5th CRAN release: fst local inbr support, popkin_A and popkin_A_min_subpops

2020-02-18 - popkin 1.3.1.9000

• Added x_local parameter to function fst, which permits estimation of FST when there is known local inbreeding (estimated from a pedigree or IBD blocks).

2020-06-19 - popkin 1.3.2.9000

• validate_kinship now tests for symmetry in input kinship matrices too.

2020-07-13 - popkin 1.3.3.9000

• Internal (non-exported) function solve_m_mem_lim now avoids a rare integer overflow caused when input number of individuals n was encoded as an integer and was greater than sqrt(.Machine$integer.max), or 46340.95.

2020-07-23 - popkin 1.3.4.9000

• validate_kinship now has sym option that, if FALSE, skips symmetry test (defaults to TRUE).
• plot_popkin has the same sym option passed to validate_kinship, but here it defaults to FALSE (there is no inherent error caused by plotting non-symmetric matrices).

2020-09-24 - popkin 1.3.5.9000

• Function popkin
  • Added want_M option, which if TRUE returns a list containing the kinship matrix as well as the pairwise complete count matrix M.
  • Added m_chunk_max option (default 1000), which sets the maximum number of loci to process at the time.
    The new default behavior reduces memory usage a lot, especially on machines with large memory, without sacrificing speed.
    Original version would use a lot of memory just because it was available, which could be inconvenient when trying to run other processes, and did not result in increased speed, so it was unnecessary at best.
  • Minor documentation improvements.

2020-11-20 - popkin 1.3.6.9000

• Added exported functions popkin_A (used to be unexported get_A) and popkin_A_min_subpops (used to be unexported min_mean_subpops)
  • These are low-level functions providing intermediate calculations used by the main popkin function.
  • Provided for researchers to try to improve the popkin method
• Function validate_kinship added option name (default "kinship") for clear error reports when the matrix being tested is not actually a kinship matrix
  • Internally used with name = "A" to validate A in popkin_A_min_subpops.
• Simplified documentation (most functions) by using markdown roxygen and replacing all LaTeX equations with simpler code equations.

2021-02-09 - popkin 1.3.7

• 5th CRAN submission.
• Updated paper citations in DESCRIPTION, README.md and the vignette, to point to the published method in PLoS Genetics, and also a related preprint of human analysis on bioRxiv.
• Minor spellcheck corrections in documentation.