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 |