R Observatory: Metrics for simplePHENOTYPES version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simplePHENOTYPES

1.3.0

Simulation of Pleiotropic, Linked and Epistatic Phenotypes

0packages depend

3.2Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Samuel FernandesFirst published 2019-12-043 releasesCRAN page ↗GitHub ↗

The number of studies involving correlated traits and the availability of tools to handle this type of data has increased considerably in the last decade. With such a demand, we need tools for testing hypotheses related to single and multi-trait (correlated) phenotypes based on many genetic settings. Thus, we implemented various options for simulation of pleiotropy and Linkage Disequilibrium under additive, dominance and epistatic models. The simulation currently takes a marker data set as an input and then uses it for simulating multiple traits as described in Fernandes and Lipka (2020) doi:10.1186/s12859-020-03804-y.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("simplePHENOTYPES", 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("samuelbfernandes/simplePHENOTYPES")

Development version from samuelbfernandes/simplePHENOTYPES. 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-simplephenotypes

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,616 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 89%
Return-value docs: 100%
References docs: 7%

Downloads

3.2K

CRAN downloads in the past year

Rank #12,919 · ~9/day · ~270/mo

Releases R versions

Daily download trend is not available in this view yet.

21930 days

79690 days

3.2K1 year

Compare downloads with other packages →

Also on139 r2u

Repository

GitHub ↗ samuelbfernandes/simplephenotypes

16Stars

5Forks

1Open issues

0Open PRs

3Releases

309Commits

6Contributors

rsimulationpleiotropy

License MIT · 309 commits · Last activity 2026-06-09 · 0% stars, 30d

Stars over time

2025-03-09 · 132026-07-07 · 16

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/samuelbfernandes/simplephenotypes on 2026-08-23.

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (6)

data.table mvtnormstatsutilsSNPRelate gdsfmt

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Samuel Fernandes

Author, Maintainer

Authors (2)

Samuel Fernandes

Author, Maintainer

Alexander Lipka

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3.0Latest
2021-01-20 · current release · diff ↗
1.2.4
2020-05-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.5
2019-12-04
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-04
Total releases: 3 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 529 KB / 1 file
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("simplePHENOTYPES")

Format

Fernandes, S., & Lipka, A. (2021). simplePHENOTYPES: Simulation of Pleiotropic, Linked and Epistatic Phenotypes (Version 1.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.simplePHENOTYPES

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 simplePHENOTYPES version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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