BreedingSchemeLanguage (version 0.9.6)

defineSpecies: Define and create species

Description

Define and create species

Usage

defineSpecies(loadData = NULL, importFounderHap = NULL,
  saveDataFileName = NULL, nSim = 1, nCore = 1, nChr = 7,
  lengthChr = 150, effPopSize = 100, nMarkers = 1000, nQTL = 50,
  propDomi = 0, nEpiLoci = 0, domModel = "HetHom")

Arguments

loadData

if null create a new species (default), else the file name of previously created species like "species1_1" (Do not put "RData" extension). A path can be specified, like "simDirectory/species1_1" (in which case "simDirectory" must exist).

importFounderHap

if null create new founder haplotypes (default), else the file name of externally sourced founder haplotypes in hapmap format (see Manual). If founder haplotypes are loaded, the `nMarkers` parameter is superseded by the number of loci in those haplotypes.

saveDataFileName

if not NULL, the name to save the species data, like "species1_1". A path can be specified, like "simDirectory/species1_1" (in which case "simDirectory" must exist). Default: NULL

nSim

the number of simulation trials

nCore

simulation processed in parallel over this number of CPUs (Check computer capacity before setting above 1.)

nChr

the number of chromosomes

lengthChr

the length of each chromosome (cM. all chromosomes are the same length)

effPopSize

the effective population size in the base population

nMarkers

the number of markers, which is used especially for genomic selection

nQTL

the number of QTLs controlling the target trait

propDomi

the probability of dominant QTL among the all QTL

nEpiLoci

the expected number of epistatic loci for each effect

domModel

the dominance model: "HetHom" means homozygotes have equal effect but opposite to that of heterozygotes, "Partial": zero means ancestral dominant over derived, one means derived dominant over ancestral, any value in between means partial dominance. At the moment, functionality for the "Partial" option is only available when using ImportFounderHap.

Value

An environment that contains a list sims with each object of the list being one replicate to initiate a simulation

Examples

# NOT RUN {
if (exists("simEnv")){
rm(list=names(simEnv), envir=simEnv)
rm(simEnv)
}
simEnv <- defineSpecies(nSim=2, nChr=5, lengthChr=100, effPopSize=20, nMarkers=100, nQTL=10)
initializePopulation(nInd=50) # popID 0 created
phenotype()
select(nSelect=20) # popID 1 selected out of popID 0
cross() # popID 2 created
phenotype(nRep=2)
select(nSelect=5) # popID 3 selected out of popID 2
cross() # popID 4 created
plotData()

# }