R Observatory: Metrics for epos version 1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epos

1.2Package record

Epilepsy Ontologies' Similarities

0packages depend

3.1Kdownloads / year

24.3%test coverage

11/13flavors OK

Overview

About

Maintained by Bernd MuellerCRAN page ↗GitHub ↗Issues ↗

Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) doi:10.4126/FRL01-006408558, Mueller, Bernd et al. (2017) doi:10.1007/978-3-319-58694-6_22, Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) doi:10.1007/978-3-030-43887-6_52, and Mueller, Bernd et al. (2022) doi:10.1186/s13326-021-00258-w.

Install

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

install.packages("epos", 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("bernd-mueller/epos")

Development version from bernd-mueller/epos. 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-epos

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-epos

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘testthat’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2

READMEYes · 313 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 41
Examples that run: 66%27 run in a plain check · 14 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #14,173 · ~9/day · ~261/mo

Releases R versions

Daily download trend is not available in this view yet.

31430 days

83390 days

3.1K1 year

Compare downloads with other packages →

Also on75 r2u

How downloads are counted

Repository

bernd-mueller/epos ↗Account: bernd-mueller

0Stars

0Forks

0Open issues

0Open PRs

3Releases

118Commits

5Commit identities

License file reads as LGPL-3.0 · 118 commits · Last activity 2025-08-29

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 79
Median days to close, 50 most recently updated closed PRs: 33

Releases over time

2025-08-29 · 32026-07-07 · 3

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/bernd-mueller/epos on 2026-10-18.

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing epos adds 82 packages (39 with compiled code, 65 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.6.0

Imports (11)

hash ggplot2 testthat gridExtra TopKLists stringr xtable mongolitestatsVennDiagram cowplot

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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 (1)

Bernd Mueller

Author, Maintainer · added in 0.1.1

Maintainer since 0.1.0 (2018)

Listed in earlier versions (1)

Bernd Müller

no longer listed · 0.1.0

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2Latest
record
2025-08-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1
record
2024-03-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0
record
2021-02-20 · diff ↗ ·
added 11 exports
drawVenn4, drawVenn4Doc, drawVenn4DrugDoc, drawVenn4Syn, drawVenn5, drawVenn5Doc, drawVenn5DrugDoc, drawVenn5Syn, drawVennGrid, printTop10Drugs, sortTableByRefMatches
0.1.3
record
2020-11-04 · diff ↗ ·
added 3 exports
calcDSEA, getRefAll, plotDSEA
0.1.2
record
2020-10-28 · diff ↗ ·
added 3 exports
calcEnrichment, getTermMatrix, plotEnrichment
unarchivedReturned to CRAN
2020-05-05
0.1.1
record
2020-05-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-03-17
depends on archived package 'hashmap'
R
R 3.6.0 released · 2019-04-26

Show 2 earlier eventsHide 2 earlier events

0.1.0
record
2018-10-08
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-08
Total releases: 7 / 8 yrs
License: LGPL (>= 3) OSI · relicensed from MIT + file LICENSE in 1.1
Minimum R: ≥ 3.6.0
Bundled data: 211 KB / 5 files
Download size: 296 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("epos")

Format

Mueller, B. (2025). epos: Epilepsy Ontologies' Similarities (Version 1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.epos

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 epos version 1.2 [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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