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AlphaSimR  

Breeding Program Simulations
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("AlphaSimR", "1.6.1")



Attach the package and use:
library("AlphaSimR")
Maintained by
Chris Gaynor
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-10-12
Latest Update: 2023-03-27
Description:
The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) ]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) ].
How to cite:
Chris Gaynor (2018). AlphaSimR: Breeding Program Simulations. R package version 1.6.1, https://cran.r-project.org/web/packages/AlphaSimR. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.8.1 (2018-10-12 15:10), 0.8.2 (2018-10-15 20:20), 0.9.0 (2019-02-07 17:23), 0.10.0 (2019-03-15 16:33), 0.11.0 (2019-10-11 17:00), 0.11.1 (2020-01-13 19:10), 0.12.1 (2020-03-30 11:10), 0.12.2 (2020-05-19 11:30), 0.13.0 (2020-10-11 06:20), 1.0.1 (2021-05-14 18:52), 1.0.2 (2021-07-28 17:20), 1.0.3 (2021-07-29 15:30), 1.0.4 (2021-09-08 17:50), 1.1.2 (2022-02-17 18:32), 1.2.1 (2022-07-06 00:30), 1.2 (2022-06-16 00:50), 1.3.1 (2022-08-25 16:52), 1.3.2 (2022-11-02 15:53), 1.3.4 (2022-12-09 14:00), 1.4.2 (2023-03-27 17:40), 1.5.2 (2023-11-01 04:20), 1.5.3 (2023-12-01 22:00), 1.6.0 (2024-08-18 00:20)
Other packages that cited AlphaSimR R package
View AlphaSimR citation profile
Other R packages that AlphaSimR depends, imports, suggests or enhances
Complete documentation for AlphaSimR
Functions, R codes and Examples using the AlphaSimR R package
Some associated functions: AlphaSimR-package . HybridPop-class . LociMap-class . MapPop-class . MegaPop-class . MultiPop-class . NamedMapPop-class . Pop-class . RRBLUP . RRBLUP2 . RRBLUPMemUse . RRBLUP_D . RRBLUP_D2 . RRBLUP_GCA . RRBLUP_GCA2 . RRBLUP_SCA . RRBLUP_SCA2 . RRsol-class . RawPop-class . SimParam . TraitA-class . TraitA2-class . TraitA2D-class . TraitAD-class . TraitADE-class . TraitADEG-class . TraitADG-class . TraitAE-class . TraitAEG-class . TraitAG-class . aa . addSegSite . attrition . bv . cChr . calcGCA . dd . dot-newPop . doubleGenome . ebv . editGenome . editGenomeTopQtl . fastRRBLUP . genParam . genicVarA . genicVarAA . genicVarD . genicVarG . getGenMap . getMisc . getNumThreads . getPed . getQtlMap . getSnpMap . gv . hybridCross . importGenMap . importHaplo . importInbredGeno . isFemale . isPop . makeCross . makeCross2 . makeDH . meanG . meanP . mergeGenome . mergePops . mutate . nInd . newEmptyPop . newMapPop . newMegaPop . newMultiPop . newPop . pedigreeCross . pheno . popVar . pullIbdHaplo . pullMarkerGeno . pullMarkerHaplo . pullQtlGeno . pullQtlHaplo . pullSegSiteGeno . pullSegSiteHaplo . pullSnpGeno . pullSnpHaplo . quickHaplo . randCross . randCross2 . reduceGenome . resetPop . runMacs . runMacs2 . sampleHaplo . selIndex . selInt . selectCross . selectFam . selectInd . selectOP . selectWithinFam . self . setEBV . setMarkerHaplo . setMisc . setPheno . setPhenoGCA . setPhenoProgTest . smithHazel . solveMKM . solveMVM . solveRRBLUP . solveRRBLUPMK . solveRRBLUPMV . solveRRBLUP_EM . solveRRBLUP_EM2 . solveRRBLUP_EM3 . solveUVM . transMat . usefulness . varA . varAA . varD . varG . varP . writePlink . writeRecords . 
Some associated R codes: AlphaSimR.R . Class-HybridPop.R . Class-LociMap.R . Class-Pop.R . Class-RRsol.R . Class-SimParam.R . GS.R . RcppExports.R . crossing.R . founderPop.R . hybrids.R . importData.R . mergePops.R . misc.R . phenotypes.R . polyploids.R . popSummary.R . pullGeno.R . selection.R . writePlink.R . writeRecords.R .  Full AlphaSimR package functions and examples
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