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PopGenHelpR 1.4.2

  • January 8th, 2025

-Updated documentation to ensure other packages are cited correctly.

PopGenHelpR 1.4.1

  • August 5th, 2025

Private.alleles

  • The function can now handle phased data.

Differentiation and Heterozygosity

  • The functions write and prefix arguments have been updated to function properly.

PopGenHelpR 1.4.0

  • July 2nd, 2025

Differentiation and Heterozygosity

  • Functions can now detect whether "|" or "" separate genotypes. This was causing functions to throw NAs.
  • Minor bug was fixed for Jost's D calculation. A parentheses was removed in the calculation of the D.bar object.

Ancestry_barchart

  • Code has been simplified, individual and population information is now coerced to character before visualization.
  • It is now an error if the individual names in the population data do not match the names in the individual data.
  • Plots are automatically sorted by cluster so that individuals and populations are plotted with others in the cluster, if there is no specified order.
  • Users can specify the individual and population order using the ind.order and pop.order arguments, respectively.
  • Users can specify the legend position using the legend_pos argument.

Mapping functions

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.

  • The maps are now built using the R package geodata to avoid the mapping NULL layer error.
  • Users can now include administrative borders like states using the country_code argument. Country codes must match those used in geodata.
  • Users can color points by group using the group argument and group_col argument to specify colors for each group (only for Plot_coordinates).
  • Users can specify the legend position using the legend_pos argument.
  • Users can add a scale bar or north arrow to plots using the 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.
  • Users can add a shapefile to the map with the 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.
  • Users can add a raster (discrete or continuous) and control it's placement in a similar fashion to shapefiles, with the 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.
  • Rasters cannot be added to the `Piechart_map output because it would require additional dependencies to accomodate two fills on the same ggplot2 object. Please email Keaka Farleigh (see package maintainer) if this poses a problem.

Pairwise_heatmap

  • Users can now specify color gradients of their preferred length (as long as they have that many colors).

PopGenHelpR 1.3.2

  • July 31st, 2024
  • Code to calculate Fst in the Differentiation function has been updated to be consistent with the rest of the function (using !is.na).

PopGenHelpR 1.3.1

  • July 26th, 2024
  • The previously deprecated Dif_stats, Dif_stats_map, Div_stats, Div_stats_map, and Plot_Ancestry functions have been removed.

PopGenHelpR 1.3.0

  • May 7th, 2024
  • The 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.
  • The Plot_coordinates function has been added to make sample maps from coordinates.
  • The 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.
  • The 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).
  • The 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.

PopGenHelpR 1.2.2

  • October 2nd, 2023
  • 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.
  • The piesize argument has been added to 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.

PopGenHelpR 1.2.1

  • August 14th, 2023
  • 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).
  • The dependency rnaturalearth is no longer used. We now use spData for mapping data.
  • The vignette has been updated to accommodate the changes noted above.

PopGenHelpR 1.1.1

  • July 17th, 2023
  • The horned lizard data was added so that examples can be run by users.
  • The write argument has been added to Div_Stats and Dif_stats so that files are not automatically written to the working directory.

PopGenHelpR 1.0.1

  • July 17th, 2023
  • PopGenHelpR has been updated to rnaturalearthhires in Suggests field of the DESCRIPTION file and now use it conditonally.

PopGenHelpR 1.0.0

  • First development of PopGenHelpR, publication on Github, and submission to the CRAN (02/06/2023)