clinspacy

1.0.2

Clinical Natural Language Processing using 'spaCy', 'scispaCy', and 'medspaCy'

0packages depend

3.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Karandeep SinghFirst published 2021-03-201 releasesCRAN page ↗GitHub ↗

Performs biomedical named entity recognition, Unified Medical Language System (UMLS) concept mapping, and negation detection using the Python 'spaCy', 'scispaCy', and 'medspaCy' packages, and transforms extracted data into a wide format for inclusion in machine learning models. The development of the 'scispaCy' package is described by Neumann (2019) doi:10.18653/v1/W19-5034. The 'medspacy' package uses 'ConText', an algorithm for determining the context of clinical statements described by Harkema (2009) doi:10.1016/j.jbi.2009.05.002. Clinspacy also supports entity embeddings from 'scispaCy' and UMLS 'cui2vec' concept embeddings developed by Beam (2018) arXiv:1804.01486.

Install

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

install.packages("clinspacy", 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("ML4LHS/clinspacy")

Development version from ML4LHS/clinspacy. 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-clinspacy

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

# 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-clinspacy

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 57 s · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

88%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 795 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 85%
Return-value docs: 100%
References docs: 0%

Downloads

3.4K

CRAN downloads in the past year

Rank #13,471 · ~9/day · ~282/mo

Releases R versions

Daily download trend is not available in this view yet.

24530 days

78390 days

3.4K1 year

Compare downloads with other packages →

Also on170 r2u12 autocran

Repository

GitHub ↗ ml4lhs/clinspacy

102Stars

21Forks

6Open issues

2Open PRs

2Releases

51Commits

2Contributors

51 commits · Last activity 2024-04-24 · +1% stars, 30d

Stars over time

2025-04-18 · 992026-07-07 · 102

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ml4lhs/clinspacy on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (6)

reticulate data.table assertthat rappdirsutilsmagrittr

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Karandeep Singh

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.2Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2021-03-20
Total releases: 1 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Download size: 42 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →