gs_BL: Estimate the average population sizes of a population under...

In hemstrow/GeneArchEst: Estimate Genomic Architecture for Quantitative Traits

Estimate the average population sizes of a population under selection according to Burger and Lynch 1995.

Description

Uses the equations laid out in Burger and Lynch 1995 to estimate the average size of a population overtime as the optimum phenotype changes. While some processes are modeled as stochastic, this returns the mean population sizes over time, and so is not stochastic itself.

Usage

gs_BL(
  phenotypes,
  h,
  K,
  omega,
  B,
  var.theta,
  k,
  gens = Inf,
  n = NULL,
  nloci = NULL,
  alpha = NULL,
  mu = NULL
)

Arguments

phenotypes	numeric. Vector of initial phenotypes.
h	numeric. Heritability of the trait.
K	numeric. Carrying capacity. Individuals surviving selection will be randomly culled to this number.
omega	numeric. Width of the selection function. Smaller numbers equate to stronger selection around the optimum.
B	numeric. Number of offspring each surviving adult has. Not stochastic.
var.theta	numeric. Variance of the stochastic selection optimum.
k	numeric. Degree by which the optimum phenotype increases each generation (where mean(opt) = k*t).
gens	numeric, default Inf. Number of generations to iterate.
n	numeric, default NULL. Initial population size. If null, equal to the number of provided phenotypes.
nloci	numeric, default NULL. Number of effective loci. If nloci, alpha, and mu are all provided, the stochastic house of cards approximation of genetic variance is used to approximate changes in genetic variance each generation based only on changes in effective population size.
alpha	numeric, default NULL. Standard deviation of the effect of new mutations. If nloci, alpha, and mu are all provided, the stochastic house of cards approximation of genetic variance is used to approximate changes in genetic variance each generation based only on changes in effective population size.
mu	numeric, default NULL. Mutation rate. If nloci, alpha, and mu are all provided, the stochastic house of cards approximation of genetic variance is used to approximate changes in genetic variance each generation based only on changes in effective population size.

Details

If nloci, alpha, and mu are all provided, the stochastic house of cards approximation of genetic variance is used to approximate changes in genetic variance each generation based only on changes in effective population size. Otherwise, genetic variance is assumed to not change in each generation and is based solely on the genetic variance calculated from the provided heritability and phenotypes.

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