R Observatory: Metrics for PhenotypeSimulator version 0.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-12-25. Its history is shown below.

Reason: issues were not addressed in time

Details below reflect version 0.3.4, its last release before removal.

PhenotypeSimulator

0.3.4

Flexible Phenotype Simulation from Different Genetic and Noise Models

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Hannah Meyer8 releasesCRAN page ↗GitHub ↗

Simulation is a critical part of method development and assessment in quantitative genetics. 'PhenotypeSimulator' allows for the flexible simulation of phenotypes under different models, including genetic variant and infinitesimal genetic effects (reflecting population structure) as well as non-genetic covariate effects, observational noise and additional correlation effects. The different phenotype components are combined into a final phenotype while controlling for the proportion of variance explained by each of the components. For each effect component, the number of variables, their distribution and the design of their effect across traits can be customised. For the simulation of the genetic effects, external genotype data from a number of standard software ('plink', 'hapgen2'/ 'impute2', 'genome', 'bimbam', simple text files) can be imported. The final simulated phenotypes and its components can be automatically saved into .rds or .csv files. In addition, they can be saved in formats compatible with commonly used genetic association software ('gemma', 'bimbam', 'plink', 'snptest', 'LiMMBo').

Install

R (source archive)pak (dev)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/PhenotypeSimulator/PhenotypeSimulator_0.3.4.tar.gz"
pkgFile <- "PhenotypeSimulator_0.3.4.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.3.4) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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

Development version from HannahVMeyer/PhenotypeSimulator. 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-phenotypesimulator

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

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.30

not tracked

Coverage

100%

Documentation · exports

13

Dependencies · direct

Documentation

READMEYes · 327 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 90%
References docs: 4%

Downloads

PhenotypeSimulator Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on370 r2u

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (13)

methodsoptparse Hmisc R.utils mvtnorm snpStats zoo data.table Rcpp cowplot ggplot2 reshape2 dplyr

LinkingTo (1)

Rcpp

Suggests (4)

testthat knitr formatR rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Hannah Meyer

Author, Maintainer

Authors (1)

Hannah Meyer

Author, Maintainer

Contributors (1)

Konrad Rudolph

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-12-25
issues were not addressed in time
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
0.3.4
2021-07-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.3.3
2019-05-15 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.1
2018-10-25 · diff ↗
0.2.2
2018-05-13 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.2.0
2018-01-07 · diff ↗
0.1.3
2017-08-05 · diff ↗

Show 3 earlier events

0.1.2
2017-06-12 · diff ↗
0.1.1
2017-05-21
R
R 3.4.0 released · 2017-04-21

Package metadata

Total releases: 8
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PhenotypeSimulator")

Format

Meyer, H., & Rudolph, K. (n.d.). PhenotypeSimulator: Flexible Phenotype Simulation from Different Genetic and Noise Models (Version 0.3.4) [Computer software]. Retrieved August 14, 2026, from https://CRAN.R-project.org/package=PhenotypeSimulator

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 PhenotypeSimulator version 0.3.4 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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