R Observatory: Metrics for LUCIDus version 3.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LUCIDus

3.2.1Package record

LUCID with Multiple Omics Data

0packages dependsuggested by 1

5.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Qiran JiaCRAN 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.

Changes in 3.2.1

A correctness follow-up to 3.2.0, focused on boot_lucid() and summary().

**Bootstrap CIs now align cluster labels.** Each bootstrap replicate is an

independent refit whose latent cluster *k* need not be the point estimate's

cluster *k*. Replicate coefficient vectors were stacked by name/position anyway,

so any coefficient whose canonical cluster ordering was weakly identified -- a

parallel layer with a near-null cluster-to-outcome effect, an upstream serial

stage ordered by a single omics feature -- could get a bimodal or sign-split

interval spanning orders of magnitude. boot_lucid() now permutes every

replicate's clusters to match the reference fit (by posterior-probability

overlap on the resampled subjects) before extracting coefficients, so each

interval brackets its own point estimate. The point estimate (bootstrap$t0)

is unchanged.

Show all changes in 3.2.1Hide the rest of the changes in 3.2.1

**summary() bootstrap CI tables.**

The exposure/transition ((3) E) and binary-outcome ((1) Y) CI tables now carry an odds-ratio view -- OR, OR_lower, OR_upper = exp() of the coefficient-scale estimate and interval bounds -- alongside the coefficient-scale columns. sig is still computed on the coefficient scale (null = 0).
Headers match the printed scale: the no-CI table says "odds ratio" (an OR column is shown), the CI table says the columns are coefficients on the log-odds scale with a bootstrap interval.
The (3) E CI table now shows the intercept and every covariate (CoG) row, so it has the same coefficient rows as summary(fit) without a bootstrap -- previously those rows silently vanished when boot.se was supplied. The covariate row is also now shown in the no-CI (3) E table for the parallel and serial models, matching the early model.
f.binary.early joins the bootstrap CI to the point estimate by row name rather than by position.

**Log-likelihood labeling.** The "Finished LUCID ... model: penalized

log-likelihood = X" completion message printed the *unpenalized* observed-data

value; it now says "observed-data log-likelihood". em_control$loglik_trace is

the unpenalized observed-data log-likelihood for every model type (it was the

penalized objective for a penalized early fit), so its last value equals

$likelihood; the penalized objective still drives the internal

convergence/dip check.

From NEWS.md in the release

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. 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-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). 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: 11.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-10
WARNING12 OK, 1 WARNING2026-05-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.2.1

READMENoVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 3.2.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 25
Examples that run: 65%11 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

5.1K

CRAN downloads in the past year

Rank #5,866 · ~14/day · ~424/mo

Releases R versions

Daily download trend is not available in this view yet.

50230 days

1.4K90 days

5.1K1 year

Compare downloads with other packages →

Also on133 r2u3 autocran46 c2d4u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing LUCIDus adds 57 packages (27 with compiled code, 58 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 3.6.0

Imports (12)

mclustnnetbootjsonlite networkD3 progressstatsutilsglasso glmnet ggplot2grDevices

LinkingTo (0)

none

Suggests (6)

testthat knitr rmarkdown plotly mix visdat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

MosaiClusteR

How these are counted

Code & Tests

Datasets

People & History

People (4)

Qiran Jia

Author, Maintainer since 3.0.1 (2023) · added in 3.0.1

Yinqi Zhao

Author · added in 2.0.0

Jesse Goodrich

Contributor · added in 2.2.1

David Conti

Thesis advisor · added in 2.2.1

Previously maintained by Yinqi Zhao (2.0.0 to 2.2.1) and Cheng Peng (0.9.0 to 1.0.0).

Listed in earlier versions (3)

Show 3 peopleHide 3 people

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

Releases (16)

Pick two releases to compare their code metrics.

3.2.1Latest
record
2026-09-02 · current release · diff ↗
3.2.0
record
2026-09-01 · diff ↗ ·
removed 7 exports
check_and_stabilize_sigma, check_convergence, fill_data, plot, safe_log_sum_exp, safe_normalize, safe_solve

added 5 exports
get_cluster_assignment, get_selected_G, get_selected_Z, get_top_omics_features, plot_cluster_omic_profile
R
R 4.6.0 released · 2026-04-24
3.1.0
record
2026-03-11 · diff ↗ ·
added 11 exports
analyze_missing_pattern, check_and_stabilize_sigma, check_convergence, check_imputation_quality, check_na, fill_data, safe_impute, safe_log_sum_exp, safe_normalize, safe_solve, summary_lucid
R
R 4.5.0 released · 2025-04-11
3.0.3
record
2024-09-23 · diff ↗
3.0.2
record
2024-07-08 · diff ↗ ·
removed 3 exports
plot_lucid, print.sumlucid, summary_lucid

added 1 export
plot
R
R 4.4.0 released · 2024-04-24
3.0.1
record
2023-10-31 · diff ↗ ·
removed 3 exports
boot.lucid, est.lucid, est_lucid

added 2 exports
estimate_lucid, print.sumlucid
R
R 4.3.0 released · 2023-04-21
2.2.1
record
2022-11-08 · diff ↗
2.2
record
2022-08-08 · diff ↗ ·
added 3 exports
boot_lucid, est_lucid, tune_lucid
2.1.5-2
record
2022-06-01 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.5-1
record
2022-04-06 · diff ↗
2.1.5
record
2022-03-28 · diff ↗

Show 9 earlier eventsHide 9 earlier events

2.1.4
record
2022-03-03 · diff ↗ ·
removed 3 exports
def.control, def.tune, tune.lucid

added 4 exports
lucid, plot_lucid, predict_lucid, summary_lucid
R
R 4.1.0 released · 2021-05-18
2.1.0
record
2020-07-22 · diff ↗
2.0.0
record
2020-05-18 · diff ↗ ·
removed 10 exports
boot_lucid, def_initial, def_tol, def_tune, est_lucid, plot_lucid, pred_lucid, sem_lucid, summary_lucid, tune_lucid

added 5 exports
boot.lucid, def.control, def.tune, est.lucid, tune.lucid
R
R 4.0.0 released · 2020-04-24
1.0.0
record
2019-12-02 · diff ↗ ·
added 1 export
boot_lucid
R
R 3.6.0 released · 2019-04-26
0.9.0
record
2018-12-21
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-12-21
Total releases: 16 / 8 yrs
License: MIT + file LICENSE OSI · relicensed from GPL-3 in 3.0.1
Minimum R: ≥ 3.6.0
Bundled data: 451 KB / 2 files
Download size: 2.9 MB

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 3.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.LUCIDus

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 LUCIDus version 3.2.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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