NEWS

gstudio 1.6 Planned
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* [REQ] Test for HWP and LD similar to that implemented in Genepop? I work with microsatellite loci that have many rare alleles, so a HWP/LD test with a MC algorithm similar to that used in Genepop would be ideal
* [ADD] Added heirfstat to genetic_structure to allow functional calling 
* [ADD] Added hooks into genetic distances from pegas through genetic_distance() for other distance measures.
* [FIX] stratum He/Ho genetic_diversity Hs
* [FIX] Add permutation to Fst() for significance
* [FIX] pies_on_map apparently is broken
* [FIX] Problem with having a misssing genotype for type="column" in first row.  Odd problem.
* [ADD] Feedback for reading in columns for read_population() when > 500 loci to provide some level of feedback to the user showing it is doing something and not just sitting there.


* [FIX] Change 'locus' to 'loci' in frequency_matrix() to be consistent with the frequencies() function argument list.
* [FIX] Catching problem where empty (instead of NA) data was causing locus(.,type="separated") to fail.

gstudio 1.5
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* [FIX] added 'structure' type of import for read_population().  Must be the two rows per individual type.
* [ADD] Added option to specify inbreeding (F) in make_population() function
* [FIX] Fixed problem with wrapper function around Nei line 9 Stratum => stratum
* [ADD] Added Fst as random anova version.
* [FIX] Added ability to pass data.frame with one or more loci to it to genotype_frequency() function
* [FIX] Refined make_population() specifying F!=0 with less suckiness.
* [ADD] Added function make_loci() to make vectors of loci outside of making populations.  Fixed problem with specifying F for small N as well.
* [ADD] Added frequency_matrix() function to reshape data.frame of allele frequencies across strata for a particular locus.
* [ADD] Added a continuity correction warning to genotype_frequencies()
* [ADD] Added multilocus_assignment() function.
* [FIX] Fixed problem with A95 parameters when evaluating a data.frame of loci
* [FIX] Fixed pies_on_map
* [FIX] Changed mate() to add additional functionality
* [FIX] Change selfing rate parameter F in mixed_mating() to s and check output.  Looks fishy right now.



gstudio 1.4
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* [FIX] Removed plot() overload for data.frame with Latitude/Longitude columns because of snotty CRAN rules that banned package from online repository
* [FIX] Changed issue with partion() to have it droplevels() to remove factors with zero occurrances. 
* [ADD] Added conversion from genind from adegenet to a data.frame object with locus objects for translation.
* [ADD] Takes centroid of coordinates in strata_coordinates (default) if more than one coordinate is provided.





gstudio 1.3
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* [ADD] Added ability to use RAD-seq style data to frequencies() function.  Here each locus is represented by the posterior likelihood of each genotype (e.g., three columns per locus).  Your locus columns will be numeric and labeled as 'LocusName_1', 'LocusName_2', and 'LocusName_3'.  It will split on the underscore and assume that the middle one (the _2) is the heterozygote.  Alleles will be A (estimated from _1 as homozygote + het) and B (estimated from _3 + het).
* [ADD] Filter to import CDPOP genotype files via read_population().
* [ADD] Added 'haploid' type for read_population().
* [ADD] Added ability to pass migration matrix to mate() function as well as constant migration.
* [ADD] Ability to call mate() with vectors of individuals at once and to specify either uniform or variable numbers of offspring per pair.
* [FIX] Problem with dist_bray() and dist_jaccard() with missing data.
* [ADD] Added function to_mv_freq() to provide multilocus frequency estimates across strata in matrix format.
* [CUTOFF]  This is where new features for Dyer (2014) stopped.  

gstudio 1.2
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* [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 
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* [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 
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* 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