R Observatory: Metrics for simfam version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simfam

1.1.6Package record

Simulate and Model Family Pedigrees with Structured Founders

0packages depend

2.4Kdownloads / year

79.7%test coverage

13/13flavors OK

Overview

About

Maintained by Alejandro OchoaCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.1.6

CRAN submission
Documentation edits
Updated hyperlink to raw genetic maps.
Fixed typos
Escaped more code to simplify spellcheck in the future.
Updated cran-comments.md

From NEWS.md in the release

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. 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-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). 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: 4.7 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.6

READMEYes · 259 wordsVignettesYes · 1 · staticNEWSYes · 67% structured · mentions 1.1.6Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 21 (1 internal)includes a package overview page
Examples that run: 100%20 run in a plain check
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

`simfam`: simulate and model family pedigrees with structured founders HTML

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #19,545 · ~7/day · ~200/mo

Releases R versions

Daily download trend is not available in this view yet.

24430 days

67490 days

2.4K1 year

Compare downloads with other packages →

Also on355 r2u4 autocran

How downloads are counted

Repository

ochoalab/simfam ↗Organization: OchoaLab

3Stars

0Forks

0Open issues

0Open PRs

3Releases

40Commits

1Commit identities

License file reads as GPL-3.0 · 40 commits · Last activity 2025-01-08 · Default branch at 1.1.16.9000, ahead of CRAN 1.1.6 (checked 2026-10-21)

Responsiveness

not measured

Stars over time

2025-01-07 · 32026-07-07 · 3

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/simfam on 2026-10-21.

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing simfam adds 11 packages (8 with compiled code, 5.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, vctrs 1.0 MB, rlang 766 KB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Alejandro Ochoa

Author, Maintainer since 1.0.2 (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
1.1.6Latest
record
2023-01-09 · current release · diff ↗ ·
added 10 exports
fam_ancestors, recomb_admix_inds, recomb_fam, recomb_geno_inds, recomb_haplo_inds, recomb_init_founders, recomb_last_gen, recomb_map_fix_ends_chr, recomb_map_inds, recomb_map_simplify_chr
R
R 4.2.0 released · 2022-04-22
1.0.3
record
2021-10-06 · diff ↗
1.0.2
record
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

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 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 simfam version 1.1.6 [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.

Report a problem with this page →