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CRAN release: improved available memory estimation on Linux, added functions `avg_kinship_subpops` and `plot_admix`

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@alexviiia alexviiia released this 27 Jan 14:00
v1.3.17
eac861b

popkin 1.3.13.9000 (2021-11-02)

  • Added function avg_kinship_subpops.
  • Function popkin_A_min_subpops:
    • Now uses avg_kinship_subpops internally to perform the bulk of the calculations
    • When subpops = NULL, calculation now returns minimum A among off-diagonal elements only (excluding diagonal) rather than the overall minimum of A. There's no difference when A is calculated from genotypes (diagonal values are much greater than off-diagonal values), but made the change for consistency when it might differ for arbitrary inputs.
  • README updated github install instructions for building vignettes.

popkin 1.3.14.9000 (2021-11-05)

  • Function plot_popkin fixed a bug when null_panel_data = TRUE in which titles that went over panels with NULL kinship were incorrectly omitted.

popkin 1.3.15.9000 (2021-12-02)

  • Improved estimation of available memory on linux, fixing a bug where popkin incorrectly believes there is not enough memory.
    • Old: retrieved MemFree (from /proc/meminfo). This could underestimate available memory when Buffers and Cached memory are large (these count as available memory!), and in some cases cause this error: 
      Error in solve_m_mem_lim : 
The resulting `m_chunk` was negative!  This is because either `mat_n_n` or `vec_n` are non-zero and `n` alone is too large for the available memory (even for `m_chunk == 0`).  The solution is to free more memory (ideal) or to reduce `n` if possible.
    • New: retrieve MemAvailable (still from /proc/meminfo), which is ideal but is absent in older linux kernels (<3.14), otherwise fallback into retrieving and returning the sum of MemFree, Buffers, and Cached. Either way available memory is greater than MemFree alone and is also more accurate.
    • Under the hood, cleaned parser considerably and check for several trouble scenarios that were previously taken for granted.

popkin 1.3.16.9000 (2022-01-15)

  • Added function plot_admix for making admixture/structure plots with most of the same options as plot_popkin!
    • Includes plotting examples in vignette.
    • Cleaned up and extended internal function print_labels_multi, print_labels.

popkin 1.3.17 (2022-01-26)

  • 8th CRAN submission.
  • Fixed some typos.
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