genomicSimulation v0.2.5

New Features

• Some culling of (unused) dependencies means we can now release genomicSimulation (R version) under the same MIT license as the C version.
• Add ability to observe the values of custom labels using see.group.data.
• Add ability to load multiple recombination maps into simulation at a time. The associated new functions are load.map and delete.recombination.map.
• New function change.allele.symbol changes the internal representation of a particular allele. It does not modify corresponding marker effects. This may be useful for tidying printed output.

Bug Fixes

• Fixed a bug where some genotypes lost their group numbers during internal data-structure tidying in large simulations.
• Input/output file paths can now include the tilde ~ character to represent the home directory, thanks to R package fs.

Improvements

• Smarter and more robust file loaders. They can now automatically detect headers and allele encodings. See R version vignette (Section: Input Files) or Templates page of C version documentation for more information.
• BREAKING CHANGE: Increased function naming consistency between R and C versions of the package. This means some R functions have changed names. Old function names still work (they directly call the new function name), but sometime in the future the old names may be removed. (Old name) -> (new recommended name) pairs for the R package are as follows:
  • see.minimum.GEBV -> see.minimal.GEBV
  • select.by.gebv -> break.group.by.GEBV
  • make.group.from.label -> break.group.by.label.value
  • make.group.from.label.range -> break.group.by.label.range
  • make.label -> create.new.label
  • load.more.genotypes -> load.genotypes
  • load.different.effects -> load.effects
  • cross.randomly -> make.random.crosses
  • cross.randomly.between -> make.random.crosses.between
  • cross.combinations -> make.targeted.crosses
  • cross.combinations.file -> make.crosses.from.file
  • cross.dc.combinations.file -> make.double.crosses.from.file
  • cross.all.pairs -> make.all.unidirectional.crosses
  • save.local.GEBVs.by.file -> save.local.GEBVs.blocks.from.file
  • save.local.GEBVs.by.chr -> save.local.GEBVs.blocks.from.chrsplit
• genomicSimulation now calls R_Calloc/R_Free for memory allocation rather than stdlib's malloc/free.
• Under-the-hood improvements to crossing functions and to the internal tidying function.
• The same script and same random seed will produce different genotypes post-v0.2.4.003, because gametes are now generated successively (first one, then the other) rather than simultaneously.
• Changed table of contents order and added details in package vignette to help new users.