AlphaSimR

2.1.0

Breeding Program Simulations

3packages depend

27.6Kdownloads / year

24.8%test coverage

13/13checks pass

Overview

About

Maintained by Chris GaynorFirst published 2018-10-1226 releasesCRAN page ↗GitHub ↗

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].

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.

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).

Health

CRAN checks

13OK

Slowest check: 8.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.05

24.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 185 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 99%
Documented parameters: 100%
Return-value docs: 53%
References docs: 1%

Downloads

27.6K

CRAN downloads in the past year

Rank #3,732 · ~76/day · ~2.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

83330 days

2.8K90 days

27.6K1 year

Compare downloads with other packages →

Also on581 r2u56 autocran26 c2d4u

Repository

GitHub ↗ gaynorr/alphasimr

68Stars

27Forks

45Open issues

2Open PRs

13Releases

537Commits

9Contributors

simulationbreedinggenomicscranrr-package

537 commits · Last activity 2026-07-19 · 0% stars, 30d

Stars over time

2025-06-19 · 492026-07-07 · 68

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/gaynorr/alphasimr on 2026-07-19.

Continuous integration (1)

GitHub Actions

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

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

3direct

0indirect

SIMplyBee evola FieldSimR

Code & Tests

Code Composition

R 13,662 (40%)C++ 9,660 (29%)Rd 8,256 (24%)Vignettes 1,040 (3%)C 971 (3%)Other 217 (1%)

Code characteristics

Object systems

S4 class18S4 method17R61

Cyclomatic complexity: 1.0 median / 25 max
Test cases: 25 / 0.05 per code line

Test coverage

Line coverage

25%

Expression

22.6%

Tests / Examples

24.8% / 48% ex

Functions

463 113 exported

Complexity

4.1 avg / 25 max

Call network

463 nodes / 498 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

463 functions

Function	Cyclo	Coverage
RRBLUP exp	5	0%
RRBLUP2 exp	10	0%
RRBLUPMemUse exp	4	0%
RRBLUP_D exp	3	0%
RRBLUP_D2 exp	13	0%
RRBLUP_GCA exp	3	0%

People & History

People (10)

Maintainer (1)

Chris Gaynor

Author, Maintainer

Authors (1)

Chris Gaynor

Author, Maintainer

Contributors (9)

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 contributors

David Wilson

Contributor

Package Timeline

26 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.1.0Latest
2025-11-08 · current release · diff ↗
2.0.0
2025-09-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.1
2024-11-01 · diff ↗
1.6.0
2024-08-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.5.3
2023-12-01 · diff ↗
1.5.2
2023-11-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.2
2023-03-27 · diff ↗
1.3.4
2022-12-09 · diff ↗
1.3.2
2022-11-02 · diff ↗
1.3.1
2022-08-25 · diff ↗
1.2.1
2022-07-06 · diff ↗
1.2
2022-06-16 · diff ↗

Show 19 earlier events

R
R 4.2.0 released · 2022-04-22
1.1.2
2022-02-17 · diff ↗
1.0.4
2021-09-08 · diff ↗
1.0.3
2021-07-29 · diff ↗
1.0.2
2021-07-28 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.1
2021-05-14 · diff ↗
0.13.0
2020-10-11 · diff ↗
0.12.2
2020-05-19 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.12.1
2020-03-30 · diff ↗
0.11.1
2020-01-13 · diff ↗
0.11.0
2019-10-11 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.10.0
2019-03-15 · diff ↗
0.9.0
2019-02-07 · diff ↗
0.8.2
2018-10-15 · diff ↗
0.8.1
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Report a problem with this page →