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SIMER

Data Simulation for Life Science and Breeding

Authors:

Design and Maintenance: Dong Yin, Xuanning Zhang, Lilin Yin ,Haohao Zhang, and Xiaolei Liu.
Contributors: Zhenshuang Tang, Jingya Xu, Xiaohui Yuan, Xiang Zhou, Xinyun Li, and Shuhong Zhao.

If you have any bug reports or questions, please feed back :point_right:here:point_left:.

:toolbox: Relevant software tools for genetic analyses and genomic breeding

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Version

Install

install.packages('simer')

Monthly Downloads

225

Version

1.0.0

License

Apache License 2.0

Issues

3

Pull Requests

0

Stars

37

Forks

10

Maintainer

Xiaolei Liu

Last Published

February 26th, 2025

Functions in simer (1.0.0)

mate.3waycro

Three-way cross
mate.assort

Assortative mating
mate

Mate
mate.4waycro

Four-way cross process
logging.print

Logging printer
mate.randmate

Random mating
logging.initialize

Logging initialization
mate.randexself

Random mating excluding self-pollination
logging.log

Logging
mate.backcro

Back cross
param.annot

Annotation parameters generator
mate.clone

Clone
mate.selfpol

Self-pollination
mate.userped

User-specified pedigree mating
mkl_env

MKL environment
mate.dh

Doubled haploid
param.sel

Selection parameters generator
param.simer

Parameter generator
pop.geno

Raw genotype matrix from outside in simdata
pop.map

Map file from outside in simdata
print_accomplished

Accomplishment
print_info

Simer information
param.pheno

Phenotype parameters generator
param.reprod

Reproduction parameters generator
paste_label

Pasting label
phenotype

Phenotype simulation
mate.disassort

Disassortative mating
selects

Selection
simer.Version

Simer version
simer.Data.Json

Data quality control
simer.Data.Impute

Genotype data imputation
simer

Simer
simer.Data.Map

simer.Data.Map: To check map file
simer.Data.Ped

Pedigree data quality control
simer.Data.Geno

Genotype data quality control
simer.Data.Env

Environmental factor selection
print_bar

Progress bar
simer.Data.Pheno

Phenotype data quality control
simer.Data

Data handling
simer.Data.Bfile2MVP

simer.Data.Bfile2MVP: To transform plink binary data to MVP package
simer.Data.SELIND

Selection index construction
genotype

Genotype simulation
param.geno

Genotype parameters generator
reproduces

Reproduction
getfam

Family index and within-family index
simer.Data.cHIBLUP

Genetic evaluation
remove_bigmatrix

Big.matrix removing
param.global

Global parameters generator
rule_wrap

Accomplishment
simer.Data.MVP2Bfile

simer.Data.MVP2Bfile: To transform MVP data to binary format
simer.Data.MVP2MVP

Genotype data conversion
write.file

File writing
build.cov

Correlation building
bigt

Genotype transportor
generate.map

Marker information
format_time

Time formating
annotation

Annotation simulation
GxG.network

Genetic interaction network
cal.eff

QTN genetic effects
checkEnv

Environmental factor checking
generate.pop

Population generator
IndPerGen

Individual number per generation
geno.cvt1

Genotype code convertor 1
mate.2waycro

Two-way cross
make_line

Line making
load_if_installed

Installation checking
geno.cvt2

Genotype code convertor 2