specifyBSP: specifyBSP function

In jeanlucj/AlfSimHlpR: Functions added to AlphaSimR to simplify simulating breeding schemes

Description

Function to manually specify a breeding scheme parameters (bsp) object in R, rather than using a control file. Currently does not handle costs. For costs (for now), run specifyCosts() on this. Ideally this is useful for programmatically varying breeding schemes.

Usage

specifyBSP(
  schemeDF,
  nParents,
  nCrosses,
  nProgeny,
  useOptContrib = FALSE,
  nCandOptCont = NULL,
  targetEffPopSize = NULL,
  useCurrentPhenoTrain = TRUE,
  nCyclesToKeepRecords,
  selCritPipeAdv,
  selCritPopImprov,
  nChr,
  effPopSize,
  segSites,
  nQTL,
  nSNP,
  genVar,
  gxeVar,
  meanDD,
  varDD
)

Arguments

schemeDF	data.frame columns: stageNames, nReps, nLocs, nChks, nEntries, entryToChkRatio, errVars
nParents	integer number of parents to cross
nCrosses	integer how many crosses to make
nProgeny	integer how many progeny per cross
useOptContrib	logical whether to use optimal contributions
nCandOptCont	integer how many candidates to consider for opt contrib
targetEffPopSize	numeric target effective population size for OC
useCurrentPhenoTrain	logical whether to use phenotypes for parent sel
nCyclesToKeepRecords	integer eliminate data on cycles above this num
selCritPipeAdv	function used to determine selection criterion for pipe
selCritPopImprov	function used to determine sel crit for pop improv
nChr	integer number of chromosomes for the species
effPopSize	numeric historic effective population size for the species
segSites	integer number of sites segregating per chromosome
nQTL	integer number of loci affecting the trait per chromosome
nSNP	integer number of observed SNPs per chromosome
genVar	numeric genetic variance of the founders
gxeVar	numeric genotype by environment variance of the founders
meanDD	numeric mean dominance deviation. Set to zero for additive
varDD	numeric variance across loci of their dominance deviation

Details

All arguments are exactly as specified in the control files. Main exception is schemeDF, which is just a tibble() or data.frame version of the set of bsp arguments which are vectors (giving values for each breeding stage). Columns must have names exactly as in the corresponding arguments in control file: stageNames, nReps, nLocs, nChks, nEntries, entryToChkRatio, errVars

Value

a named list of of the parameters to specify a breeding scheme simulation

Examples

schemeDF <- tibble(stageNames=c("SDN", "CET", "PYT"),
                 nReps=c(1, 1, 2),
                 nLocs=c(1, 1, 2),
                 nChks=c(1, 1, 2),
                 nEntries=c(100, 50, 20),
                 entryToChkRatio=c(50, 20, 10),
                 errVars=c(150,75,40))
bsp <- specifyBSP(schemeDF,nParents = 10, nCrosses = 10, nProgeny = 10,
                useOptContrib = FALSE,
                useCurrentPhenoTrain = TRUE,
                nCyclesToKeepRecords = 1,
                selCritPipeAdv = selCritGRM,
                selCritPopImprov = selCritGRM,
                nChr = 2,effPopSize = 50,
                segSites = 100, nQTL = 5, nSNP = 10,
                genVar = 50, gxeVar = 0, meanDD = 0.05, varDD = 0.25)
test <- runBreedingScheme(replication = 1,nCycles = 1,
                        initializeFunc = initFuncADChk,
                        productPipeline = prodPipeFncChk,
                        populationImprovement = popImprov1Cyc,
                        bsp = bsp)

jeanlucj/AlfSimHlpR documentation built on Nov. 7, 2021, 5:10 p.m.