R Observatory: Metrics for LTFGRS version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LTFGRS

1.0.1

Implementation of Several Phenotype-Based Family Genetic Risk Scores

0packages depend

2.3Kdownloads / year

16.9%test coverage

13/13checks pass

Overview

About

Maintained by Emil Michael PedersenFirst published 2025-07-072 releasesCRAN page ↗GitHub ↗

Implementation of several phenotype-based family genetic risk scores with unified input data and data preparation functions to help facilitate the required data preparation and management. The implemented family genetic risk scores are the extended liability threshold model conditional on family history from Pedersen (2022) doi:10.1016/j.ajhg.2022.01.009 and Pedersen (2023) https://www.nature.com/articles/s41467-023-41210-z, Pearson-Aitken Family Genetic Risk Scores from Krebs (2024) doi:10.1016/j.ajhg.2024.09.009, and family genetic risk score from Kendler (2021) doi:10.1001/jamapsychiatry.2021.0336.

Install

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

install.packages("LTFGRS", 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("EmilMiP/LTFGRS")

Development version from EmilMiP/LTFGRS. 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-ltfgrs

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-LTFGRS

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-LTFGRS

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

Health

CRAN checks

13OK

Slowest check: 4.9 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.10

16.9%

Coverage · measured lines

100%

Documentation · exports

16

Dependencies · direct

Check history

OK2026-08-05
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 · 186 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 100%
References docs: 5%

Downloads

2.3K

CRAN downloads in the past year

Rank #17,076 · ~6/day · ~194/mo

Releases R versions

Daily download trend is not available in this view yet.

19730 days

62690 days

2.3K1 year

Compare downloads with other packages →

Also on375 r2u19 autocran

Repository

GitHub ↗ emilmip/ltfgrs

2Stars

0Forks

1Open issues

0Open PRs

0Releases

52Commits

1Contributors

52 commits · Last activity 2026-03-18 · 0% stars, 30d

Stars over time

2025-05-09 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/emilmip/ltfgrs on 2026-08-16.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (16)

batchmeans dplyr future.apply future lubridate purrr Rcpp rlangstatsstringr tibble tmvtnorm tidyselect igraph xgboost tidyr

LinkingTo (1)

Rcpp

Suggests (4)

knitr rmarkdown testthatMASS

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Emil Michael Pedersen

Author, Maintainer

Authors (3)

Emil Michael Pedersen

Author, Maintainer

Morten Dybdahl Krebs

Author

Jette Steinbach

Author

Contributors (1)

Lucas Rasmussen

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
2025-08-29 · current release · diff ↗
unarchivedReturned to CRAN
2025-08-29
archivedRemoved from CRAN
2025-08-25
errors were not corrected in time
1.0.0
2025-07-07
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-07
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Download size: 126 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LTFGRS")

Format

Pedersen, E. M., Krebs, M. D., Rasmussen, L., & Steinbach, J. (2025). LTFGRS: Implementation of Several Phenotype-Based Family Genetic Risk Scores (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.LTFGRS

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 LTFGRS version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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