optiSel: Optimum Contribution Selection and Population Genetics
Version 0.9

A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.

AuthorRobin Wellmann
Date of publication2017-05-24 10:14:36 UTC
MaintainerRobin Wellmann <r.wellmann@uni-hohenheim.de>
LicenseGPL-2
Version0.9
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("optiSel")

Getting started

Package overview
1. Pedigree-based Evaluations"
2. Marker-based Evaluations"
3. Optimum Contribution Selection"

Popular man pages

completeness: Calculates Pedigree Completeness
conttac: Calculates *Cont*ributions *T*o *A*ge *C*ohorts
kinlist: Combines Kinship Matrices into a List
opticont4mb: Calculates Optimum Contributions of Selection Candidates...
segIBDatN: Calculates Segment Based Kinship at Native Alleles.
sim2dis: Converts a Similarity Matrix into a Dissimilarity Matrix
summary.Pedig: Calculates Summary Statistics for Pedigrees.
See all...

All man pages Function index File listing

Man pages

Cattle: Phenotypes of Genotyped Cattle
Chr1.phased: Phased Cattle Genotypes from Chromosome 1
Chr2.phased: Phased Cattle Genotypes from Chromosome 2
completeness: Calculates Pedigree Completeness
conttac: Calculates *Cont*ributions *T*o *A*ge *C*ohorts
ExamplePed: Pedigree of Hinterwald Cattle
freqlist: Combines Objects Computed with Function haplofreq() into a...
genecont: Calculates Genetic Contributions using Pedigrees.
haplofreq: Evaluates the Occurrence of Haplotype Segments in Particular...
help.opticont: Displays Available Objective Functions and Constraints for...
help.opticont4mb: Displays Available Objective Functions and Constraints for...
Kin: A list of class kinMatrices containing kinship matrices
kinlist: Combines Kinship Matrices into a List
kinwac: Calculates Kinships With Age Cohorts
makeA: Calculates the Pedigree-based Additive Relationship Matrix
map: Marker Map for Cattle
matings: Mate Allocation
noffspring: Calculates Optimum Numbers of Offspring
opticomp: Calculates the Optimum Breed Composition
opticont: Calculates Optimum Contributions of Selection Candidates
opticont4mb: Calculates Optimum Contributions of Selection Candidates...
optiSel-package: Optimum Contribution Selection and Population Genetics
pedBreedComp: Calculates the Pedigree Based Breed Composition of...
pedIBD: Calculates the Pedigree-based Kinship Matrix
pedIBDatN: Calculates the Pedigree Based Kinship at Native Alleles
pedIBDorM: Calculates Kinships taking Allele Origin into Account
PedigWithErrors: Pedigree of Hinterwald cattle
pedInbreeding: Calculates Pedigree Based Inbreeding
pedplot: Plots a Pedigree
Phen: Simulated Phenotypes of Hinterwald Cattle
plot.HaploFreq: Plots Frequencies of Haplotype Segments in Specified Breeds
prePed: *Pre*pares a *Ped*igree
read.indiv: Reads Individual IDs from a Genotype File
sampleIndiv: Sample Individuals from Pedigree
segBreedComp: Calculates the Segment Based Breed Composition of Individuals
segIBD: Calculates the Segment Based Kinship Matrix
segIBDandN: Calculates Probabilities that Alleles belong to a Shared...
segIBDatN: Calculates Segment Based Kinship at Native Alleles.
segInbreeding: Calculates Segment Based Inbreeding
segN: Calculates Probabilities of Alleles to belong to Native...
sim2dis: Converts a Similarity Matrix into a Dissimilarity Matrix
subPed: Creates a Subset of a Large Pedigree
summary.kinMatrices: Calculates Genetic Parameters for Age Cohorts
summary.opticont: Summary Statistics and Check of Validity for Optimum...
summary.Pedig: Calculates Summary Statistics for Pedigrees.

Functions

Cattle Man page
Chr1.phased Man page
Chr2.phased Man page
ExamplePed Man page
Kin Man page
PedigWithErrors Man page
Phen Man page
completeness Man page
conttac Man page
freqlist Man page
genecont Man page
haplofreq Man page
help.opticont Man page
help.opticont4mb Man page
kinlist Man page
kinwac Man page
makeA Man page Source code
map Man page
matings Man page
nativeNe Source code
noffspring Man page Source code
onAttach Source code
optiSel Man page
optiSel-package Man page
opticomp Man page
opticont Man page
opticont4mb Man page
pedBreedComp Man page
pedIBD Man page
pedIBDatN Man page
pedIBDorM Man page
pedInbreeding Man page
pedplot Man page
plot.HaploFreq Man page
prePed Man page
rcpp_completeness Source code
rcpp_genecont Source code
rcpp_haplofreq Source code
rcpp_makeA Source code
rcpp_makeA_lowMem Source code
rcpp_nativecont Source code
rcpp_segBreedComp Source code
rcpp_segIBD Source code
rcpp_segIBDandN Source code
rcpp_segIBDandNVersion2 Source code
rcpp_segInbreeding Source code
rcpp_segN Source code
read.indiv Man page
sampleIndiv Man page
segBreedComp Man page
segIBD Man page
segIBDandN Man page
segIBDatN Man page
segInbreeding Man page
segN Man page
sim2dis Man page
subPed Man page
summary.Pedig Man page
summary.kinMatrices Man page
summary.opticont Man page

Files

inst
inst/extdata
inst/extdata/Chr2.phased
inst/extdata/Chr1.phased
inst/doc
inst/doc/seg-vignette.Rmd
inst/doc/ped-vignette.Rmd
inst/doc/ocs-vignette.html
inst/doc/seg-vignette.R
inst/doc/ocs-vignette.R
inst/doc/ocs-vignette.Rmd
inst/doc/ped-vignette_files
inst/doc/ped-vignette_files/figure-html
inst/doc/ped-vignette_files/figure-html/unnamed-chunk-4-1.png
inst/doc/ped-vignette_files/figure-html/unnamed-chunk-7-1.png
inst/doc/ped-vignette.html
inst/doc/seg-vignette.html
inst/doc/ped-vignette.R
src
src/rcpp_genecont.cpp
src/Makevars
src/rcpp_segIBD.cpp
src/rcpp_segIBDandN.cpp
src/rcpp_segInbreeding.cpp
src/rcpp_makeA.cpp
src/rcpp_makeA_lowMem.cpp
src/rcpp_haplofreq.cpp
src/rcpp_segBreedComp.cpp
src/rcpp_completeness.cpp
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/rcpp_nativecont.cpp
src/rcpp_segN.cpp
src/rcpp_segIBDandNVersion2.cpp
NAMESPACE
data
data/PedigWithErrors.rda
data/map.rda
data/ExamplePed.rda
data/Phen.rda
data/Kin.rda
data/Cattle.rda
R
R/opticomp.R
R/segInbreeding.R
R/matings.R
R/getNe.R
R/pedBreedComp.R
R/pedIBDatN.R
R/segIBDatN.R
R/segN.R
R/summary.opticont.R
R/onAttach.R
R/freqlist.R
R/segBreedComp.R
R/genecontALT.R
R/pedIBD.R
R/help.opticont.R
R/sampleIndiv.R
R/pedplot.R
R/segIBD.R
R/help.opticont4mb.R
R/opticont.R
R/summary.kinMatrices.R
R/read.indiv.R
R/opticont4mb.R
R/kinlist.R
R/RcppExports.R
R/genecont.R
R/kinwac.R
R/pedInbreeding.R
R/opticontx.R
R/getskip.R
R/plot.HaploFreq.R
R/prePed.R
R/pedIBDorM.R
R/subPed.R
R/sim2dis.R
R/noffspring.R
R/getcskip.R
R/completeness.R
R/makeA.R
R/summary.Pedig.R
R/haplofreq.R
R/segIBDandN.R
R/conttac.R
vignettes
vignettes/seg-vignette.Rmd
vignettes/ped-vignette.Rmd
vignettes/ocs-vignette.Rmd
vignettes/HaplotypeEval
vignettes/HaplotypeEval/freq.Angler.Chr1.in.others.txt
vignettes/HaplotypeEval/freq.Angler.Chr2.in.others.txt
vignettes/HaplotypeEval/match.Angler.Chr2.in.others.txt
vignettes/HaplotypeEval/match.Angler.Chr1.in.others.txt
vignettes/references.bib
MD5
build
build/vignette.rds
build/partial.rdb
DESCRIPTION
man
man/pedBreedComp.Rd
man/subPed.Rd
man/kinlist.Rd
man/map.Rd
man/opticont.Rd
man/makeA.Rd
man/noffspring.Rd
man/pedIBDorM.Rd
man/Chr2.phased.Rd
man/segIBDatN.Rd
man/genecont.Rd
man/Chr1.phased.Rd
man/Cattle.Rd
man/plot.HaploFreq.Rd
man/segIBDandN.Rd
man/optiSel-package.Rd
man/pedIBD.Rd
man/sampleIndiv.Rd
man/Phen.Rd
man/help.opticont4mb.Rd
man/PedigWithErrors.Rd
man/segBreedComp.Rd
man/opticomp.Rd
man/freqlist.Rd
man/segInbreeding.Rd
man/pedIBDatN.Rd
man/prePed.Rd
man/summary.opticont.Rd
man/ExamplePed.Rd
man/segN.Rd
man/Kin.Rd
man/conttac.Rd
man/read.indiv.Rd
man/sim2dis.Rd
man/completeness.Rd
man/matings.Rd
man/haplofreq.Rd
man/segIBD.Rd
man/pedplot.Rd
man/help.opticont.Rd
man/pedInbreeding.Rd
man/summary.Pedig.Rd
man/summary.kinMatrices.Rd
man/opticont4mb.Rd
man/kinwac.Rd
optiSel documentation built on May 24, 2017, 5:01 p.m.

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