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genomicSimulation v0.2.4

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@vllrs vllrs released this 06 Feb 00:48
· 63 commits to main since this release
v0.2.4
a24365b

v0.2.4 introduces the ability to use multiple sets of marker effects at once in the simulation.

New Features

  • Add ability to load multiple effect files. Multiple sets of marker effects can now be available at one time. Loading an effect file will return a marker effect set identifier that represents that particular set of marker effects. Sets of marker effects can be removed from memory using the new function delete.effect.set.

Improvements

  • BREAKING CHANGE: When load.data is called with an effect file, the return value is now a list containing an element $groupNum (identical to the old return value) and an element $effectID (representing the identifier of the marker effect set loaded).
  • The save-as-you-go setting for saving breeding values in GenOptions now takes the identifier for a set of marker effects, if you wish to save the breeding values from that set of marker effects, or 0, to not use the save-as-you-go functionality.

Bug Fixes

  • Standardised file-output functions so that genotype names are consistently substituted with their PedigreeIDs, if the genotype does not have a name.
  • Stopped save-as-you-go genotype saving repeating the header row (of genetic marker names) every 1000 rows. The header row now only appears in the first row.
  • Semicolon separators appear correctly in the output of save_marker_blocks
  • Pedigrees are printed consistently between group-specific and whole-simulation variants of the same function. Parents are no longer skipped in favour of starting with grandparents in group-specific functions.
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