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3rd CRAN release, massive naming style normalization
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@alexviiia alexviiia released this 15 May 17:50
v1.1.1
9d8cdbf

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).
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