Other packages > Find by keyword >

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]
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 29 Apr. 2025.
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
Downloads during the last 30 days
03/3003/3104/0104/0204/0304/0404/0504/0604/0704/0804/0904/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/2004/2104/2204/2304/2404/2504/2604/2704/28Downloads for AlphaSimR0102030405060708090100110120130TrendBars

Today's Hot Picks in Authors and Packages

PCAmatchR  
Match Cases to Controls Based on Genotype Principal Components
Matches cases to controls based on genotype principal components (PC). In order to produce better r ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
NBBDesigns  
Neighbour Balanced Block Designs (NBBDesigns)
Neighbour-balanced designs ensure that no treatment is disadvantaged unfairly by its surroundings. T ...
Download / Learn more Package Citations See dependency  
bigGP  
Distributed Gaussian Process Calculations
Distributes Gaussian process calculations across nodes in a distributed memory setting, using Rmpi. ...
Download / Learn more Package Citations See dependency  
knockoff  
The Knockoff Filter for Controlled Variable Selection
The knockoff filter is a general procedure for controlling the false discovery rate (FDR) when perf ...
Download / Learn more Package Citations See dependency  
phecodemap  
Visualization for PheCode Mapping with ICD-9 and ICD-10-CM Codes
To build a shiny app for visualization of the hierarchy of PheCode Mapping with International Classi ...
Download / Learn more Package Citations See dependency  

24,142

R Packages

207,311

Dependencies

65,176

Author Associations

24,143

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA