relatedness() for Ritland 1996 and Lynch & Ritland 1999 marker estimators.



gstudio 1.0 
-----------------

* This is a complete rewrite of the gstudio (ver. 0.X) package.  What I have done is to remake
  the fundamental locus object as an S3 object rather than an S4 class. 
* Too much has changed to interate through all of the changes.  To get a good idea of how to 
  use the new functionality see http://dyerlab.github.io/gstudio/
* Integrated, where possible, spatial connections to both the raster and sp packages such that 
  direct analyses of spatial population genetic processes can be accessed.
* This first version has the following functional components.
    - locus(), alleles(), frequencies()
    - heterozygosity in terms of He(), Fis(), Ho()
    - genetic_diversity() for parameters Ae(), A(), A95() with rarefaction()
    - genetic_distance() for dist_amova(), dist_bray(), dist_euclidean(), dist_cgd(), dist_nei(), dist_jaccard(), dist_Dps()
    - genetic_structure() for Gst(), Gst_prime(), and Dest()
    - spatial plotting and mapping using sp, raster, and google_maps API's
    - paternity() with transition_probability() for both strict and fractional paternity.
    - parent offspring stuff with with minus_mom()
    - added make_population() and mate() for making random populations


