Skip to content

poppr version 2.8.0
Compare
Choose a tag to compare
@zkamvar zkamvar released this 20 May 00:39
v.2.8.0
578a7c4
This commit was signed with the committer’s verified signature. The key has expired.
zkamvar Zhian N. Kamvar
GPG key ID: 88EFAD5774DF822F
Expired
Learn about vigilant mode.

This release contains an updated win.ia(), AMOVA for genlight objects, and a faster and more efficient calculation of Euclidean distance for genlight objects (see image).

image

NEWS

BUG FIX

  • win.ia() now has more consistent behavior with chromosome structure and will
    no longer result in an integer overflow.
    (see #179). Thanks to @MarisaMiller
    for the detailed bug report.
  • plot_filter_stats() will plot stats if supplied a list of thresholds.

ALGORITHMIC CHANGE

  • win.ia() may result in slightly different results because of two changes:
    1. The windows will now always start at position one on any given chromosome.
      This will result in some windows at the beginning of chromosomes having a
      value of NA if the first variant starts beyond the first window.
    2. Windows are now calculated for each chromosome independently. The previous
      version first concatenated chromosomes with at least a window-sized gap
      between the chromosomes, but failed to ensure that the window always started
      at the beginning of the chromosome. This version fixes that issue.
      (see #179).

DEPRECATION

  • The chromosome_buffer argument for win.ia() has been permanently set to
    TRUE and deprecated as it is no longer used.

NEW FEATURES

  • poppr.amova() will now handle genlight/snpclone objects.
    See #185 for details.

  • bitwise.dist() now has two new options: euclidean and scale_missing.
    When both of these are set to TRUE, the distance measured will be Euclidean
    scaled for the amount of missing data in each comparison. This matches the
    output of base R's dist() function at a fraction of time and memory.
    See #176 for details.

  • make_haplotypes() is now a generic defined for both genind and genlight.

  • genind2genalex() will no longer write to "genalex.csv" by default. Instead,
    it will warn the user and write to a temporary file.
    See #175 for details.

  • genind2genalex() now has an overwrite parameter set to FALSE to prevent
    accidental overwriting of files.

  • win.ia() has a new argument name_window, which will give each element in
    the result the designation of the terminal position of that window. Thanks to
    @MarisaMiller for the suggestion!

  • pair.ia() can now calculate p-values via permutations (I forgot to add this in the official NEWS)

DOCUMENTATION

  • cutoff_predictor() was added to the MLG vignette
Assets 2
Loading