Run a breeding scheme including a burn-in period

Allows users to switch selection critera after a designated set of cycles and continue for additional cycles. Use case envisioned is to run phenotypic selection for an initial period and then switch to e.g. GS. Adds a few other bells and whistles to the original runBreedingScheme function.

runBreedingScheme_wBurnIn(
  replication = NULL,
  bsp,
  nBurnInCycles,
  nPostBurnInCycles,
  selCritPopPre,
  selCritPopPost,
  selCritPipePre = "selCritIID",
  selCritPipePost = "selCritIID",
  iniFunc = "initializeScheme",
  productFunc = "productPipeline",
  popImprovFunc = "popImprov1Cyc",
  nBLASthreads = NULL,
  nThreadsMacs2 = NULL
)

Arguments

replication

Integer replication of running the breeding scheme
bsp

A list of breeding scheme parameters.
nBurnInCycles

Integer number of cycles to as 'burn-in' using the selCritPopPre and selCritPipePre settings.
nPostBurnInCycles

Integer number of cycles to as 'burn-in' using the selCritPopPost and selCritPipePost settings.
selCritPopPre

string, overrides the selCrit in bsp for the burn-in stage.
selCritPopPost

string, overrides the selCrit in bsp for the burn-in stage.
selCritPipePre

string, overrides the selCrit in bsp for the burn-in stage. DEFAULT: selCritIID
selCritPipePost

string, overrides the selCrit in bsp for the burn-in stage. DEFAULT: selCritIID
nBLASthreads

number of cores for each worker to use for multi-thread BLAS. Will speed up, for example, genomic predictions when using selCritGRM. Careful to balance with other forms of parallel processing.
nThreadsMacs2

uses the nThreads argument in runMacs2, parallelizes founder sim by chrom.
initializeFunc

Function to initialize the breeding program.
productPipeline

Function to advance the product pipeline by one generation
populationImprovement

Function to improve the breeding population and select parents to initiate the next cycle of the breeding scheme

Value

A records object containing the phenotypic records retained of the breeding scheme

Details

A wrapper to initiate the breeding program then iterate cycles of product pipeline and population improvement