2017-09-11 - bnpsd 1.0.0.9000

• Public release!

2018-01-15 - bnpsd 1.0.1

• Minor non-code changes for first CRAN submission.

2018-02-01 - bnpsd 1.0.1.9000

• README.md now contains instructions for installing from CRAN as well as from GitHub.

2019-02-06 - bnpsd 1.0.2.9000

• Added option noFixed to function rbnpsd to redraw loci that were drawn fixed for a single allele. These loci are not polymorphic so they would normally not be considered in analyses.

• Added function fixed_loci to test for fixed loci within rbnpsd.

2019-02-07 - bnpsd 1.0.3.9000

• Added function coanc_to_kinship to easily obtain kinship matrices from coancestry matrices.

2019-02-11 - bnpsd 1.0.4

• Second CRAN submission.

2019-02-13 - bnpsd 1.0.4.9000

• Converted the vignette from PDF to HTML

2019-04-11 - bnpsd 1.0.5.9000

• qis now returns a numeric admixture proportions matrix (used to be logical).
• q1d and q1dc now handle sigma = 0 special case.
• q1d and q1dc now provide more informative out-of-bounds messages when sigma is missing (and s is provided)
• sigma root finding in q1d and q1dc (when s is provided) is now more robust, explicitly tested at boundaries (min s > 0 achieved at sigma = 0 and max s = 1 achieved at sigma = Inf).
  • Removed arguments interval and tol from both q1d and q1dc (users would never need to set them now that procedure is more robust).
• Updated coding style, renamed some internal functions and variables.

2019-04-16 - bnpsd 1.1.0.9000

• Renamed most functions for clarity:
  • coanc -> coanc_admix
  • q1d -> admix_prop_1d_linear
  • q1dc -> admix_prop_1d_circular
  • qis -> admix_prop_indep_subpops
  • rpanc -> draw_p_anc
  • rpint -> draw_p_subpops
  • rpiaf -> make_p_ind_admix
  • rgeno -> draw_genotypes_admix
  • rbnpsd -> draw_all_admix
  • fst -> fst_admix (no deprecated version available in this case, to eliminate conflict with popkin::fst)
  • Functions with old names remain for now as deprecated functions (to be removed in the future).
• Renamed several recurrent argument names for clarity:
  • Q -> admix_proportions
  • F -> coanc_subpops (if general matrix is accepted), inbr_subpops (vector or scalar versions required)
  • s -> bias_coeff
  • w -> weights
  • Theta -> coancestry
  • m -> m_loci
  • n -> n_ind
  • k -> k_subpops
  • pAnc -> p_anc
  • B -> p_subpops
  • P -> p_ind
  • Deprecated functions still accept old argument names.
• Fixed a sigma = 0 bug in admix_prop_1d_circular.
• Changed default values for draw_all_admix (compared to deprecated rbnpsd, which retains old defaults):
  • require_polymorphic_loci (old noFixed) is now TRUE by default.
  • want_p_ind and want_p_subpops (old wantP and wantB) are now FALSE by default.
  • Names (following above conventions) and order of items in return list changed.
• draw_p_subpops now admits scalar inputs p_anc and inbr_subpops, while number of loci and number of subpopulations can be provided as additional options.
• Added more input checks to functions, informative error messages.
• Updated documentation, particularly on whether intermediate subpopulation coancestries are accepted generally (coanc_subpops) or if the diagonal matrix case is required (specified as vector or scalar inbr_subpops).

2019-05-15 - bnpsd 1.1.1

• Third CRAN submission.
• Added ORCIDs to authors.
• Corrected doc typos.
• Adjusted layout of subpopulations and individuals (default limits) for circular 1D geography (admix_prop_1d_circular) to prevent overlapping individuals on the edges, and to better agree visually with the linear version (admix_prop_1d_linear).

2019-06-05 - bnpsd 1.1.2

• Non-code changes:
  • Edited .Rbuildignore to stop ignoring README; also removed non-existent files from list
  • Removed unused .travis.yml and bnpsd.Rproj files

2019-08-13 - bnpsd 1.1.2.9000

• Improved memory efficiency of default draw_genotypes_admix
  • Old approach was by default very memory-hungry (created IAF matrix whole when admixture proportions were provided). The low_mem option could be set but filled slowly by locus only.
  • New approach is always low-memory (so the explicit option was removed). This was made faster by filling by individual when there are fewer individuals than loci, or filling by locus otherwise, therefore always vectorizing as much as possible. Test showed this was always as fast as the original full memory approach, so the latter was removed as an option.
• draw_all_admix is also now automatically low-memory whenever want_p_ind = FALSE, and the explicit low_mem option has also been removed.
• Updated documentation to use RMarkdown
• Other code tidying

2019-09-06 - bnpsd 1.1.3.9000

• Added option beta in function draw_p_anc to trigger a symmetric Beta distribution for the ancestral allele frequencies, with the desired shape parameter. The beta option can also be set on the wrapper function draw_all_admix. This option allows simulation of a distribution heavier on rare variants (when beta is much smaller than 1), more similar to real human data.

2019-12-17 - bnpsd 1.2.0

• Fourth CRAN submission.
• Removed deprecated function names: q1dc, q1d, qis, coanc, rbnpsd, rgeno, rpanc, rpint, rpiaf.
• Moved logo to man/figures/
• Minor Roxygen-related updates.

2020-01-08 - bnpsd 1.2.1

• Fourth CRAN submission, second attempt.
• Fixed a rare bug in bias_coeff_admix_fit, which caused it to die if the desired bias coefficient was an extreme value (particularly 1). The error message was: f() values at end points not of opposite sign. The actual bug was not observed in the regular R build, but rather in a limited precision setting where R was configured with --disable-long-double.