Package: simer 0.9.0.5

Xiaolei Liu

simer: Data Simulation for Life Science and Breeding

Data simulator including genotype, phenotype, pedigree, selection and reproduction in R. It simulates most of reproduction process of animals or plants and provides data for GS (Genomic Selection), GWAS (Genome-Wide Association Study), and Breeding. For ADI model, please see Kao C and Zeng Z (2002) <doi:10.1093/genetics/160.3.1243>. For build.cov, please see B. D. Ripley (1987) <ISBN:9780470009604>.

Authors:Dong Yin [aut], Xuanning Zhang [aut], Lilin Yin [aut], Haohao Zhang [aut], Zhenshuang Tang [aut], Jingya Xu [aut], Xiaohui Yuan [aut], Xiang Zhou [aut], Xinyun Li [aut], Shuhong Zhao [aut], Xiaolei Liu [cre, aut, cph]

simer_0.9.0.5.tar.gz
simer_0.9.0.5.tar.gz(r-4.5-noble)simer_0.9.0.5.tar.gz(r-4.4-noble)
simer.pdf |simer.html✨
simer/json (API)

# Install 'simer' in R:
install.packages('simer', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/xiaolei-lab/simer/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • pop.geno - Raw genotype matrix from outside in simdata
  • pop.map - Map file from outside in simdata

cppopenmp

1.70 score 2 scripts 172 downloads 57 exports 11 dependencies

Last updated 3 months agofrom:9248cd005a. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 30 2024
R-4.5-linux-x86_64OKDec 30 2024

Exports:annotationbuild.covcal.effcheckEnvformat_timegenerate.mapgenerate.popgeno.cvt1geno.cvt2genotypegetfamGxG.networkIndPerGenlogging.loglogging.printmatemate.2waycromate.3waycromate.4waycromate.assortmate.backcromate.clonemate.dhmate.disassortmate.randexselfmate.randmatemate.selfpolmate.userpedparam.annotparam.genoparam.globalparam.phenoparam.reprodparam.selparam.simerphenotypeprint_inforemove_bigmatrixreproducesselectssimersimer.Datasimer.Data.Bfile2MVPsimer.Data.cHIBLUPsimer.Data.Envsimer.Data.Genosimer.Data.Imputesimer.Data.Jsonsimer.Data.Kinsimer.Data.Mapsimer.Data.MVP2Bfilesimer.Data.MVP2MVPsimer.Data.Pedsimer.Data.Phenosimer.Data.SELINDsimer.Versionwrite.file

Dependencies:BHbigmemorybigmemory.srijsonlitelatticeMASSMatrixRcppRcppArmadilloRcppProgressuuid

Readme and manuals

Help Manual

Help pageTopics
Annotation simulationannotation
Correlation buildingbuild.cov
QTN genetic effectscal.eff
Environmental factor checkingcheckEnv
Marker informationgenerate.map
Population generatorgenerate.pop
Genotype code convertor 1geno.cvt1
Genotype code convertor 2geno.cvt2
Genotype simulationgenotype
Family index and within-family indexgetfam
Genetic interaction networkGxG.network
Individual number per generationIndPerGen
Logging initializationlogging.initialize
Logginglogging.log
Logging printerlogging.print
Matemate
Two-way crossmate.2waycro
Three-way crossmate.3waycro
Four-way cross processmate.4waycro
Assortative matingmate.assort
Back crossmate.backcro
Clonemate.clone
Doubled haploidmate.dh
Disassortative matingmate.disassort
Random mating excluding self-pollinationmate.randexself
Random matingmate.randmate
Self-pollinationmate.selfpol
User-specified pedigree matingmate.userped
Annotation parameters generatorparam.annot
Genotype parameters generatorparam.geno
Global parameters generatorparam.global
Phenotype parameters generatorparam.pheno
Reproduction parameters generatorparam.reprod
Selection parameters generatorparam.sel
Parameter generatorparam.simer
Phenotype simulationphenotype
Raw genotype matrix from outside in simdatapop.geno
Map file from outside in simdatapop.map
Big.matrix removingremove_bigmatrix
Reproductionreproduces
Selectionselects
Simersimer
Data handlingsimer.Data
simer.Data.Bfile2MVP: To transform plink binary data to MVP packagesimer.Data.Bfile2MVP
Genetic evaluationsimer.Data.cHIBLUP
Environmental factor selectionsimer.Data.Env
Genotype data quality controlsimer.Data.Geno
Genotype data imputationsimer.Data.Impute
Data quality controlsimer.Data.Json
simer.Data.EMMA: To construct EMMA kinship matrixsimer.Data.Kin
simer.Data.Map: To check map filesimer.Data.Map
simer.Data.MVP2Bfile: To transform MVP data to binary formatsimer.Data.MVP2Bfile
Genotype data conversionsimer.Data.MVP2MVP
Pedigree data quality controlsimer.Data.Ped
Phenotype data quality controlsimer.Data.Pheno
Selection index constructionsimer.Data.SELIND
Simer versionsimer.Version
File writingwrite.file