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MoBPS (version 1.13.1)

Modular Breeding Program Simulator

Description

Framework for the simulation framework for the simulation of complex breeding programs and compare their economic and genetic impact. Associated publication: Pook et al. (2020) .

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Version

Install

install.packages('MoBPS')

Monthly Downloads

350

Version

1.13.1

License

GPL (>= 3)

Maintainer

Torsten Pook

Last Published

October 29th, 2025

Functions in MoBPS (1.13.1)

breeding.intern5

Internal function to simulate one meiosis
breeding.intern

Internal function to simulate one meiosis
breeding.intern2

Internal function to simulate one meiosis
bit.storing

Bitwise-storing in R
breeding.intern6

Internal function to simulate one meiosis
bit.snps

Decoding of bitwise-storing in R
breeding.intern1

Internal function to simulate one meiosis
breeding.diploid

Breeding function
breeding.intern4

Internal function to simulate one meiosis
breeding.intern3

Internal function to simulate one meiosis
bv.development

Development of genetic/breeding value
clean.up

Clean-up recombination points
chicken_chip

chicken chip
breeding.intern7

Internal function to simulate one meiosis
creating.trait

Generation of genomic traits
bv.development.box

Development of genetic/breeding value using a boxplot
breeding.intern8

Internal function to simulate one meiosis
decodeOriginsR

Origins-Decoding(R)
creating.diploid

Generation of the starting population
bv.standardization

BV standardization
effective.size

Estimate effective population size
creating.phenotypic.transform

Create a phenotypic transformation
diag.mobps

Diagonal matrix
demiraculix

Remove miraculix-coding for genotypes
find.snpbefore

Position detection (SNPs)
derive.loop.elements

Derive loop elements
founder.simulation

Founder simulation
exist.cohort

Function to extract if a cohort exists
epi

Martini-Test function
cattle_chip

Cattle chip
check.parents

Relatedness check between two individuals
get.cohorts

Export Cohort-names
get.class

Derive class
get.fixed.effects.p

Export parametrization of fixed effects
find.chromo

Position detection (chromosome)
get.geno

Derive genotypes of selected individuals
computing.snps

Compute genotype/haplotype
ex_json

ex_json
ex_pop

ex_pop
get.admixture

Admixture Plot
computing.snps_single

Compute genotype/haplotype in gene editing application
generation.individual

Function to generate a new individual
get.creating.type

Derive creating type
get.dendrogram.trait

Dendrogram
get.culling.time

Derive culling time
computing.costs

Compute costs of a breeding program
get.infos

Extract bv/pheno/geno of selected individuals
get.is.first

First copy
get.distance

Calculate Nei distance between two or more population
get.id

Derive ID on an individual
get.index

Putting together indices for GxE / multi trait
combine.traits

Combine traits
codeOriginsR

Origins-coding(R)
get.age.point

Derive age point
calculate.bv

Calculate breeding values
get.map

Map generation
edges.fromto

Detection of parental/child nodes
get.dendrogram

Dendrogram
get.dendrogram.heatmap

Dendrogram Heatmap
get.ngen

Number of generations
get.culling.type

Derive culling type
get.allele.freq

Calculate allele frequencies
get.pedigree

Derive pedigree
get.pheno.off.count

Export underlying number of used offspring for offspring phenotypes
get.pedigree.visual

Draw pedigree
get.pheno.single

Export underlying phenotypes
get.cohorts.individual

Derive ID on an individual
get.computing.time

Derive computing time
get.effect.freq

Compute marker frequency in QTL-markers
get.effective.size

Estimate effective population size
get.qtl.variance

QTL effect variance extraction
get.qtl.effects

QTL effect extraction
get.pen.effect

Export pen-effects
get.pen

Export pen ID
get.is.last

Last copy
get.trafo.p

Export parametrization of fixed effects
get.time.point

Derive time point of generation
get.nindi

Number of individuals
get.pool

Export founder pool
get.plink

Generate binary plink-file
get.haplo

Derive haplotypes of selected individuals
get.cullingtime

Derive time of culling
get.uhat

Export estimated SNP effects
get.variance

Derive variances components (add/dom)
get.genotyped.snp

Derive which markers are genotyped of selected individuals
get.snapshot

Derive snapshot of selected individuals
get.snapshot.single

Derive snapshot of selected individuals
computing.costs.cohorts

Compute costs of a breeding program by cohorts
get.bve

Export estimated breeding values
get.bv

Export underlying true breeding values
get.database

gen/database/cohorts conversion
edit_animal

Internal gene editing function
effect.estimate.add

Estimation of marker effects
get.death.point

Derive death point
insert.bve

Manually enter estimated breeding values
insert.pheno

Manually enter phenotypes
get.pedigree_old

Derive pedigree
get.pedmap

Generate plink-file (pedmap)
get.litter

Export litter
get.pedigree2

Derive pedigree including grandparents
get.pedigree3

Derive pedigree parents and grandparents
insert.bv

Manually enter breeding values
inbreeding.exp

Expected inbreeding
get.pheno

Export underlying phenotypes
get.npheno

Export underlying number of observations per phenotype
maize_chip

maize chip
matrix.posdef

Projection positive definite
kinship.exp

Derive expected kinship
ld.decay

Generate LD plot
get.pheno.off

Export underlying offspring phenotypes
get.genotyped

Derive genotyping status
get.geno.time

Derive genotyping timepoint
get.litter.effect

Export litter effect
get.maf

Calculate minor allele frequencies
get.selectionbve

Export derived breeding values based on the selection index
merging.cohorts

Merging of cohorts
merging.trait

Generation of genomic traits
get.selectionindex

Export underlying last used selection index
get.trait.name

Name of traits
group.diff

Exclude individuals from a database
get.trafo.p.single

Export parametrization of fixed effects
ogc.mobps

Breeding function
optimize.cores

Optimize generation cores
get.qtl

QTL extraction
get.variance.components

Derive variance components
get.pool.founder

Derive founder pool
recalculate.manual

Recalculate genomic values
set.default

Set defaults
set.class

Set class
miesenberger.index

Miesenberger Index
miraculix

Add miraculix-coding for genotypes
recombination.function.haldane

Haldane recombination function
get.ntrait

Number of traits
get.phylogenetic.tree

Phylogenetic Tree
get.recombi

Derive genetic origins
get.pca

Principle components analysis
get.pheno.time

Derive phenotyping time point
get.vcf

Generate vcf-file
summary.population

Summary Population
plot.population

Plot Population
recalculate.bv

Recalculate genomic values
pedmap.to.phasedbeaglevcf

Internal function to perform imputing/phasing
pig_chip

pig chip
ssGBLUP

Single Step GBLUP
inbreeding.emp

Empirical kinship
kinship.emp.fast

Approximate empirical kinship
kinship.emp.fast.between

Approximate empirical kinship
scaling.relationship

scaling.relationship
pedigree.simulation

Simulation of a given pedigree
pedigree.matrix

Derive pedigree relationship matrix
set.age.point

Set age points
get.reliability

Export underlying reliabilities
get.sex

Extraction of individual sex
get.size

Number of individuals in each generation
set.mean.pool

Set differences between founder pool
set.time.point

Set time point
kinship.emp

Empirical kinship
kinship.development

Development of genetic/breeding value
json.simulation

Simulation of a breeding program based on a JSON-file from MoBPSweb
new.base.generation

Set new base generation
insert.pheno.single

Manually enter phenotypes
mutation.intro

Mutation intro
vlist

Generation of a sublist
renaming.cohort

Rename a cohort
write.pedigree

write.pedigree.mixblup
sortd

Apply sort and unique
rowMedian

Row-wise Median
sheep_chip

sheep chip
analyze.bv

Analyze genomic values
analyze.population

Analyze allele frequency of a single marker
add.combi

Add a trait as a linear combination of other traits
alpha_to_beta

Moore-Penrose-Transfomration
add.diag

Add something to the diagonal
add.array

Add a genotyping array
add.founder.kinship

Add a relationship matrix for founder individuals
OGC

Optimal genetic contribution
add.fixed.effects

Add fixed effects to traits
add.diversity

Add additional diverse material to a population