R Observatory: Metrics for lgpr version 1.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

lgpr

1.2.5Package record

Longitudinal Gaussian Process Regression

0packages depend

3.3Kdownloads / year

89.2%test coverage

13/13flavors OK

Overview

About

Maintained by Juho TimonenCRAN page ↗GitHub ↗Issues ↗

Interpretable nonparametric modeling of longitudinal data using additive Gaussian process regression. Contains functionality for inferring covariate effects and assessing covariate relevances. Models are specified using a convenient formula syntax, and can include shared, group-specific, non-stationary, heterogeneous and temporally uncertain effects. Bayesian inference for model parameters is performed using 'Stan'. The modeling approach and methods are described in detail in Timonen et al. (2021) doi:10.1093/bioinformatics/btab021.

Install

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

install.packages("lgpr", 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("jtimonen/lgpr")

Development version from jtimonen/lgpr. 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-lgpr

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-lgpr

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-lgpr

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: 20.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.5

READMEYes · 316 wordsVignettesYes · 1 · dynamicNEWS· In the repository, left out of the releaseCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 68includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 7%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 1%

Vignettes (1)

Mathematical description of lgpr models

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #11,903 · ~9/day · ~271/mo

Releases R versions

Daily download trend is not available in this view yet.

32730 days

92490 days

3.3K1 year

Compare downloads with other packages →

Also on379 r2u3 autocran

How downloads are counted

Repository

jtimonen/lgpr ↗Account: jtimonen

28Stars

2Forks

3Open issues

0Open PRs

23Releases

521Commits

2Commit identities

stanlongitudinal-datagaussian-processesbayesian-inferencer-packages

521 commits · Last activity 2025-10-30 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 57
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-03 · 262026-07-07 · 28

How these are measured

PracticesBeta

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

Checks run against github.com/jtimonen/lgpr on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Contributing guideIssue templates

Docs source (1)

pkgdown

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing lgpr adds 62 packages (33 with compiled code, 67 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (2)

R >= 3.4.0methods

Imports (10)

Rcpp RcppParallel RCurl rstan rstantools bayesplotMASSstatsggplot2 gridExtra

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.26.0)

Suggests (4)

knitr rmarkdown testthat covr

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 (2)

Juho Timonen

Author, Maintainer since 1.1.3 (2021)

Andrew Johnson

Contributor · added in 1.2.3

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.5Latest
record
2025-10-31 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.4
record
2023-09-24 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.3
record
2023-04-06 · diff ↗ ·
added 6 exports
add_factor_crossing, split_by_factor, split_data, split_random, split_within_factor, split_within_factor_random
R
R 4.2.0 released · 2022-04-22
1.1.5
record
2021-09-23 · diff ↗
1.1.4
record
2021-08-11 · diff ↗
1.1.3
record
2021-06-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-06-21
Total releases: 6 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.4.0
Bundled data: 2.6 KB / 2 files
Download size: 200 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("lgpr")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btab021.

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 lgpr version 1.2.5 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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