Package: MoBPS 1.6.64

MoBPS: Modular Breeding Program Simulator

Framework for the simulation framework for the simulation of complex breeding programs and compare their economic and genetic impact. The package is also used as the background simulator for our a web-based interface <http:www.mobps.de>. Associated publication: Pook et al. (2020) <doi:10.1534/g3.120.401193>.

Authors:Torsten Pook

MoBPS_1.6.64.tar.gz
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MoBPS.pdf |MoBPS.html✨
MoBPS/json (API)

# Install 'MoBPS' in R:
install.packages('MoBPS', repos = c('https://tpook92.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.34 score 44 scripts 216 downloads 5 mentions 87 exports 0 dependencies

Last updated 3 years agofrom:c2aeedfcba. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winWARNINGNov 16 2024
R-4.5-linuxWARNINGNov 16 2024
R-4.4-winWARNINGNov 16 2024
R-4.4-macWARNINGNov 16 2024
R-4.3-winWARNINGNov 16 2024
R-4.3-macWARNINGNov 16 2024

Exports:add.arrayadd.combiadd.diagadd.founder.kinshipanalyze.bvanalyze.populationbreeding.diploidbreeding.internbv.developmentbv.development.boxbv.standardizationcalculate.bvcheck.parentsclean.upcodeOriginsRcombine.traitscompute.costscompute.costs.cohortscompute.snpscreating.diploidcreating.phenotypic.transformcreating.traitdecodeOriginsRdemiraculixderive.loop.elementsdiag.mobpseffect.estimate.addfounder.simulationget.admixtureget.age.pointget.bvget.bveget.classget.cohortsget.creating.typeget.cullingtimeget.databaseget.death.pointget.dendrogramget.dendrogram.heatmapget.dendrogram.traitget.distanceget.effect.freqget.effective.sizeget.genoget.genotypedget.genotyped.snpget.haploget.idget.individual.locget.infosget.mapget.nphenoget.pcaget.pedigreeget.pedigree2get.pedigree3get.pedmapget.phenoget.pheno.offget.pheno.off.countget.phylogenetic.treeget.qtlget.qtl.effectsget.qtl.varianceget.recombiget.reliabilitiesget.selectionbveget.selectionindexget.time.pointget.vcfgroup.diffinsert.bvejson.simulationkinship.developmentkinship.empkinship.emp.fastkinship.expld.decaymiraculixmutation.intronew.base.generationpedigree.simulationset.classset.defaultsortdvlist

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Add a genotyping arrayadd.array
Add a trait as a linear combination of other traitsadd.combi
Add something to the diagonaladd.diag
Add a relationship matrix for founder individualsadd.founder.kinship
Moore-Penrose-Transfomrationalpha_to_beta
Analyze genomic valuesanalyze.bv
Analyze allele frequency of a single markeranalyze.population
Decoding of bitwise-storing in Rbit.snps
Bitwise-storing in Rbit.storing
Breeding functionbreeding.diploid
Internal function to simulate one meiosisbreeding.intern
Development of genetic/breeding valuebv.development
Development of genetic/breeding value using a boxplotbv.development.box
BV standardizationbv.standardization
Calculate breeding valuescalculate.bv
Cattle chipcattle_chip
Relatedness check between two individualscheck.parents
chicken chipchicken_chip
Clean-up recombination pointsclean.up
Origins-coding(R)codeOriginsR
Combine traitscombine.traits
Compute costs of a breeding programcompute.costs
Compute costs of a breeding program by cohortscompute.costs.cohorts
Compute genotype/haplotypecompute.snps
Compute genotype/haplotype in gene editing applicationcompute.snps_single
Generation of the starting populationcreating.diploid
Create a phenotypic transformationcreating.phenotypic.transform
Generation of genomic traitscreating.trait
Origins-Decoding(R)decodeOriginsR
Remove miraculix-coding for genotypesdemiraculix
Derive loop elementsderive.loop.elements
Add a genotyping arraydiag.mobps
Detection of parental/child nodesedges.fromto
Internal gene editing functionedit_animal
Estimation of marker effectseffect.estimate.add
Estimate effective population sizeeffective.size
Martini-Test functionepi
ex_jsonex_json
ex_popex_pop
Position detection (chromosome)find.chromo
Position detection (SNPs)find.snpbefore
Founder simulationfounder.simulation
Function to generate a new individualgeneration.individual
Admixture Plotget.admixture
Derive age pointget.age.point
Export underlying true breeding valuesget.bv
Export estimated breeding valuesget.bve
Derive classget.class
Export Cohort-namesget.cohorts
Derive creating typeget.creating.type
Derive time of cullingget.cullingtime
gen/database/cohorts conversionget.database
Derive death pointget.death.point
Dendrogramget.dendrogram
Dendrogram Heatmapget.dendrogram.heatmap
Dendrogramget.dendrogram.trait
Calculate Nei distance between two or more populationget.distance
Compute marker frequency in QTL-markersget.effect.freq
Estimate effective population sizeget.effective.size
Derive genotypes of selected individualsget.geno
Derive genotyping statusget.genotyped
Derive which markers are genotyped of selected individualsget.genotyped.snp
Derive haplotypes of selected individualsget.haplo
Derive ID on an individualget.id
Export location of individuals from the population listget.individual.loc
Extract bv/pheno/geno of selected individualsget.infos
Map generationget.map
Export underlying number of observations per phenotypeget.npheno
Principle components analysisget.pca
Derive pedigreeget.pedigree
Derive pedigree including grandparentsget.pedigree2
Derive pedigree parents and grandparentsget.pedigree3
Generate plink-file (pedmap)get.pedmap
Export underlying phenotypesget.pheno
Export underlying offspring phenotypesget.pheno.off
Export underlying number of used offspring for offspring phenotypesget.pheno.off.count
Phylogenetic Treeget.phylogenetic.tree
QTL extractionget.qtl
QTL effect extractionget.qtl.effects
QTL effect variance extractionget.qtl.variance
Derive genetic originsget.recombi
Export underlying reliabilitiesget.reliabilities
Export derived breeding values based on the selection indexget.selectionbve
Export underlying last used selection indexget.selectionindex
Derive time pointget.time.point
Generate vcf-fileget.vcf
Function to exclude individuals from a databasegroup.diff
Manually enter estimated breeding valuesinsert.bve
Simulation of a breeding program based on a JSON-file from MoBPSwebjson.simulation
Devolopment of genetic/breeding valuekinship.development
Empirical kinshipkinship.emp
Approximate empirical kinshipkinship.emp.fast
Derive expected kinshipkinship.exp
Generate LD plotld.decay
maize chipmaize_chip
Miesenberger Indexmiesenberger.index
Add miraculix-coding for genotypesmiraculix
Mutation intromutation.intro
Set new base generationnew.base.generation
Optimal genetic contributionOGC
Simulation of a given pedigreepedigree.simulation
Internal function to perform imputing/phasingpedmap.to.phasedbeaglevcf
pig chippig_chip
Plot Populationplot.population
Export estimated breeding valuesset.class
Set defaultsset.default
sheep chipsheep_chip
Apply sort and uniquesortd
Single Step GBLUPssGBLUP
Summary Populationsummary.population
Generation of a sublistvlist