simcross (version 0.6)

sim_do_pedigree_fix_n: Simulate a pedigree for Diversity Outbreds for a target sample size

Description

Simulate a pedigree for Diversity Outbred (DO) mice (a table of individual, mom, dad, sex) so that the last generation reaches a desired sample size.

Usage

sim_do_pedigree_fix_n(
  ngen = 12,
  nkids_per = 5,
  nccgen = 15,
  nsample_ngen = 150,
  npairs = NULL,
  method = c("last2", "sub2", "fixcc"),
  design = c("nosib", "random"),
  selc.method = c("byfamily", "byindiv")
)

Value

A data frame with six columns: individual ID, mother ID, father ID, sex, generation, and TRUE/FALSE indicator for whether DO or pre-DO. Founders have 0 for mother and father ID. Sex is coded 0 for female and 1 for male.

Arguments

ngen

Number of generations of outbreeding

nkids_per

Number of offspring per pair for the last generation

nccgen

The number of generations for each CC line, only used when method is not "fixcc".

nsample_ngen

Number of individuals desired at the last generation

npairs

Number of breeding pairs at each generation. If missing, we use 30 when method="last2" and 300 when method="sub2".

method

Method used to generate the pedigree: either expand at the last two generations or generate a pedigree with a large number of pairs and then select a subset to have the desired sample size. With method="fixcc", we use the pre-CC generations as performed at the Jackson Lab.

design

How to choose crosses: either random but avoiding siblings, or completely at random

selc.method

Method used to select the individuals from last generation.

Details

The default number of breeding pairs depends on the chosen method. With method="last2", the default is npairs=30; with method="sub2", the default is npairs=300; with method="fixcc", npairs is ignored and is fixed at 144.

See Also

sim_from_pedigree(), sim_ril_pedigree(), sim_ail_pedigree(), sim_do_pedigree(), sim_4way_pedigree(), sim_ail_pedigree_fix_n()

Examples

tab <- sim_do_pedigree_fix_n(8)