R Observatory: Metrics for simtrait version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simtrait

1.1.3Package record

Simulate Complex Traits from Genotypes

0packages depend

2.5Kdownloads / year

89.4%test coverage

13/13flavors OK

Overview

About

Maintained by Alejandro OchoaCRAN page ↗GitHub ↗Issues ↗

Simulate complex traits given a SNP genotype matrix and model parameters (the desired heritability, number of causal loci, and either the true ancestral allele frequencies used to generate the genotypes or the mean kinship for a real dataset). Emphasis on avoiding common biases due to the use of estimated allele frequencies. The code selects random loci to be causal, constructs coefficients for these loci and random independent non-genetic effects, and can optionally generate random group effects. Traits can follow three models: random coefficients, fixed effect sizes, and infinitesimal (multivariate normal). GWAS method benchmarking functions are also provided. Described in Yao and Ochoa (2022) doi:10.1101/2022.03.25.485885.

Changes in 1.1.3

Updated CRAN comments, for CRAN submission

From NEWS.md in the release

Install

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

install.packages("simtrait", 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("OchoaLab/simtrait")

Development version from OchoaLab/simtrait. 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-simtrait

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-simtrait

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-simtrait

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: 1.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.3

READMEYes · 204 wordsVignettesYes · 1 · staticNEWSYes · 67% structured · mentions 1.1.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12includes a package overview page
Examples that run: 100%12 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

`simtrait`: Simulate Complex Traits from Genotypes HTML

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #20,326 · ~7/day · ~207/mo

Releases R versions

Daily download trend is not available in this view yet.

23230 days

65990 days

2.5K1 year

Compare downloads with other packages →

Also on77 r2u10 autocran

How downloads are counted

Repository

ochoalab/simtrait ↗Organization: OchoaLab

7Stars

1Forks

0Open issues

0Open PRs

3Releases

77Commits

1Commit identities

License file reads as GPL-3.0 · 77 commits · Last activity 2025-07-08 · 0% stars, 30d · Default branch at 1.1.11.9000, ahead of CRAN 1.1.3 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 56
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-01-05 · 52026-09-18 · 7

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/ochoalab/simtrait on 2026-10-25.

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing simtrait adds 2 packages (1 with compiled code, 1.2 MB of source tarballs). Heaviest: rlang 766 KB, PRROC 510 KB.

Depends (0)

none

Imports (1)

PRROC

LinkingTo (0)

none

Suggests (6)

popkin testthat knitr rmarkdown bnpsd BEDMatrix

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Alejandro Ochoa

Author, Maintainer since 1.0.21 (2021)

Releases (3)

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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.3Latest
record
2023-01-06 · current release · diff ↗
1.1.0
record
2022-08-23 · diff ↗ ·
added 2 exports
pval_power_calib, pval_type_1_err
R
R 4.2.0 released · 2022-04-22
1.0.21
record
2021-08-16
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-16
Total releases: 3 / 5 yrs
License: GPL-3 OSI
Download size: 323 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("simtrait")

Format

Ochoa, A. (2023). simtrait: Simulate Complex Traits from Genotypes (Version 1.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.simtrait

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 simtrait version 1.1.3 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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