R Observatory: Metrics for LongDat version 1.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LongDat

1.1.4Package record

A Tool for 'Covariate'-Sensitive Longitudinal Analysis on 'omics' Data

0packages depend

7Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Chia-Yu ChenCRAN page ↗GitHub ↗Issues ↗

This tool takes longitudinal dataset as input and analyzes if there is significant change of the features over time (a proxy for treatments), while detects and controls for 'covariates' simultaneously. 'LongDat' is able to take in several data types as input, including count, proportion, binary, ordinal and continuous data. The output table contains p values, effect sizes and 'covariates' of each feature, making the downstream analysis easy.

Changes in 1.1.4

Updated the maintainer email address (previous address bounced).

From NEWS.md in the release

Install

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

install.packages("LongDat", 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("CCY-dev/LongDat")

Development version from CCY-dev/LongDat. 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-longdat

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-LongDat

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-LongDat

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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘ConModelTest_cont.Rd’ ‘ConModelTest_disc.Rd’ ‘NuModelTest_cont.Rd’
  ‘NuModelTest_disc.Rd’ ‘cliff_cal.Rd’ ‘cuneiform_plot.Rd’
  ‘random_neg_ctrl_cont.Rd’ ‘random_neg_ctrl_disc.Rd’
  ‘rm_sparse_cont.Rd’ ‘rm_sparse_disc.Rd’ ‘theta_plot.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 4.8 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-30
ERROR13 OK, 1 ERROR2026-03-28

Show 1 earlier changeHide 1 earlier change

OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.4

READMEYes · 132 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.1.4Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 28
Examples that run: 45%5 run in a plain check · 6 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

7K

CRAN downloads in the past year

Rank #11,207 · ~19/day · ~582/mo

Releases R versions

Daily download trend is not available in this view yet.

38830 days

93490 days

7K1 year

Compare downloads with other packages →

Also on89 r2u7 autocran

How downloads are counted

Repository

ccy-dev/longdat ↗Account: CCY-dev

3Stars

1Forks

1Open issues

0Open PRs

0Releases

201Commits

2Commit identities

201 commits · Last activity 2024-11-19 · 0% stars, 30d · The default branch showed an older version (1.1.3) than CRAN on 2026-10-11 · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 192
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-11-17 · 32026-07-07 · 3

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/ccy-dev/longdat on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing LongDat adds 111 packages (53 with compiled code, 90 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.0.0

Imports (20)

lme4 reshape2 glmmTMB emmeans bestNormalizeMASSggplot2 stringr magrittr tibble dplyrgraphicsutilsstatsrlang car rstatix effsize tidyr patchwork

LinkingTo (0)

none

Suggests (3)

rmarkdown knitr kableExtra

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)

Chia-Yu Chen

Author, Maintainer since 1.0.0 (2022)

Sofia Forslund

Contributor

Releases (11)

Pick two releases to compare their code metrics.

1.1.4Latest
record
2026-07-08 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.3
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2024-11-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.2
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2023-07-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.1
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2023-04-17 · diff ↗
1.1.0
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2022-07-14 · diff ↗
1.0.5
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2022-06-21 · diff ↗
1.0.4
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2022-06-01 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.3
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2022-02-26 · diff ↗
1.0.2
record
2022-02-17 · diff ↗
1.0.1
record
2022-02-02 · diff ↗
1.0.0
record
2022-01-18

Show 1 earlier eventHide 1 earlier event

R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-18
Total releases: 11 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.0.0
Bundled data: 2.5 KB / 6 files
Download size: 635 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("LongDat")

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

It points to 10.1093/bioadv/vbad063.

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 LongDat version 1.1.4 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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