makeInbreeding: makeInbreeding A function to create inbred mates in the...

In R-Computing-Lab/BGMisc: An R Package for Extended Behavior Genetics Analysis

makeInbreeding A function to create inbred mates in the simulated pedigree data.frame. Inbred mates can be created by specifying their IDs or the generation the inbred mate should be created. When specifying the generation, inbreeding between siblings or 1st cousin needs to be specified. This is a supplementary function for simulatePedigree.

Description

makeInbreeding A function to create inbred mates in the simulated pedigree data.frame. Inbred mates can be created by specifying their IDs or the generation the inbred mate should be created. When specifying the generation, inbreeding between siblings or 1st cousin needs to be specified. This is a supplementary function for simulatePedigree.

Usage

makeInbreeding(
  ped,
  ID_mate1 = NA_integer_,
  ID_mate2 = NA_integer_,
  verbose = FALSE,
  gen_inbred = 2,
  type_inbred = "sib"
)

Arguments

ped	A data.frame in the same format as the output of simulatePedigree.
ID_mate1	A vector of ID of the first mate. If not provided, the function will randomly select two individuals from the second generation.
ID_mate2	A vector of ID of the second mate.
verbose	logical. If TRUE, print progress through stages of algorithm
gen_inbred	A vector of generation of the twin to be imputed.
type_inbred	A character vector indicating the type of inbreeding. "sib" for sibling inbreeding and "cousin" for cousin inbreeding.

Details

This function creates inbred mates in the simulated pedigree data.frame. This function's purpose is to evaluate the effect of inbreeding on model fitting and parameter estimation. In case it needs to be said, we do not condone inbreeding in real life. But we recognize that it is a common practice in some fields to create inbred strains for research purposes.

Value

Returns a data.frame with some inbred mates.

R-Computing-Lab/BGMisc documentation built on April 3, 2025, 3:12 p.m.