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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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.