Package: clinspacy
Type: Package
Title: Clinical Natural Language Processing using 'spaCy', 'scispaCy',
        and 'medspaCy'
Version: 1.0.2.9000
Authors@R: c(person("Karandeep", "Singh",
            email = "kdpsingh@umich.edu", role = c("aut", "cre")),
            person("Benjamin", "Kompa", role = c("aut")),
            person("Andrew", "Beam", role = c("aut")),
            person("Allen", "Schmaltz", role = c("aut")))
Description: 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>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: reticulate (>= 1.19), data.table, assertthat, rappdirs, utils,
        magrittr
RoxygenNote: 7.1.1
URL: https://github.com/ML4LHS/clinspacy
BugReports: https://github.com/ML4LHS/clinspacy/issues
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
Config/pak/sysreqs: libpng-dev python3
Repository: https://kdpsingh.r-universe.dev
Date/Publication: 2021-08-21 19:15:52 UTC
RemoteUrl: https://github.com/kdpsingh/clinspacy
RemoteRef: HEAD
RemoteSha: 2efc73a3dbd152cb57aa65e263ae37310e068c61
NeedsCompilation: no
Packaged: 2026-10-05 10:28:09 UTC; root
Author: Karandeep Singh [aut, cre],
  Benjamin Kompa [aut],
  Andrew Beam [aut],
  Allen Schmaltz [aut]
Maintainer: Karandeep Singh <kdpsingh@umich.edu>