R Observatory: Metrics for simer version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simer

1.0.0Package record

Data Simulation for Life Science and Breeding

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Xiaolei LiuCRAN page ↗GitHub ↗Issues ↗

Data simulator including genotype, phenotype, pedigree, selection and reproduction in R. It simulates most of reproduction process of animals or plants and provides data for GS (Genomic Selection), GWAS (Genome-Wide Association Study), and Breeding. For ADI model, please see Kao C and Zeng Z (2002) doi:10.1093/genetics/160.3.1243. For build.cov, please see B. D. Ripley (1987) <ISBN:9780470009604>.

Install

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

install.packages("simer", 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("xiaolei-lab/SIMER")

Development version from xiaolei-lab/SIMER. 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-simer

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-simer

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-simer

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: 5.0 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
NOTE12 OK, 1 NOTE2026-06-08
OK12 OK2026-04-25

Show 5 earlier changesHide 5 earlier changes

NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-04-10
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-09
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 9,059 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 67 (9 internal)
Examples that run: 54%32 run in a plain check · 27 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 4%

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #15,293 · ~8/day · ~239/mo

Releases R versions

Daily download trend is not available in this view yet.

27030 days

79090 days

2.9K1 year

Compare downloads with other packages →

Also on381 r2u7 autocran

How downloads are counted

Repository

xiaolei-lab/simer ↗Organization: xiaolei-lab

45Stars

11Forks

3Open issues

0Open PRs

1Releases

728Commits

5Commit identities

License file reads as Apache-2.0 · 728 commits · Last activity 2025-06-13 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 18
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-04 · 392026-07-09 · 45

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/xiaolei-lab/simer on 2026-10-18.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing simer adds 8 packages (5 with compiled code, 18 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

Depends (1)

R >= 3.5.0

Imports (8)

utilsstatsMatrixmethodsMASSbigmemory jsonlite Rcpp

LinkingTo (5)

Rcpp RcppArmadillo RcppProgress BH bigmemory

Suggests (2)

knitr igraph

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (11)

Author

Author

Author

Author

Author

Author

Author

Author

Author

Author · added in 0.9.0.3

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.0Latest
record
2025-02-26 · current release · diff ↗
0.9.0.6
record
2025-01-30 · diff ↗ ·
removed 1 export
simer.Data.Kin

added 1 export
bigt
0.9.0.5
record
2024-09-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.9.0.4
record
2023-11-29 · diff ↗
0.9.0.3
record
2023-10-12 · diff ↗ ·
added 3 exports
mate.assort, mate.disassort, simer.Data.Kin
R
R 4.3.0 released · 2023-04-21
0.9.0.2
record
2022-08-08 · diff ↗ ·
added 3 exports
simer.Data.Bfile2MVP, simer.Data.MVP2Bfile, simer.Data.Map
0.9.0.0
record
2022-05-12
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-12
Total releases: 7 / 4 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 3.5.0
Bundled data: 244 KB / 2 files
Download size: 3.9 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("simer")

Format

Liu, X., Li, X., Tang, Z., Xu, J., Yin, D., Yin, L., Yuan, X., Zhang, H., Zhang, X., Zhao, S., & Zhou, X. (2025). simer: Data Simulation for Life Science and Breeding (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.simer

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 simer version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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