R Observatory: Metrics for TriadSim version 0.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TriadSim

0.3.1Package record

Simulating Triad Genomewide Genotypes

0packages depend

2.9Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Min ShiCRAN page ↗

Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.

Changes in 0.3.1

Important update on some key functions.
Fix a bug.

From NEWS.md in the release

Install

R (CRAN)Ubuntu (r2u)

install.packages("TriadSim", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-triadsim

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

Package required but not available: ‘snpStats’

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

CRAN check page ↗

Slowest check: 5.1 min · r-oldrel-macos-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR12 OK, 2 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.1

READMEYes · 168 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 0.3.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

TriadSim Vignette HTML

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #17,471 · ~8/day · ~239/mo

Releases R versions

Daily download trend is not available in this view yet.

28730 days

73790 days

2.9K1 year

Compare downloads with other packages →

Also on79 r2u

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing TriadSim adds 3 packages (0 with compiled code, 541 KB of source tarballs). Heaviest: iterators 293 KB, doParallel 160 KB, foreach 88 KB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.2.2

Imports (5)

methodsparallelsnpStats foreach doParallel

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 (1)

Min Shi

Author, Maintainer since 0.0.1 (2017)

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.1Latest
record
2026-02-22 · current release · diff ↗
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
0.3.0
record
2021-09-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2020-07-12
0.2.0
record
2020-07-12 · diff ↗
archivedRemoved from CRAN
2020-07-07
the request of the maintainer
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1.1
record
2017-05-25 · diff ↗
0.0.1
record
2017-05-13

Show 1 earlier eventHide 1 earlier event

R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-13
Total releases: 5 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.2.2
Bundled data: 16 KB / 2 files
Download size: 705 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TriadSim")

Format

Shi, M. (2026). TriadSim: Simulating Triad Genomewide Genotypes (Version 0.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.TriadSim

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 TriadSim version 0.3.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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