MoBPS (version 1.13.1)

json.simulation: Simulation of a breeding program based on a JSON-file from MoBPSweb

Description

Function to simulate a breeding program based on a JSON-file from MoBPSweb

Usage

json.simulation(
  file = NULL,
  log = NULL,
  total = NULL,
  fast.mode = FALSE,
  progress.bars = FALSE,
  size.scaling = NULL,
  rep.max = 1,
  verbose = TRUE,
  miraculix.cores = NULL,
  miraculix.chol = NULL,
  skip.population = FALSE,
  time.check = FALSE,
  time.max = 7200,
  export.population = FALSE,
  export.gen = NULL,
  export.timepoint = NULL,
  export.cor = FALSE,
  fixed.generation.order = NULL,
  generation.cores = NULL,
  manual.select.check = FALSE
)

Value

Population-list

Arguments

file

Path to a json-file generated by the user-interface

log

Provide Path where to write a log-file of your simulation (or false to not write a log-file)

total

Json-file imported via jsonlite::read_json

fast.mode

Set to TRUE work on a small genome with few markers

progress.bars

Set to TRUE to display progress bars

size.scaling

Scale the size of nodes by this factor (especially for testing smaller examples)

rep.max

Maximum number of repeats to use in fast.mode

verbose

Set to FALSE to not display any prints

miraculix.cores

Number of cores used in miraculix applications (default: 1)

miraculix.chol

Set to FALSE to manually deactive the use of miraculix for any cholesky decompostion even though miraculix is active

skip.population

Set to TRUE to not execute breeding actions (only cost/time estimation will be performed)

time.check

Set to TRUE to automatically check simulation run-time before executing breeding actions

time.max

Maximum length of the simulation in seconds when time.check is active

export.population

Path were to export the population to (at state selected in export.gen/timepoint)

export.gen

Last generation to simulate before exporting population to file

export.timepoint

Last timepoint to simulate before exporting population to file

export.cor

Set TRUE to export correlation matrices

fixed.generation.order

Vector containing the order of cohorts to generate (Advanced // Testing Parameter!)

generation.cores

Number of cores used for the generation of new individuals (This will only be active when generating more than 500 individuals)

manual.select.check

Set to FALSE to not automatically remove cohorts from Manual select with they lead to an invalid breeding scheme

Examples

data(ex_json)
population <- json.simulation(total=ex_json)