R Observatory: Metrics for LTFHPlus version 2.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LTFHPlus

2.2.0Package record

Implementation of LT-FH++

0packages depend

3.2Kdownloads / year

16.6%test coverage

13/13flavors OK

Overview

About

Maintained by Emil Michael PedersenCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 2.2.0

Added several functions to assist labelling relatives, summarising per-family relatives, and summary pedigree information visualisation
get_generations()
label_relatives()
get_relations()
get_family_graphs()
Relation_per_proband_plot()
Added vignette on pedigree visualisation and labelling relatives

From NEWS.md in the release

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

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.0

READMEYes · 215 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 2.2.0Citation fileNoWebsiteYes · pkgdown

Help pages: 36 (1 internal)includes a package overview page
Examples that run: 82%27 run in a plain check · 6 hold no code
Exported functions with examples: 97%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 6%

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #13,872 · ~9/day · ~264/mo

Releases R versions

Daily download trend is not available in this view yet.

25630 days

85590 days

3.2K1 year

Compare downloads with other packages →

Also on355 r2u5 autocran

How downloads are counted

Repository

emilmip/ltfhplus ↗Account: EmilMiP

11Stars

3Forks

1Open issues

1Open PRs

7Releases

395Commits

6Commit identities

395 commits · Last activity 2025-11-17

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-27 · 112026-07-07 · 11

How these are measured

PracticesBeta

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

Checks run against github.com/emilmip/ltfhplus on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-11-17 · The repository has a site deploy workflow

pkgdown site last built 2025-11-17

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing LTFHPlus adds 46 packages (26 with compiled code, 48 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

People & History

People (6)

Emil Michael Pedersen

Author, Maintainer since 2.1.1 (2024)

Florian Privé

Author, Thesis advisor

Jette Steinbach

Author

Lucas Rasmussen

Contributor

Esben Agerbo

Thesis advisor

Bjarni Jóhann Vilhjálmsson

Thesis advisor

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.2.0Latest
record
2025-11-17 · current release · diff ↗ ·
added 7 exports
Relation_per_proband_plot, attach_attributes, familywise_attach_attributes, get_family_graphs, get_generations, get_relations, label_relatives
2.1.4
record
2025-05-26 · diff ↗
2.1.3
record
2025-05-13 · diff ↗ ·
added 1 export
graph_to_trio
R
R 4.5.0 released · 2025-04-11
2.1.2
record
2024-11-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1.1
record
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

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 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 LTFHPlus version 2.2.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, 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 →