R Observatory: Metrics for LTFHPlus version 2.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LTFHPlus

2.2.0

Implementation of LT-FH++

0packages depend

3.6Kdownloads / year

16.6%test coverage

13/13checks pass

Overview

About

Maintained by Emil Michael PedersenFirst published 2024-02-125 releasesCRAN page ↗GitHub ↗

Implementation of LT-FH++, an extension of the liability threshold family history (LT-FH) model. LT-FH++ uses a Gibbs sampler for sampling from the truncated multivariate normal distribution and allows for flexible family structures. LT-FH++ was first described in Pedersen, Emil M., et al. (2022) doi:10.1016/j.ajhg.2022.01.009 as an extension to LT-FH with more flexible family structures, and again as the age-dependent liability threshold (ADuLT) model Pedersen, Emil M., et al. (2023) https://www.nature.com/articles/s41467-023-41210-z as an alternative to traditional time-to-event genome-wide association studies, where family history was not considered.

Install

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

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

Development version from EmilMiP/LTFHPlus. 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-ltfhplus

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-LTFHPlus

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-LTFHPlus

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 0.10

16.6%

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 · 215 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 100%
References docs: 6%

Downloads

3.6K

CRAN downloads in the past year

Rank #16,700 · ~10/day · ~302/mo

Releases R versions

Daily download trend is not available in this view yet.

18230 days

63790 days

3.6K1 year

Compare downloads with other packages →

Also on398 r2u15 autocran

Repository

GitHub ↗ emilmip/ltfhplus

11Stars

3Forks

1Open issues

1Open PRs

7Releases

395Commits

6Contributors

395 commits · Last activity 2025-11-17

Stars over time

2025-05-27 · 112026-07-07 · 11

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

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

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (16)

batchmeans dplyr future.apply future purrr Rcpp rlangstatsstringr tibble tmvtnorm tidyselect igraph xgboost tidyr ggplot2

LinkingTo (1)

Rcpp

Suggests (5)

MASSknitr rmarkdown kinship2 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Emil Michael Pedersen

Author, Maintainer

Authors (3)

Emil Michael Pedersen

Author, Maintainer

Florian Privé

Author, Thesis advisor

Jette Steinbach

Author

Contributors (1)

Lucas Rasmussen

Contributor

Other (2)

Esben Agerbo

Thesis advisor

Bjarni Jóhann Vilhjálmsson

Thesis advisor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.2.0Latest
2025-11-17 · current release · diff ↗
2.1.4
2025-05-26 · diff ↗
2.1.3
2025-05-13 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.1.2
2024-11-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1.1
2024-02-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-12
Total releases: 5 / 2 yrs
License: GPL-3 OSI
Download size: 84 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LTFHPlus")

Format

Pedersen, E. M., Agerbo, E., Privé, F., Rasmussen, L., Steinbach, J., & Vilhjálmsson, B. J. (2025). LTFHPlus: Implementation of LT-FH++ (Version 2.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.LTFHPlus

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 LTFHPlus version 2.2.0 [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.

Report a problem with this page →