# Data Simulation for Life Science and Breeding

## Documentation for package ‘simer’ version 0.9.0.4

- DESCRIPTION file.

## Help Pages

annotation | Annotation simulation
build.cov | Correlation building
cal.eff | QTN genetic effects
checkEnv | Environmental factor checking
generate.map | Marker information
generate.pop | Population generator
geno.cvt1 | Genotype code convertor 1
geno.cvt2 | Genotype code convertor 2
genotype | Genotype simulation
getfam | Family index and within-family index
GxG.network | Genetic interaction network
IndPerGen | Individual number per generation
logging.initialize | Logging initialization
logging.log | Logging
logging.print | Logging printer
mate | Mate
mate.2waycro | Two-way cross
mate.3waycro | Three-way cross
mate.4waycro | Four-way cross process
mate.assort | Assortative mating
mate.backcro | Back cross
mate.clone | Clone
mate.dh | Doubled haploid
mate.disassort | Disassortative mating
mate.randexself | Random mating excluding self-pollination
mate.randmate | Random mating
mate.selfpol | Self-pollination
mate.userped | User-specified pedigree mating
param.annot | Annotation parameters generator
param.geno | Genotype parameters generator
param.global | Global parameters generator
param.pheno | Phenotype parameters generator
param.reprod | Reproduction parameters generator
param.sel | Selection parameters generator
param.simer | Parameter generator
phenotype | Phenotype simulation
pop.geno | Raw genotype matrix from outside in simdata
pop.map | Map file from outside in simdata
remove_bigmatrix | Big.matrix removing
reproduces | Reproduction
selects | Selection
simer | Simer
simer.Data | Data handling
simer.Data.Bfile2MVP | simer.Data.Bfile2MVP: To transform plink binary data to MVP package
simer.Data.cHIBLUP | Genetic evaluation
simer.Data.Env | Environmental factor selection
simer.Data.Geno | Genotype data quality control
simer.Data.Impute | Genotype data imputation
simer.Data.Json | Data quality control
simer.Data.Kin | simer.Data.EMMA: To construct EMMA kinship matrix
simer.Data.Map | simer.Data.Map: To check map file
simer.Data.MVP2Bfile | simer.Data.MVP2Bfile: To transform MVP data to binary format
simer.Data.MVP2MVP | Genotype data conversion
simer.Data.Ped | Pedigree data quality control
simer.Data.Pheno | Phenotype data quality control
simer.Data.SELIND | Selection index construction
simer.Version | Simer version
write.file | File writing