# Modular Breeding Program Simulator

## Documentation for package ‘MoBPS’ version 1.13.1

- DESCRIPTION file.

## Help Pages

A B C D E F G I J K L M N O P R S V W

## -- A --

add.array | Add a genotyping array
add.combi | Add a trait as a linear combination of other traits
add.diag | Add something to the diagonal
add.diversity | Add additional diverse material to a population
add.fixed.effects | Add fixed effects to traits
add.founder.kinship | Add a relationship matrix for founder individuals
alpha_to_beta | Moore-Penrose-Transfomration
analyze.bv | Analyze genomic values
analyze.population | Analyze allele frequency of a single marker

## -- B --

bit.snps | Decoding of bitwise-storing in R
bit.storing | Bitwise-storing in R
breeding.diploid | Breeding function
breeding.intern | Internal function to simulate one meiosis
breeding.intern1 | Internal function to simulate one meiosis
breeding.intern2 | Internal function to simulate one meiosis
breeding.intern3 | Internal function to simulate one meiosis
breeding.intern4 | Internal function to simulate one meiosis
breeding.intern5 | Internal function to simulate one meiosis
breeding.intern6 | Internal function to simulate one meiosis
breeding.intern7 | Internal function to simulate one meiosis
breeding.intern8 | Internal function to simulate one meiosis
bv.development | Development of genetic/breeding value
bv.development.box | Development of genetic/breeding value using a boxplot
bv.standardization | BV standardization

## -- C --

calculate.bv | Calculate breeding values
cattle_chip | Cattle chip
check.parents | Relatedness check between two individuals
chicken_chip | chicken chip
clean.up | Clean-up recombination points
codeOriginsR | Origins-coding(R)
combine.traits | Combine traits
computing.costs | Compute costs of a breeding program
computing.costs.cohorts | Compute costs of a breeding program by cohorts
computing.snps | Compute genotype/haplotype
computing.snps_single | Compute genotype/haplotype in gene editing application
creating.diploid | Generation of the starting population
creating.phenotypic.transform | Create a phenotypic transformation
creating.trait | Generation of genomic traits

## -- D --

decodeOriginsR | Origins-Decoding(R)
demiraculix | Remove miraculix-coding for genotypes
derive.loop.elements | Derive loop elements
diag.mobps | Diagonal matrix

## -- E --

edges.fromto | Detection of parental/child nodes
edit_animal | Internal gene editing function
effect.estimate.add | Estimation of marker effects
effective.size | Estimate effective population size
epi | Martini-Test function
exist.cohort | Function to extract if a cohort exists
ex_json | ex_json
ex_pop | ex_pop

## -- F --

find.chromo | Position detection (chromosome)
find.snpbefore | Position detection (SNPs)
founder.simulation | Founder simulation

## -- G --

generation.individual | Function to generate a new individual
get.admixture | Admixture Plot
get.age.point | Derive age point
get.allele.freq | Calculate allele frequencies
get.bv | Export underlying true breeding values
get.bve | Export estimated breeding values
get.class | Derive class
get.cohorts | Export Cohort-names
get.cohorts.individual | Derive ID on an individual
get.computing.time | Derive computing time
get.creating.type | Derive creating type
get.culling.time | Derive culling time
get.culling.type | Derive culling type
get.cullingtime | Derive time of culling
get.database | gen/database/cohorts conversion
get.death.point | Derive death point
get.dendrogram | Dendrogram
get.dendrogram.heatmap | Dendrogram Heatmap
get.dendrogram.trait | Dendrogram
get.distance | Calculate Nei distance between two or more population
get.effect.freq | Compute marker frequency in QTL-markers
get.effective.size | Estimate effective population size
get.fixed.effects.p | Export parametrization of fixed effects
get.geno | Derive genotypes of selected individuals
get.geno.time | Derive genotyping timepoint
get.genotyped | Derive genotyping status
get.genotyped.snp | Derive which markers are genotyped of selected individuals
get.haplo | Derive haplotypes of selected individuals
get.id | Derive ID on an individual
get.index | Putting together indices for GxE / multi trait
get.infos | Extract bv/pheno/geno of selected individuals
get.is.first | First copy
get.is.last | Last copy
get.litter | Export litter
get.litter.effect | Export litter effect
get.maf | Calculate minor allele frequencies
get.map | Map generation
get.ngen | Number of generations
get.nindi | Number of individuals
get.npheno | Export underlying number of observations per phenotype
get.ntrait | Number of traits
get.pca | Principle components analysis
get.pedigree | Derive pedigree
get.pedigree.visual | Draw pedigree
get.pedigree2 | Derive pedigree including grandparents
get.pedigree3 | Derive pedigree parents and grandparents
get.pedigree_old | Derive pedigree
get.pedmap | Generate plink-file (pedmap)
get.pen | Export pen ID
get.pen.effect | Export pen-effects
get.pheno | Export underlying phenotypes
get.pheno.off | Export underlying offspring phenotypes
get.pheno.off.count | Export underlying number of used offspring for offspring phenotypes
get.pheno.single | Export underlying phenotypes
get.pheno.time | Derive phenotyping time point
get.phylogenetic.tree | Phylogenetic Tree
get.plink | Generate binary plink-file
get.pool | Export founder pool
get.pool.founder | Derive founder pool
get.qtl | QTL extraction
get.qtl.effects | QTL effect extraction
get.qtl.variance | QTL effect variance extraction
get.recombi | Derive genetic origins
get.reliability | Export underlying reliabilities
get.selectionbve | Export derived breeding values based on the selection index
get.selectionindex | Export underlying last used selection index
get.sex | Extraction of individual sex
get.size | Number of individuals in each generation
get.snapshot | Derive snapshot of selected individuals
get.snapshot.single | Derive snapshot of selected individuals
get.time.point | Derive time point of generation
get.trafo.p | Export parametrization of fixed effects
get.trafo.p.single | Export parametrization of fixed effects
get.trait.name | Name of traits
get.uhat | Export estimated SNP effects
get.variance | Derive variances components (add/dom)
get.variance.components | Derive variance components
get.vcf | Generate vcf-file
group.diff | Exclude individuals from a database

## -- I --

inbreeding.emp | Empirical kinship
inbreeding.exp | Expected inbreeding
insert.bv | Manually enter breeding values
insert.bve | Manually enter estimated breeding values
insert.pheno | Manually enter phenotypes
insert.pheno.single | Manually enter phenotypes

## -- J --

json.simulation | Simulation of a breeding program based on a JSON-file from MoBPSweb

## -- K --

kinship.development | Development of genetic/breeding value
kinship.emp | Empirical kinship
kinship.emp.fast | Approximate empirical kinship
kinship.emp.fast.between | Approximate empirical kinship
kinship.exp | Derive expected kinship

## -- L --

ld.decay | Generate LD plot

## -- M --

maize_chip | maize chip
matrix.posdef | Projection positive definite
merging.cohorts | Merging of cohorts
merging.trait | Generation of genomic traits
miesenberger.index | Miesenberger Index
miraculix | Add miraculix-coding for genotypes
mutation.intro | Mutation intro

## -- N --

new.base.generation | Set new base generation

## -- O --

OGC | Optimal genetic contribution
ogc.mobps | Breeding function
optimize.cores | Optimize generation cores

## -- P --

pedigree.matrix | Derive pedigree relationship matrix
pedigree.simulation | Simulation of a given pedigree
pedmap.to.phasedbeaglevcf | Internal function to perform imputing/phasing
pig_chip | pig chip
plot.population | Plot Population

## -- R --

recalculate.bv | Recalculate genomic values
recalculate.manual | Recalculate genomic values
recombination.function.haldane | Haldane recombination function
renaming.cohort | Rename a cohort
rowMedian | Row-wise Median

## -- S --

scaling.relationship | scaling.relationship
set.age.point | Set age points
set.class | Set class
set.default | Set defaults
set.mean.pool | Set differences between founder pool
set.time.point | Set time point
sheep_chip | sheep chip
sortd | Apply sort and unique
ssGBLUP | Single Step GBLUP
summary.population | Summary Population

## -- V --

vlist | Generation of a sublist

## -- W --

write.pedigree | write.pedigree.mixblup