add.diversity: Add additional diverse material to a population

In MoBPS: Modular Breeding Program Simulator

Add additional diverse material to a population

Description

Function to simulate and add additional diverse material to a population

Usage

add.diversity(
  population,
  breeding.size = 100,
  selection.rate = 0.5,
  pool.gen = NULL,
  pool.database = NULL,
  pool.cohorts = NULL,
  target.gen = NULL,
  target.database = NULL,
  target.cohorts = NULL,
  target.value = NULL,
  reduction.multiplier = 5,
  name.cohort = NULL,
  sex.quota = NULL,
  add.gen = 1,
  target.direction = NULL,
  verbose = TRUE,
  store.comp.times = TRUE,
  use.recalculate.manual = FALSE,
  pop1 = NULL,
  export.pop1 = FALSE
)

Arguments

population	Population list
breeding.size	Number of individuals to generate (default: 100)
selection.rate	Proportion of individuals to select in each breeding cycle (default: 0.5)
pool.gen	Generations of individuals to consider as founder pool to start from (default: NULL)
pool.database	Groups of individuals to consider as founder pool to start from (default: NULL)
pool.cohorts	Cohorts of individuals to consider as founder pool to start from (default: NULL)
target.gen	Generations of individuals to consider to calculate target genomic value to get to (default: NULL)
target.database	Groups of individuals to consider to calculate target genomic value to get to (default: NULL)
target.cohorts	Cohorts of individuals to consider to calculate target genomic value to get to (default: NULL)
target.value	Target genomic value to get (default: NULL - calculated based on target.gen/database/cohorts)
reduction.multiplier	Traits that already exceed the target are bred against. Weighting is scaled by this factor.
name.cohort	Name of the newly added cohort
sex.quota	Share of newly added female individuals (default: 0.5)
add.gen	Generation you want to add the new individuals to (default: 1)
target.direction	Manual select with traits are supposed to increase / decrease (1 target high, -1 target low)
verbose	Set to FALSE to not display any prints
store.comp.times	If TRUE store computation times in $info$comp.times.general (default: TRUE)
use.recalculate.manual	Set to TRUE to use recalculate.manual to calculate genomic values (all individuals and traits jointly, default: FALSE)
pop1	Population to start with as founder pool (default: NULL - generation from pool.gen/database/cohorts)
export.pop1	Default: FALSE. Exporting this is helpful if add.diversity is used frequently to avoid initializing this multiple times

Value

population list with newly added individuals

Examples

data(ex_pop)
population <- add.diversity(ex_pop, pool.gen  = 1, target.gen = 5)

MoBPS documentation built on Nov. 5, 2025, 6:26 p.m.