R Observatory: Metrics for AlphaSimR version 2.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AlphaSimR

2.1.0Package record

Breeding Program Simulations

2packages dependsuggested by 1

23Kdownloads / year

24.8%test coverage

13/13flavors OK

Overview

About

Maintained by Chris GaynorCRAN page ↗GitHub ↗Website ↗

The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) doi:10.3835/plantgenome2016.02.0013]. 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) doi:10.1101/gr.083634.108].

Changes in 2.1.0

*changed R6 and methods from Depends to Imports to match current best practices for R packages

*Change order of call to finalizePop in .newPop to allow access to recombination tracking data

*added parentAverage and mendelianSampling functions

*fixed bug in c for RawPop, MapPop, and NamedMapPop

*changed popVar to an R wrapper to automate casting of vectors to matrices

*corrected bibliography entry month from sept to sep

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("AlphaSimR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("gaynorr/AlphaSimR")

Development version from gaynorr/AlphaSimR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-alphasimr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-AlphaSimR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-AlphaSimR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 8.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.0

READMEYes · 185 wordsVignettesYes · 2 · dynamicNEWSYes · 67% structured · mentions 2.1.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 146 (20 internal)includes a package overview page
Examples that run: 97%94 run in a plain check · 3 never run
Exported functions with examples: 86%
Documented parameters: 100%
Return-value docs: 53%
Help pages citing references: 1% with a bibliography file

Vignettes (2)

Introduction HTML
Traits PDF

How these are measured

Downloads

23K

CRAN downloads in the past year

Rank #3,283 · ~63/day · ~1.9K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.5K30 days

3.5K90 days

23K1 year

Compare downloads with other packages →

Also on589 r2u33 autocran71 c2d4u

How downloads are counted

Repository

gaynorr/alphasimr ↗Account: gaynorr

75Stars

31Forks

5Open issues

1Open PRs

13Releases

537Commits

9Commit identities

simulationbreedinggenomicscranrr-package

537 commits · Last activity 2025-11-24 · +2.7% stars, 30d · Discussions: 55 posts

Responsiveness

How these are sampled

PRs merged (all time): 85%
Median days to close, 50 most recently updated closed issues: 886
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2025-10-01 · 552026-10-09 · 75

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/gaynorr/alphasimr on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Issue templates

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-11-24 · The repository has a site deploy workflow

pkgdown site last built 2025-11-24

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing AlphaSimR adds 6 packages (3 with compiled code, 18 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, rbibutils 1.1 MB.

Depends (1)

R >= 4.0.0

Imports (4)

Rcpp RdpackmethodsR6

LinkingTo (3)

Rcpp RcppArmadillo BH

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Depends 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

evola SIMplyBee

Suggests, most downloaded first

FieldSimR

How these are counted

Code & Tests

People & History

People (10)

Chris Gaynor

Author, Maintainer since 0.8.1 (2018)

Ros Craddock

Contributor · added in 2.0.0

Gregor Gorjanc

Contributor

Philip Greenspoon

Contributor · added in 1.5.2

John Hickey

Contributor

Audrey Martin

Contributor · added in 1.4.2

Daniel Money

Contributor

Jana Obsteter

Contributor · added in 2.1.0

Thiago Oliveira

Contributor · added in 1.2

Show 1 more contributorHide 1 contributor

David Wilson

Contributor

Releases (26)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.1.0Latest
record
2025-11-08 · current release · diff ↗ ·
added 2 exports
mendelianSampling, parentAverage
2.0.0
record
2025-09-02 · diff ↗ ·
removed 1 export
transMat

added 1 export
asCategorical
R
R 4.5.0 released · 2025-04-11
1.6.1
record
2024-11-01 · diff ↗
1.6.0
record
2024-08-18 · diff ↗ ·
removed 2 exports
getMisc, setMisc

added 2 exports
meanEBV, varEBV
R
R 4.4.0 released · 2024-04-24
1.5.3
record
2023-12-01 · diff ↗
1.5.2
record
2023-11-01 · diff ↗ ·
removed 2 exports
isMegaPop, newMegaPop

added 2 exports
isMultiPop, newMultiPop
R
R 4.3.0 released · 2023-04-21
1.4.2
record
2023-03-27 · diff ↗
1.3.4
record
2022-12-09 · diff ↗
1.3.2
record
2022-11-02 · diff ↗
1.3.1
record
2022-08-25 · diff ↗ ·
added 11 exports
addSegSite, getGenMap, getPed, isHybridPop, isMapPop, isMegaPop, isNamedMapPop, isPop, isRawPop, newEmptyPop, setMarkerHaplo
1.2.1
record
2022-07-06 · diff ↗
1.2
record
2022-06-16 · diff ↗ ·
added 10 exports
getMisc, importGenMap, importHaplo, importInbredGeno, isFemale, isMale, pullMarkerGeno, pullMarkerHaplo, setMisc, transMat

Show 19 earlier eventsHide 19 earlier events

R
R 4.2.0 released · 2022-04-22
1.1.2
record
2022-02-17 · diff ↗ ·
added 10 exports
getNumThreads, solveMKM, solveMVM, solveRRBLUP, solveRRBLUPMK, solveRRBLUPMV, solveRRBLUP_EM, solveRRBLUP_EM2, solveRRBLUP_EM3, solveUVM
1.0.4
record
2021-09-08 · diff ↗
1.0.3
record
2021-07-29 · diff ↗
1.0.2
record
2021-07-28 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.1
record
2021-05-14 · diff ↗ ·
added 3 exports
attrition, newMegaPop, setPhenoProgTest
0.13.0
record
2020-10-11 · diff ↗
0.12.2
record
2020-05-19 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.12.1
record
2020-03-30 · diff ↗ ·
added 1 export
mergeGenome
0.11.1
record
2020-01-13 · diff ↗ ·
removed 2 exports
pullMultipleSnpGeno, pullMultipleSnpHaplo

added 3 exports
cChr, doubleGenome, reduceGenome
0.11.0
record
2019-10-11 · diff ↗ ·
added 2 exports
RRBLUP_SCA2, mutate
R
R 3.6.0 released · 2019-04-26
0.10.0
record
2019-03-15 · diff ↗ ·
removed 1 export
trackHaploPop

added 7 exports
RRBLUP_D2, aa, fastRRBLUP, genicVarAA, getQtlMap, getSnpMap, varAA
0.9.0
record
2019-02-07 · diff ↗ ·
added 1 export
RRBLUP_GCA2
0.8.2
record
2018-10-15 · diff ↗
0.8.1
record
2018-10-12
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-12
Total releases: 26 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 511 KB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("AlphaSimR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/g3journal/jkaa017, 10.1002/csc2.21312.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for AlphaSimR version 2.1.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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