R Observatory: Metrics for LUCIDus version 3.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LUCIDus

3.1.0

LUCID with Multiple Omics Data

1packages depend

4.5Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Qiran JiaFirst published 2018-12-2114 releasesCRAN page ↗

Implements Latent Unknown Clusters By Integrating Multi-omics Data (LUCID; Peng (2019) doi:10.1093/bioinformatics/btz667) for integrative clustering with exposures, multi-omics data, and health outcomes. Supports three integration strategies: early, parallel, and serial. Provides model fitting and tuning, lasso-type regularization for exposure and omics feature selection, handling of missing data, including both sporadic and complete-case patterns, prediction, and g-computation for estimating causal effects of exposures, bootstrap inference for uncertainty estimation, and S3 summary and plot methods. For the multi-omics integration framework, see Jia (2024) https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf. For the missing-data imputation mechanism, see Jia (2024) doi:10.1093/bioadv/vbae123.

Install

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

install.packages("LUCIDus", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-lucidus

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-LUCIDus

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-LUCIDus

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

Health

CRAN checks

13OK

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.60

0.0%

Coverage · measured lines

100%

Documentation · exports

10

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
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-09
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 38%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.5K

CRAN downloads in the past year

Rank #6,394 · ~12/day · ~377/mo

Releases R versions

Daily download trend is not available in this view yet.

25930 days

1.3K90 days

4.5K1 year

Compare downloads with other packages →

Also on138 r2u16 autocran25 c2d4u

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (10)

mclustnnetbootjsonlite networkD3 progressstatsutilsglasso glmnet

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

MosaiClusteR

Code & Tests

People & History

People (4)

Maintainer (1)

Qiran Jia

Author, Maintainer · added in 3.0.1

Authors (2)

Qiran Jia

Author, Maintainer · added in 3.0.1

Yinqi Zhao

Author · added in 2.0.0

Contributors (1)

Jesse Goodrich

Contributor · added in 2.2.1

Other (1)

David Conti

Thesis advisor · added in 2.2.1

Listed in earlier versions (3)

David V. Conti

no longer listed · 0.9.0 to 2.2

Cheng Peng

no longer listed · 0.9.0 to 2.2.1

Zhao Yang

no longer listed · 0.9.0 to 2.2

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
3.1.0Latest
2026-03-11 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.3
2024-09-23 · diff ↗
3.0.2
2024-07-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.0.1
2023-10-31 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.2.1
2022-11-08 · diff ↗
2.2
2022-08-08 · diff ↗
2.1.5-2
2022-06-01 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.5-1
2022-04-06 · diff ↗
2.1.5
2022-03-28 · diff ↗
2.1.4
2022-03-03 · diff ↗
R
R 4.1.0 released · 2021-05-18

Show 7 earlier events

2.1.0
2020-07-22 · diff ↗
2.0.0
2020-05-18 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.0
2019-12-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.9.0
2018-12-21
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-12-21
Total releases: 14 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 451 KB / 2 files
Download size: 552 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LUCIDus")

Format

Jia, Q., Conti, D., Goodrich, J., & Zhao, Y. (2026). LUCIDus: LUCID with Multiple Omics Data (Version 3.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.LUCIDus

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 LUCIDus version 3.1.0 [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.

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