SimParam: Simulation parameters

Description

Container for global simulation parameters. Saving this object as SP will allow it to be accessed by function defaults.

Usage

SimParam

Arguments

Format

An object of class R6ClassGenerator of length 24.

Fields

nChr: number of chromosomes

nTraits

number of traits

nSnpChips

number of SNP chips

segSites

segregating sites per chromosome

gender

is gender used for mating

genMap

"matrix" of chromosome genetic maps

femaleMap

"matrix" of chromosome genetic maps for females

maleMap

"matrix" of chromosome genetic maps for males

sepMap

are there seperate genetic maps for males and females

femaleCentromere

position of centromere on female genetic map

maleCentromere

position of centromere on male genetic map

recombRatio

ratio of genetic recombination in females relative to male

traits

list of trait

snpChips

list of SNP chips

potQtl

list of potential QTL segregating sites

potSnp

list of potential SNP segregating sites

lastId

last ID number assigned

isTrackPed

is pedigree being tracked

pedigree

pedigree matrix for all individuals

isTrackRec

is recombination being tracked

recHist

list of historic recombination events

varA

additive genetic variance in founderPop

varG

total genetic variance in founderPop

varE

default error variance

founderPop

the founder population used for scaling traits

quadProb

the probability of quadrivalent formation

nThreads

number of threads used on platforms with OpenMP support

version

the version of AlphaSimR used to generate this object