gs: Simulate selection and population growth

In hemstrow/GeneArchEst: Estimate Genomic Architecture for Quantitative Traits

Simulate selection and population growth

Description

Simulate selection and population growth

Usage

gs(
  genotypes,
  meta,
  phenotypes = NULL,
  BVs = NULL,
  h,
  gens,
  chr.length,
  growth.function = function(n) logistic_growth(n, 500, 2),
  survival.function = function(phenotypes, opt_pheno, ...) BL_survival(phenotypes,
    opt_pheno, omega = 1),
  selection.shift.function = function(opt, iv) optimum_constant_slide(opt, iv, 0.3),
  rec.dist = function(n) rpois(n, lambda = 1),
  var.theta = 0,
  plot_during_progress = FALSE,
  facet = "group",
  do.sexes = TRUE,
  init = FALSE,
  verbose = FALSE,
  print.all.freqs = F,
  model = NULL,
  K_thin_post_surv = NULL
)

Arguments

genotypes	unphased matrix of genotypes, one row per snp and one column per chromosome/gene copy. Copies from individuals must be sequential.
meta	data.frame of snp metadata, with the first column containing chromosome info, the second containing position in base pairs, and the third, named "effects" optionally containing effect sizes.
chr.length	numeric vector of chromosome lengths in the same order as would be given by unique(meta[,1]).

hemstrow/GeneArchEst documentation built on June 10, 2025, 5:06 a.m.