-Updated documentation to ensure other packages are cited correctly.
write and prefix arguments have been updated to function properly.D.bar object.ind.order and pop.order arguments, respectively.legend_pos argument.The following updates laregly apply for the Plot_coordinates, Piechart_map, Point_map, and Network_map functions. We note where any updates are function specific.
country_code argument. Country codes must match those used in geodata.group argument and group_col argument to specify colors for each group (only for Plot_coordinates).legend_pos argument.scale_bar and north_arrow arguments. Users can also modify the position and style of the north arrow using north_arrow_position and north_arrow_style arguments, respectively.shapefile argument. Users can also control where the shapefile is placed using shape_file_position, the fill color (shapefile_col), and the outline color (shapefile_outline_col). Shapefiles can be character strings or spatVector objects.raster, raster_col, and raster_plot_position arguments. Custom breaks can be set with raster_breaks and users can indicate if rasters are discrete using discrete_raster. Note that sometimes terra interprets continuous rasters as discrete, and users should use the discrete_raster argument to accommodate this. Rasters can be characters or spatRaster objects.Differentiation function has been updated to be consistent with the rest of the function (using !is.na).Dif_stats, Dif_stats_map, Div_stats, Div_stats_map, and Plot_Ancestry functions have been removed.Longitude_col and Latitude_col arguments have been added to mapping functions; Plot_coordinates, Ancestry_Piemap, Piechart_map, Network_map, and Point_map.Ind_order and Pop_order arguments have been added to Ancestry_Barchart to allow users to specify the order of individuals and populations in the barchart.Plot_coordinates function has been added to make sample maps from coordinates.Point_map function has replaced Div_stats_map and a statistic argument has been added to highlight the functions utility and allow users to name the map legend.Dif_stats_map has been changed to Network_map and a statistic argument has been added to highlight the functions utility and allow users to name the map legend.Plot_ancestry has been split into Piechart_Map and Ancestry_barchart so that it is easier for users to determine which function is most appropriate for their analysis.Differentiation has been added to estimate Fst, Nei's D, and Jost's D. Please see the documentation for more details.Heterozygosity has been added to estimate 7 different measures of heterozygosity. Please see the documentation for more details.Private.alleles has been added to calculate the number of private alleles in each population.Dif_Stats function has been deprecated, please used the Differentiation function to calculate pairwise differentiation between populations (Fst, Nei's D, Jost's D) or individuals (Nei's D).Div_Stats function has been deprecated, please use the Heterozygosity function if you wish to estimate heterozygosity or the Private.alleles function if you wish to calculate the number of private alleles per population. Please use the Point_Map function if you wish to visualize the results on a map or plot.Dif_stats_Map, Div_Stats_Map, and Plot_ancestry have been updated to use a base color of #f4f4f4 instead of grey99 which was throwing an error for some users.Plot_ancestry, the original value of 0.35 was found to be too high, especially in cases where users were mapping a smaller geographic area.Div_Stats and Dif_stats have been updated to accept a vcf file or vcfR object as input.Div_Stats and Dif_stats have been updated to accept a csv file or data frame for population assignment.Plot_ancestry has been updated to generate structure-like plots using ggplot2 instead of base R and to handle character and numeric values for individual and population names. Note that individual and populations must be of the same type (i.e., both numeric or both characters).rnaturalearth is no longer used. We now use spData for mapping data.Div_Stats and Dif_stats so that files are not automatically written to the working directory.