popkin 1.3.17.9000 (2022-01-31)

Function plot_admix added options leg_title_line and leg_las, and changed the default of leg_mar, to better accommodate numerous long ancestry labels.

popkin 1.3.18.9000 (2022-01-31)

Added functions to complement plot_admix:
- admix_order_cols: to automatically order ancestries given ordered individuals.
- admix_label_cols: to automatically assign labels to ancestries given labels to individuals.

Functions popkin, popkin_A:
- Added option mean_of_ratios, default FALSE is original estimator, TRUE gives a new estimator that upweighs rare variants, which resembles in this way the standard kinship estimator, and which appears to improve performance in association testing.
- Fixed minor bug that M (one of the return values when want_M = TRUE) did not inherit individual names from X even though A and kinship did, and similarly all inherit names when X is a function (fixed accidentally when replacing Rcpp code with pure R).
- Internally, for original (mean_of_ratios = FALSE) replaced Rcpp code with pure R version, which results in large speedups, at a cost of higher memory use (despite my best attempts at improving the original Rcpp code, the simpler R code is doing something magically fast I don't understand).
  Rcpp, RcppEigen dependencies have been dropped as a consequence.
Tests were separated into more files (contexts), had some cleanups

Internal function print_labels fixed bug when even = TRUE and the minimum xb_ind is not zero, which caused the maximum to be off by xb_ind.
- This bug didn't affect the exported functions that use this function (plot_popkin or plot_admix) because the minimum xb_ind was always zero in those cases.
- Fixed to handle a new application outside this package.

Function plot_popkin
- Added option ylab_per_panel to allow single-panel figures to place y-axis label in inner margin (before that case was forced to use outer margin).
- Added clarifications to existing options oma and layout_add, as in some cases you may want to turn off both features to avoid unexpected behaviors (though there are cases where turning off one but not the other also makes sense).

Function plot_phylo added option edge_width, which defaults to 1.
- This restores the plotting behavior under the dependency package ape version 5.5 and prior, where its function plot.phylo (which popkin::plot_phylo wraps) had its parameter edge.width default to 1.
- In contrast, starting on ape version 5.6 (2021-12-20), edge.width defaults to NULL, with results in setting it to par('lwd'), which had undesirable consequences in my use cases and which is why the old default is overridden in popkin.
- By extension, plot_popkin's old default edge widths for trees of class phylo is also restored.

9th CRAN submission.
Added hgdp_subset sample data, copied from lfa.
- Removed lfa dependency, which was only used for this sample data.
  lfa has become unreliable in external testing servers, particularly as it is on Bioconductor and sometimes hard to install on R-devel, so its removal simplifies automatic testing considerably.
Functions popkin, popkin_A, and popkin_af
- Removed internal code that obtained available memory on Windows systems, which started to fail recently. Now only Linux retrieves available memory from system, on all other systems a default of 1GB memory is assumed to be available.
- Updated documentation.
Fixed some typos, escaped more function/code names to simplify spellcheck in the future.
Function plot_popkin clarified documentation.