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optiSel  

Optimum Contribution Selection and Population Genetics
View on CRAN: Click here


Download and install optiSel package within the R console
Install from CRAN:
install.packages("optiSel")

Install from Github:
library("remotes")
install_github("cran/optiSel")

Install by package version:
library("remotes")
install_version("optiSel", "2.0.9")



Attach the package and use:
library("optiSel")
Maintained by
Robin Wellmann
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-06-27
Latest Update: 2023-05-08
Description:
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.
How to cite:
Robin Wellmann (2016). optiSel: Optimum Contribution Selection and Population Genetics. R package version 2.0.9, https://cran.r-project.org/web/packages/optiSel. Accessed 03 Feb. 2025.
Previous versions and publish date:
0.1 (2016-06-27 17:22), 0.3 (2017-02-23 17:31), 0.5 (2017-03-23 15:56), 0.6.1 (2017-03-30 13:28), 0.6.2 (2017-03-31 12:03), 0.7.1 (2017-04-15 08:36), 0.7 (2017-04-06 15:25), 0.8.1 (2017-04-24 20:42), 0.8 (2017-04-24 14:18), 0.9.1 (2017-05-26 09:26), 0.9 (2017-05-24 12:14), 1.0.0 (2017-08-15 14:18), 2.0.1 (2018-06-28 12:35), 2.0.2 (2018-08-24 14:20), 2.0.3 (2020-03-12 12:20), 2.0.5 (2021-01-12 15:20), 2.0.6 (2023-01-27 18:10), 2.0.7 (2023-05-08 12:40), 2.0.8 (2024-06-12 13:00), 2.0 (2017-12-15 18:24)
Other packages that cited optiSel R package
View optiSel citation profile
Other R packages that optiSel depends, imports, suggests or enhances
Complete documentation for optiSel
Functions, R codes and Examples using the optiSel R package
Some associated functions: Cattle . Chr1.phased . Chr2.phased . ExamplePed . PedigWithErrors . Phen . agecont . candes . completeness . conttac . freqlist . genecont . haplofreq . makeA . map . matings . noffspring . optiSel-package . opticomp . opticont . pedBreedComp . pedIBD . pedIBDatN . pedIBDorM . pedInbreeding . pedplot . plot.HaploFreq . prePed . read.indiv . sampleIndiv . segBreedComp . segIBD . segIBDandN . segIBDatN . segInbreeding . segN . sim2dis . subPed . summary.Pedig . summary.candes . 
Some associated R codes: NPOdata.R . NPOpopALT.R . RcppExports.R . addClasses.R . addContributions.R . agecont.R . bc4candes.R . bounds4cand.R . candes.R . characterizeBreeds.R . characterizeClasses.R . checkbc.R . checkcon.R . checkcont.R . checkphen.R . completeness.R . con2df.R . conttac.R . extractKinships.R . f4cand.R . freqlist.R . fun4Kin.R . fun4KinatN.R . genecont.R . genecontALT.R . getNe.R . getcskip.R . getskip.R . gettraits.R . haplofreq.R . lc4cand.R . makeA.R . matings.R . meankin.R . noffspring.R . onAttach.R . opticomp.R . opticont.R . pPOpop.R . param4candes.R . pedBreedComp.R . pedIBD.R . pedIBDatN.R . pedIBDorM.R . pedInbreeding.R . pedplot.R . plot.HaploFreq.R . prePed.R . printParam4candes.R . qcrc4cand.R . read.indiv.R . sampleIndiv.R . segBreedComp.R . segIBD.R . segIBDandN.R . segIBDatN.R . segInbreeding.R . segN.R . sim2dis.R . subPed.R . summary.Pedig.R . summary.candes.R . summary4opticont.R .  Full optiSel package functions and examples
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