simer.Data.Env: Environmental factor selection

In simer: Data Simulation for Life Science and Breeding

Environmental factor selection

Description

To find appropriate fixed effects, covariates, and random effects.

Usage

simer.Data.Env(
  jsonList = NULL,
  hiblupPath = "",
  header = TRUE,
  sep = "\t",
  ncpus = 10,
  verbose = TRUE
)

Arguments

jsonList	the list of environmental factor selection parameters.
hiblupPath	the path of HIBLUP software.
header	the header of file.
sep	the separator of file.
ncpus	the number of threads used, if NULL, (logical core number - 1) is automatically used.
verbose	whether to print detail.

Details

Build date: July 17, 2021 Last update: Apr 28, 2022

Value

the function returns a list containing

$genotype

the path of genotype data.

$pedigree

the filename of pedigree data.

$selection_index

the selection index for all traits.

$breeding_value_index

the breeding value index for all traits.

$quality_control_plan

a list of parameters for data quality control.

$breeding_plan

a list of parameters for genetic evaluation.

Author(s)

Dong Yin

Examples

# Read JSON file
jsonFile <- system.file("extdata", "04breeding_plan", "plan1.json", package = "simer")
jsonList <- jsonlite::fromJSON(txt = jsonFile, simplifyVector = FALSE)

## Not run: 
# It needs "hiblup" solfware
jsonList <- simer.Data.Env(jsonList = jsonList)

## End(Not run)

simer documentation built on April 3, 2025, 9:24 p.m.