freqbasedsim_AlleleSample: Simulate Multi-Generational Hybrids - Proportional Sampling,...

In bwringe/hybriddetective: Automates the process of detecting hybrids from genetic data

Simulate Multi-Generational Hybrids - Proportional Sampling, Alleles Sampled Without Replacement

Description

freqbasedsim_AlleleSample generates simulated, centred Pure1, Pure2, F1, F2, BC1 and BC2 offspring based on the genotype frequencies of two ancestral populations provided by sampling alleles without replacement. Centred Pure1 and Pure2 created by sampling a proportion of indivduals that comprise the known reference samples. Alleles are sampled without replacement

Usage

freqbasedsim_AlleleSample(GPD, pop.groups = c("PopA", "PopB"),
  outputName = NULL, NumSims = 1, NumReps = 1, prop.sample = 0.9,
  sample.sizePure1 = NULL, sample.sizePure2 = NULL, sample.sizeF1 = NULL,
  sample.sizeF2 = NULL, sample.sizeBC1 = NULL, sample.sizeBC2 = NULL)

Arguments

GPD	file path to a GenePop formatted file containing genotypes from two (2) ancestral populations. This is the data from which the simulated hybrids will be constructed
pop.groups	Optional character vector denoting how the two ancestral populations should be named. The default is "PopA" and "PopB"
outputName	an optional character vector to be applied as the name of the output. The default is NULL, in which case the output name is constructed from the name of the input, with the suffix _SiRj_NH added where i is the number of simulations corresponding to the output, and j is the number of replicates of the ith simulation. NH refers to the fact that the output is in NewHybrids format
NumSims	an integer number of simulated datasets to be created. The default is 1
NumReps	an integer number of replicates of each of the NumSims simulated dataset to be created. The default is 1
prop.sample	The proportion of individuals in both ancestral PopA and PopB to sample to create the simulated, centred Pure1 and Pure2. The default is 0.9
sample.sizePure1	An optional integer to specify the number of simulated Pure1 individuals (centred ancestral PopA) to be output when the desired number is less than the number of individuals in Ancestral Population 1 * prop.sample. The default is NULL, where the number output = number of individuals in Ancestral Population 1 * prop.sample. If a number greater than number of individuals in Ancestral Population 1 * prop.sample is requested, the number of individuals in Ancestral Population 1 * prop.sample are output.
sample.sizePure2	An optional integer to specify the number of specify the number of simulated Pure2 individuals (centred ancestral PopB) to be output when the desired number is less than the number of individuals in Ancestral Population 2 * prop.sample. The default is NULL, where the number output = number of individuals in Ancestral Population 2 * prop.sample. If a number greater than number of individuals in Ancestral Population 2 * prop.sample is requested, the number of individuals in Ancestral Population 2 * prop.sample are output.
sample.sizeF1	An optional integer to specify the number of simulated F1 individuals to be output when the desired number of simulated F1 individuals is less than (number of individuals in Ancestral PopA + number of individuals in Ancestral PopB) * prop.sample. The default is NULL where the number returned = (number of individuals in Ancestral PopA + number of individuals in Ancestral PopB) * prop.sample. Unless sample.sizeF1 is explicitly stated, even when sample.sizePure1 and sample.sizePure2 are specified, the number of simulated F1 individuals returned will be equal to (number of individuals in Ancestral PopA + number of individuals in Ancestral PopB) * prop.sample.
sample.sizeF2	An optional integer to specify the number of simulated F2 individuals to be output when the desired number of simulated F2 individuals is less than (number of individuals in Ancestral PopA + number of individuals in Ancestral PopB) * prop.sample. The default is NULL where the number returned = (number of individuals in Ancestral PopA + number of individuals in Ancestral PopB) * prop.sample. Unless sample.sizeF2 is explicitly stated, even when sample.sizePure1 and sample.sizePure2 are specified, the number of simulated F2 individuals returned will be equal to (number of individuals in Ancestral PopA + number of individuals in Ancestral PopB) * prop.sample.
sample.sizeBC1	An optional integer to specify the number of simulated BC1 (PopA X F1) individuals to be output when the desired number of simulated BC1 individuals is less than the number of individuals in Ancestral PopA * prop.sample. The default is NULL where the number returned = number of individuals in Ancestral PopA * prop.sample. Unless sample.sizeBC1 is explicitly stated, even when sample.sizePure1 and sample.sizeF1 are specified, the number of simulated BC1 individuals returned will be equal to number of individuals in Ancestral PopA * prop.sample.
sample.sizeBC2	An optional integer to specify the number of simulated BC2 (PopB X F1) individuals to be output when the desired number of simulated BC2 individuals is less than the number of individuals in Ancestral PopB * prop.sample. The default is NULL where the number returned = number of individuals in Ancestral PopB * prop.sample. Unless sample.sizeBC2 is explicitly stated, even when sample.sizePure2 and sample.sizeF1 are specified, the number of simulated BC2 individuals returned will be equal to number of individuals in Ancestral PopB * prop.sample.

bwringe/hybriddetective documentation built on March 22, 2023, 6:52 a.m.