NEWS.md

In PopGenHelpR: Streamline Population Genomic and Genetic Analyses

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)

PopGenHelpR documentation built on Sept. 11, 2024, 7:51 p.m.