- 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).
- July 26th, 2024
- The previously deprecated
Dif_stats
,Dif_stats_map
,Div_stats
,Div_stats_map
, andPlot_Ancestry
functions have been removed.
- May 7th, 2024
- The
Longitude_col
andLatitude_col
arguments have been added to mapping functions;Plot_coordinates
,Ancestry_Piemap
,Piechart_map
,Network_map
, andPoint_map
. Ind_order
andPop_order
arguments have been added toAncestry_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 replacedDiv_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 toNetwork_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 intoPiechart_Map
andAncestry_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 theDifferentiation
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 theHeterozygosity
function if you wish to estimate heterozygosity or thePrivate.alleles
function if you wish to calculate the number of private alleles per population. Please use thePoint_Map
function if you wish to visualize the results on a map or plot.
- October 2nd, 2023
Dif_stats_Map
,Div_Stats_Map
, andPlot_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.
- August 14th, 2023
Div_Stats
andDif_stats
have been updated to accept a vcf file or vcfR object as input.Div_Stats
andDif_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 usespData
for mapping data. - The vignette has been updated to accommodate the changes noted above.
- 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
andDif_stats
so that files are not automatically written to the working directory.
- July 17th, 2023
- PopGenHelpR has been updated to rnaturalearthhires in Suggests field of the DESCRIPTION file and now use it conditonally.
- First development of PopGenHelpR, publication on Github, and submission to the CRAN (02/06/2023)