R Observatory: Metrics for simplePHENOTYPES version 1.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simplePHENOTYPES

1.3.1Package record

Simulation of Pleiotropic, Linked and Epistatic Phenotypes

0packages depend

3.6Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Samuel FernandesCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.3.1

Minor changes

Updated the maintainer e-mail address.

Replaced class(x) == "matrix" / "try-error" comparisons with inherits(), which also avoids a length-2 condition error under R >= 4.2.

Use an absolute URL for the README logo.

From NEWS.md in the release

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. 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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64

Packages required but not available: 'SNPRelate', 'gdsfmt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-macos-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR10 OK, 2 NOTE, 1 ERROR2026-10-05
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.1

READMEYes · 1,624 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 1.3.1Citation fileYes · cites a publication

Help pages: 15 (14 internal)
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 89%
Return-value docs: 100%
Help pages citing references: 7%

Vignettes (1)

Introduction to simplePHENOTYPES

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #8,060 · ~10/day · ~298/mo

Releases R versions

Daily download trend is not available in this view yet.

57630 days

1.1K90 days

3.6K1 year

Compare downloads with other packages →

Also on99 r2u

How downloads are counted

Repository

samuelbfernandes/simplephenotypes ↗Account: samuelbfernandes

17Stars

4Forks

0Open issues

0Open PRs

3Releases

518Commits

5Commit identities

rsimulationpleiotropy

518 commits · Last activity 2026-10-09 · 0% stars, 30d · Default branch at 2.0.0.9003, ahead of CRAN 1.3.1 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 97%
Median days to close, 50 most recently updated closed issues: 58
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-03-09 · 132026-09-11 · 17

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/samuelbfernandes/simplephenotypes on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (3)

README.Rmd

GitHub Pages site last deployed 2026-10-09 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Research and citation (1)

CITATION.cff

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing simplePHENOTYPES adds 2 packages (2 with compiled code, 6.7 MB of source tarballs). Heaviest: data.table 5.7 MB, mvtnorm 1.0 MB. 2 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Samuel Fernandes

Author, Maintainer since 1.0.5 (2019)

Alexander Lipka

Author

Releases (4)

Pick two releases to compare their code metrics.

1.3.1Latest
record
2026-10-04 · current release · diff ↗ ·
23 hours in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-03 21:57 to 2026-10-04 20:43 UTC, in 6 readings.
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
1.3.0
record
2021-01-20 · diff ↗
1.2.4
record
2020-05-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.5
record
2019-12-04
R
R 3.6.0 released · 2019-04-26

Across CRAN, the median accepted release of the past year spent 23 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2019-12-04
Total releases: 4 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 529 KB / 1 file
Download size: 1.4 MB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("simplePHENOTYPES")

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

It points to 10.1186/s12859-020-03804-y.

The repository also keeps a CITATION.cff.

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 1.3.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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