R Observatory: Metrics for simfam version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simfam

1.1.6

Simulate and Model Family Pedigrees with Structured Founders

0packages depend

2.4Kdownloads / year

79.7%test coverage

13/13checks pass

Overview

About

Maintained by Alejandro OchoaFirst published 2021-09-023 releasesCRAN page ↗GitHub ↗

The focus is on simulating and modeling families with founders drawn from a structured population (for example, with different ancestries or other potentially non-family relatedness), in contrast to traditional pedigree analysis that treats all founders as equally unrelated. Main function simulates a random pedigree for many generations, avoiding close relatives, pairing closest individuals according to a 1D geography and their randomly-drawn sex, and with variable children sizes to result in a target population size per generation. Auxiliary functions calculate kinship matrices, admixture matrices, and draw random genotypes across arbitrary pedigree structures starting from the corresponding founder values. The code is built around the plink FAM table format for pedigrees. Described in Yao and Ochoa (2022) doi:10.1101/2022.03.25.485885.

Install

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

install.packages("simfam", 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/simfam")

Development version from OchoaLab/simfam. 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-simfam

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

# 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-simfam

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-simfam

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.8 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.61

79.7%

Coverage · measured lines

100%

Documentation · exports

3

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 259 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #19,027 · ~7/day · ~201/mo

Releases R versions

Daily download trend is not available in this view yet.

11730 days

57990 days

2.4K1 year

Compare downloads with other packages →

Also on386 r2u20 autocran

Repository

GitHub ↗ ochoalab/simfam

3Stars

0Forks

0Open issues

0Open PRs

3Releases

40Commits

1Contributors

License GPL-3.0 · 40 commits · Last activity 2025-01-08

Stars over time

2025-01-07 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/ochoalab/simfam on 2026-08-16.

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (3)

Rcppstatstibble

LinkingTo (1)

Rcpp

Suggests (7)

testthat popkin bnpsd kinship2 RColorBrewer knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Alejandro Ochoa

Author, Maintainer

Authors (1)

Alejandro Ochoa

Author, Maintainer

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
1.1.6Latest
2023-01-09 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.3
2021-10-06 · diff ↗
1.0.2
2021-09-02
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-02
Total releases: 3 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 289 KB / 2 files
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("simfam")

Format

Ochoa, A. (2023). simfam: Simulate and Model Family Pedigrees with Structured Founders (Version 1.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.simfam

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 simfam version 1.1.6 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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