MoBPS (version 1.13.1)

add.diversity: 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
)

Value

population list with newly added individuals

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

Examples

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