{ "_id": "6a253dc84b233be198399490", "Package": "clinspacy", "Type": "Package", "Title": "Clinical Natural Language Processing using 'spaCy', 'scispaCy',\nand 'medspaCy'", "Version": "1.0.2.9000", "Authors@R": "c(person(\"Karandeep\", \"Singh\",\nemail = \"kdpsingh@umich.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Benjamin\", \"Kompa\", role = c(\"aut\")),\nperson(\"Andrew\", \"Beam\", role = c(\"aut\")),\nperson(\"Allen\", \"Schmaltz\", role = c(\"aut\")))", "Description": "Performs biomedical named entity recognition, Unified\nMedical Language System (UMLS) concept mapping, and negation\ndetection using the Python 'spaCy', 'scispaCy', and 'medspaCy'\npackages, and transforms extracted data into a wide format for\ninclusion in machine learning models. The development of the\n'scispaCy' package is described by Neumann (2019)\n. The 'medspacy' package uses\n'ConText', an algorithm for determining the context of clinical\nstatements described by Harkema (2009)\n. Clinspacy also supports entity\nembeddings from 'scispaCy' and UMLS 'cui2vec' concept\nembeddings developed by Beam (2018) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "URL": "https://github.com/ML4LHS/clinspacy", "BugReports": "https://github.com/ML4LHS/clinspacy/issues", "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": { "Date": "2026-06-07 09:43:08 UTC", "User": "root" }, "Author": "Karandeep Singh [aut, cre],\nBenjamin Kompa [aut],\nAndrew Beam [aut],\nAllen Schmaltz [aut]", "Maintainer": "Karandeep Singh ", "MD5sum": "e7665a68433d6c4229959effda347ec1", "_user": "kdpsingh", "_type": "src", "_file": "clinspacy_1.0.2.9000.tar.gz", "_fileid": "f8a3befc6a4db3eef60546119ca0f511cd1c0110df8dec448c5880b1e8ede3f5", "_filesize": 212424, "_sha256": "f8a3befc6a4db3eef60546119ca0f511cd1c0110df8dec448c5880b1e8ede3f5", "_created": "2026-06-07T09:43:08.000Z", "_published": "2026-06-07T09:45:44.750Z", "_distro": "noble", "_jobs": [ { "job": 79948796449, "time": 109, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7462942698" }, { "job": 79948796454, "time": 112, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7462943008" }, { "job": 79948796461, "time": 123, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7462941860" }, { "job": 79948796451, "time": 113, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7462941206" }, { "job": 79948647535, "time": 155, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7462929377" }, { "job": 79948796458, "time": 99, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7462941517" }, { "job": 79948796453, "time": 89, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7462940354" }, { "job": 79948796459, "time": 70, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7462938182" }, { "job": 79948796457, "time": 61, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7462937044" } ], "_buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/kdpsingh/clinspacy", "_commit": { "id": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "author": "Karandeep Singh ", "committer": "Karandeep Singh ", "message": "Attempt to fix https://github.com/ML4LHS/clinspacy/issues/11 by updating reticulate to v1.19 and setting clinspacy conda env to Python 3.8\n", "time": 1629573352 }, "_maintainer": { "name": "Karandeep Singh", "email": "kdpsingh@umich.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "reticulate", "version": ">= 1.19", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "rappdirs", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "kdpsingh", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 102, "_userbio": { "uuid": 3826233, "type": "user", "name": "Karandeep Singh", "description": "Chief Health AI Officer at UCSD Health" }, "_downloads": { "count": 192, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/clinspacy" }, "_devurl": "https://github.com/ml4lhs/clinspacy", "_searchresults": 36, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/clinspacy.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/kdpsingh/clinspacy", "_realowner": "kdpsingh", "_cranurl": true, "_releases": [ { "version": "1.0.2", "date": "2021-03-20" } ], "_exports": [ "%>%", "bind_clinspacy", "bind_clinspacy_embeddings", "clinspacy", "clinspacy_init", "dataset_cui2vec_definitions", "dataset_cui2vec_embeddings", "dataset_mtsamples" ], "_help": [ { "page": "bind_clinspacy", "title": "This function binds columns containing either the lemma of the entity or the UMLS concept unique identifier (CUI) with frequencies to a data frame. The resulting data frame can be used to train a machine learning model or for additional feature selection.", "topics": [ "bind_clinspacy" ] }, { "page": "bind_clinspacy_embeddings", "title": "This function binds columns containing entity or concept embeddings to a data frame. The entity embeddings are derived from the scispacy package, and the concept embeddings are derived from the 'dataset_cui2vec_embeddings' dataset included with this package.", "topics": [ "bind_clinspacy_embeddings" ] }, { "page": "clinspacy", "title": "This is the primary function for processing both data frames and character vectors in the 'clinspacy' package.", "topics": [ "clinspacy" ] }, { "page": "clinspacy_init", "title": "Initializes clinspacy. This function is optional to run but gives you more control over the parameters used by scispacy at initiation. If you do not run this function, it will be run with default parameters the first time that any of the package functions are run.", "topics": [ "clinspacy_init" ] }, { "page": "dataset_cui2vec_definitions", "title": "Cui2vec concept definitions", "topics": [ "dataset_cui2vec_definitions" ] }, { "page": "dataset_cui2vec_embeddings", "title": "Cui2vec concept embeddings", "topics": [ "dataset_cui2vec_embeddings" ] }, { "page": "dataset_mtsamples", "title": "Medical transcription samples.", "topics": [ "dataset_mtsamples" ] } ], "_readme": "https://github.com/kdpsingh/clinspacy/raw/HEAD/README.md", "_rundeps": [ "assertthat", "data.table", "here", "jsonlite", "lattice", "magrittr", "Matrix", "png", "rappdirs", "Rcpp", "RcppTOML", "reticulate", "rlang", "rprojroot", "withr" ], "_score": 5.2638726768652235, "_indexed": true, "_nocasepkg": "clinspacy", "_universes": [ "kdpsingh", "ml4lhs" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2.9000", "date": "2026-06-07T09:45:04.000Z", "distro": "noble", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "6d4dc7aec5d9d232e76ceef19111c4424f4e009d05fbfb8f4f6cebbb34798c6a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" }, { "r": "4.6.0", "os": "linux", "version": "1.0.2.9000", "date": "2026-06-07T09:45:06.000Z", "distro": "noble", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "13bc23000e3c3db9b22960b21dd52179ff87661fb2fc2d2fa92c656aa560e818", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2.9000", "date": "2026-06-07T09:44:58.000Z", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "d8e9a40d2eb1544592d5babcce348e19c6b75501b92f8d759429561fd2b722da", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" }, { "r": "4.6.0", "os": "mac", "version": "1.0.2.9000", "date": "2026-06-07T09:44:53.000Z", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "642f3ae0ef3c2ffea621f33a47a698a6aac61f543a2bbd033efbf53f0762fe20", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2.9000", "date": "2026-06-07T09:45:03.000Z", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "157802761be9f3d9cdc10f1d191d832308c14a4a11fa0244e945394210be5aba", "status": "success", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" }, { "r": "4.7.0", "os": "win", "version": "1.0.2.9000", "date": "2026-06-07T09:44:33.000Z", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "cc0ee3a1e7dca22848d298fc1e1efbf75d010b2b18510fc351b3dc3034fd1620", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" }, { "r": "4.5.3", "os": "win", "version": "1.0.2.9000", "date": "2026-06-07T09:44:20.000Z", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "2e52a6ab492319687466e68132a8ead5f4c12124c462b8f6008726228ba875b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" }, { "r": "4.6.0", "os": "win", "version": "1.0.2.9000", "date": "2026-06-07T09:44:09.000Z", "commit": "2efc73a3dbd152cb57aa65e263ae37310e068c61", "fileid": "3e55602686d8ed4f8a1c7ffc0300a506e2f7aacde6af744f6a1e136a43ef4c5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kdpsingh/actions/runs/27088899615" } ] }