simer.Data.Env {simer}

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)