CRAN release: added function popkin_af, tree plotting capability, weights_subpops now supports two-level hierarchy

popkin 1.3.8.9000 (2021-02-16)

• Documentation updates:
  • Fixed links to functions, in many cases these were broken because of incompatible mixed Rd and markdown syntax (now markdown is used more fully).

popkin 1.3.9.9000 (2021-03-16)

• Added function popkin_af, which is the analog of popkin but for allele frequency matrices instead of genotypes, and as a consequence it estimates coancestry instead of kinship.

popkin 1.3.10.9000 (2021-05-25)

Overall added tree plotting capabilities and more plotting fine control.

• Added function plot_phylo for plotting phylo trees.
  This is a wrapper around ape::plot.phylo that makes several adjustments so plots agree more with accompanying kinship matrices (package ape is now a dependency for this feature).
• Function plot_popkin had the following updates:
  • Objects of type phylo and function are now accepted elements in input list kinship (first argument).
    If phylo, these trees are plotted via plot_phylo.
    If function, its code is executed without arguments, which is expected to plot a single panel.
  • Added option ylab_side to allow placing labels on x-axis (bottom, but also top, and right side) instead of the default y-axis (left side).
  • Added option leg_column for placing legend/color key in any column (default last column, which was the only choice before).
  • Added option panel_letters_adj for positioning panel letters more finely, farther into the margin.
    Also, previous hardcoded default of 0 (inside x-axis range) was changed now to -0.1 (just outside the x-axis range in most cases).
  • Matrix row and column names (when names = TRUE) are now always plotted entirely, even if overlapping.
    The old behavior (R's default) plotted names in order and skipped overlapping labels (see ?axis), which looks prettier but was confusing for this plot as it suggested incorrectly that some individuals or subpopulations were not present.
    The solution is unfortunately a hack, to pass gap.axis = -1 to axis (suggested in ?axis), which hopefully does not break in the future.
• Function validate_kinship now has option logical = TRUE to return a logical value instead of throwing errors.

popkin 1.3.11.9000 (2021-06-04)

• Updated citations in inst/CITATION (missed last time I updated them in other locations).

popkin 1.3.12.9000 (2021-06-09)

• Function weights_subpops updates:
  • Now accepts a second optional vector subsubpops for calculating weights on two levels.
  • Return value is now a numeric vector (used to be of class table).

popkin 1.3.13 (2021-07-27)

• 7th CRAN submission.
• Removed "LazyData: true" from DESCRIPTION (to avoid a new "NOTE" on CRAN).
• Reformatted this NEWS.md slightly to improve its automatic parsing.
• Fixed spelling in documentation.