Package: optiSel 2.0.9

Robin Wellmann

optiSel: Optimum Contribution Selection and Population Genetics

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. The methods are described in:\n Wellmann, R., and Pfeiffer, I. (2009) <doi:10.1017/S0016672309000202>.\n Wellmann, R., and Bennewitz, J. (2011) <doi:10.2527/jas.2010-3709>.\n Wellmann, R., Hartwig, S., Bennewitz, J. (2012) <doi:10.1186/1297-9686-44-34>.\n de Cara, M. A. R., Villanueva, B., Toro, M. A., Fernandez, J. (2013) <doi:10.1111/mec.12560>.\n Wellmann, R., Bennewitz, J., Meuwissen, T.H.E. (2014) <doi:10.1017/S0016672314000196>.\n Wellmann, R. (2019) <doi:10.1186/s12859-018-2450-5>.

Authors:Robin Wellmann [aut, cre]

optiSel_2.0.9.tar.gz
optiSel_2.0.9.tar.gz(r-4.5-noble)optiSel_2.0.9.tar.gz(r-4.4-noble)
optiSel_2.0.9.tgz(r-4.4-emscripten)optiSel_2.0.9.tgz(r-4.3-emscripten)
optiSel.pdf |optiSel.html
optiSel/json (API)

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • Cattle - Phenotypes of Genotyped Cattle
  • ExamplePed - Pedigree of Hinterwald Cattle
  • PedigWithErrors - Pedigree of Hinterwald cattle
  • Phen - Simulated Phenotypes of Hinterwald Cattle
  • map - Marker Map for Cattle

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

cpp

4.31 score 49 scripts 705 downloads 7 mentions 31 exports 63 dependencies

Last updated 5 months agofrom:23d81e8cdf. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-linux-x86_64OKDec 06 2024

Exports:agecontcandescompletenessconttacfreqlistgeneconthaplofreqmakeAmatingsnoffspringopticompopticontpedBreedComppedIBDpedIBDatNpedIBDorMpedInbreedingpedplotprePedread.indivsampleIndivsegBreedCompsegIBDsegIBDandNsegIBDatNsegInbreedingsegNsim2dissubPedsummary.candessummary.Pedig

Dependencies:abindalabamabase64encbslibcachemcccpclicodetoolsdata.tabledigestdoParallelECOSolveRevaluatefastmapfontawesomeforeachfsglueHaploSimhighrhtmltoolshtmlwidgetsiteratorsjquerylibjsonlitekinship2knitrlatticelifecyclemagicmagrittrMASSMatrixmemoisemimeminpack.lmnadivnloptrnumDerivoptiSolvepedigreeplyrpsplinepurrrquadprogR6rappdirsRcppRcppArmadilloreshapereshape2rglrlangrmarkdownsassscatterplot3dshapesstringistringrtinytexvctrsxfunyaml

Pedigree-based Evaluations

Rendered fromped-vignette.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-06-13
Started: 2017-03-23

Marker-based Evaluations

Rendered fromseg-vignette.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2017-12-15
Started: 2017-03-23

Optimum Contribution Selection

Rendered fromocs-vignette.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2020-03-12
Started: 2017-03-23

Readme and manuals

Help Manual

Help pageTopics
Optimum Contribution Selection and Population GeneticsoptiSel-package optiSel
Contributions of age cohorts to the populationagecont
Candidate Descriptioncandes
Phenotypes of Genotyped CattleCattle
Phased Cattle Genotypes from Chromosome 1Chr1.phased
Phased Cattle Genotypes from Chromosome 2Chr2.phased
Calculates Pedigree Completenesscompleteness
Calculates *Cont*ributions *T*o *A*ge *C*ohortsconttac
Pedigree of Hinterwald CattleExamplePed
Combines Objects Computed with Function haplofreq() into a Listfreqlist
Calculates Genetic Contributions using Pedigrees.genecont
Evaluates the Occurrence of Haplotype Segments in Particular Breedshaplofreq
Calculates the Pedigree-based Additive Relationship MatrixmakeA
Marker Map for Cattlemap
Mate Allocationmatings
Calculates Optimum Numbers of Offspringnoffspring
Calculates the Optimum Breed Compositionopticomp
Optimum Contributions of Selection Candidatesopticont
Calculates the Pedigree Based Breed Composition of IndividualspedBreedComp
Calculates the Pedigree-based Kinship MatrixpedIBD
Calculates the Pedigree Based Kinship at Native AllelespedIBDatN
Calculates Kinships taking Allele Origin into AccountpedIBDorM
Pedigree of Hinterwald cattlePedigWithErrors
Calculates Pedigree Based InbreedingpedInbreeding
Plots a Pedigreepedplot
Simulated Phenotypes of Hinterwald CattlePhen
Plots Frequencies of Haplotype Segments in Specified Breedsplot.HaploFreq
*Pre*pares a *Ped*igreeprePed
Reads Individual IDs from a Genotype Fileread.indiv
Sample Individuals from PedigreesampleIndiv
Calculates the Segment-Based Breed Composition of IndividualssegBreedComp
Calculates the Segment Based Kinship MatrixsegIBD
Calculates Probabilities that Alleles belong to a Shared Native SegmentsegIBDandN
Segment-Based Kinship at Native Alleles.segIBDatN
Calculates Segment Based InbreedingsegInbreeding
Calculates Probabilities of Alleles to belong to Native SegmentssegN
Converts a Similarity Matrix into a Dissimilarity Matrixsim2dis
Creates a Subset of a Large PedigreesubPed
Population Genetic Parameters at Different Timessummary.candes
Calculates Summary Statistics for Pedigrees.summary.Pedig