R Observatory: Metrics for LBDiscover version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LBDiscover

0.1.0Package record

Literature-Based Discovery Tools for Biomedical Research

0packages depend

2.4Kdownloads / year

28.8%test coverage

13/13flavors OK

Overview

About

Maintained by Chao LiuCRAN page ↗GitHub ↗Website ↗Issues ↗

A suite of tools for literature-based discovery in biomedical research. Provides functions for retrieving scientific articles from 'PubMed' and other NCBI databases, extracting biomedical entities (diseases, drugs, genes, etc.), building co-occurrence networks, and applying various discovery models including 'ABC', 'AnC', 'LSI', and 'BITOLA'. The package also includes visualization tools for exploring discovered connections.

Changes in 0.1.0

Initial CRAN submission.

From NEWS.md in the release

Install

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

install.packages("LBDiscover", 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("chaoliu-cl/LBDiscover")

Development version from chaoliu-cl/LBDiscover. 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-lbdiscover

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-LBDiscover

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-LBDiscover

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: 2.3 min · r-oldrel-windows-x86_64

Status changes

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

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 374 wordsVignettesNoNEWSYes · 67% structured · mentions 0.1.0Citation fileNoWebsiteYes · pkgdown

Help pages: 105 (31 internal)
Examples that run: 25%1 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 4%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #21,140 · ~7/day · ~202/mo

Releases R versions

Daily download trend is not available in this view yet.

23930 days

60890 days

2.4K1 year

Compare downloads with other packages →

Also on71 r2u8 autocran

How downloads are counted

Repository

chaoliu-cl/lbdiscover ↗Account: chaoliu-cl

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2025-10-05

Responsiveness

not measured

How these are measured

PracticesBeta

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

Checks run against github.com/chaoliu-cl/lbdiscover 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

Governance and community (1)

Contributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-10-05 · The repository has a site deploy workflow

pkgdown site last built 2025-10-05

Coverage (1)

Coverage reporting

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing LBDiscover adds 20 packages (14 with compiled code, 12 MB of source tarballs). Heaviest: igraph 4.8 MB, openssl 1.1 MB, jsonlite 1.0 MB.

Depends (1)

R >= 4.1.0

Imports (11)

httr xml2 igraphMatrixutilsstatsgrDevicesgraphicstoolsrentrez jsonlite

LinkingTo (0)

none

Suggests (17)

openxlsx SnowballC visNetwork (>= 2.1.0)spacyrparalleldigest irlba knitr rmarkdown base64enc reticulate testthat mockery covr htmltools data.table tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Chao Liu

Author, Maintainer since 0.1.0 (2025)

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
2025-06-16 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-06-16
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 553 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LBDiscover")

Format

Chao Liu. (2025). LBDiscover: Literature-Based Discovery Tools for Biomedical Research (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.LBDiscover

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 LBDiscover version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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