Process Generations for Pedigree Simulation

This function iterates through generations in a pedigree simulation, assigning IDs, creating data frames, determining sexes, and managing pairing within each generation.

Usage

buildWithinGenerations(
  beta = FALSE,
  sizeGens,
  marR,
  sexR,
  Ngen,
  verbose = FALSE,
  personID = "ID",
  momID = "momID",
  dadID = "dadID",
  code_male = "M",
  code_female = "F",
  fam_shift = 1L
)

Arguments

beta

logical or character. Controls which algorithm version to use:

• FALSE, "base", or "original" (default): Use the original algorithm. Slower but ensures exact reproducibility with set.seed().

• TRUE or "optimized": Use the optimized algorithm with 4-5x speedup. Produces statistically equivalent results but not identical to base version due to different random number consumption. Recommended for large simulations where speed matters more than exact reproducibility.

Note: Both versions are mathematically correct and produce valid pedigrees with the same statistical properties (sex ratios, mating rates, etc.). The optimized version uses vectorized operations instead of loops, making it much faster for large pedigrees.

sizeGens

A numeric vector containing the sizes of each generation within the pedigree.

marR

Mating rate. A numeric value ranging from 0 to 1 which determines the proportion of mated (fertilized) couples in the pedigree within each generation. For instance, marR = 0.5 suggests 50 percent of the offspring in a specific generation will be mated and have their offspring.

sexR

Sex ratio of offspring. A numeric value ranging from 0 to 1 that determines the proportion of males in all offspring in this pedigree. For instance, 0.4 means 40 percent of the offspring will be male.

Ngen

Number of generations. An integer >= 2 that determines how many generations the simulated pedigree will have. The first generation is always a fertilized couple. The last generation has no mated individuals.

verbose

logical If TRUE, message progress through stages of algorithm

personID

character. Name of the column in ped for the person ID variable

momID

character. Name of the column in ped for the mother ID variable

dadID

character. Name of the column in ped for the father ID variable

code_male

The value to use for males. Default is "M"

code_female

The value to use for females. Default is "F"

fam_shift

An integer to shift the person ID. Default is 1L. This is useful when simulating multiple pedigrees to avoid ID conflicts.

Value

A data frame representing the simulated pedigree, including columns for family ID (`fam`),