{ "_id": "6a197496acfb0bcc41df0542", "Package": "Rdiagnosislist", "Title": "Manipulate SNOMED CT Diagnosis Lists", "Version": "1.4.0", "Authors@R": "person(given = c(\"Anoop\", \"D.\"),\nfamily = \"Shah\",\nrole = c(\"aut\", \"cre\"),\nemail = \"anoop@doctors.org.uk\",\ncomment = structure(\"0000-0002-8907-5724\", .Names = \"ORCID\"))", "Description": "Functions and methods for manipulating 'SNOMED CT'\nconcepts. The package contains functions for loading the\n'SNOMED CT' release into a convenient R environment, selecting\n'SNOMED CT' concepts using regular expressions, and navigating\nthe 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3\nclass for a vector of 'SNOMED CT' concepts (stored as 64-bit\nintegers) and the 'SNOMEDcodelist' S3 class for a table of\nconcepts IDs with descriptions. The package can be used to\nconstruct sets of 'SNOMED CT' concepts for research\n(). For more information about\n'SNOMED CT' visit .", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.1", "Author": "Anoop D. Shah [aut, cre]\n()", "Maintainer": "Anoop D. Shah ", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 11:09:22 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-01-29 08:30:07 UTC", "RemoteUrl": "https://github.com/cran/Rdiagnosislist", "RemoteRef": "HEAD", "RemoteSha": "944b78d906e67470e910547a01c07278cb66cbbc", "MD5sum": "437598bf0b1de6235906d85b1022746f", "_user": "cran", "_type": "src", "_file": "Rdiagnosislist_1.4.0.tar.gz", "_fileid": "2f275ce9ee02175aa71fa04ad05d9920e6f1d20bf5fad516f2c34eb180cdcb8b", "_filesize": 489457, "_sha256": "2f275ce9ee02175aa71fa04ad05d9920e6f1d20bf5fad516f2c34eb180cdcb8b", "_created": "2026-05-29T11:09:22.000Z", "_published": "2026-05-29T11:12:22.254Z", "_distro": "noble", "_jobs": [ { "job": 78489160348, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7289308582" }, { "job": 78489160324, "time": 136, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7289306431" }, { "job": 78487969193, "time": 502, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7289266581" }, { "job": 78489160331, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7289299321" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26633504658", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/Rdiagnosislist", "_commit": { "id": "944b78d906e67470e910547a01c07278cb66cbbc", "author": "Anoop D. Shah ", "committer": "cran-robot ", "message": "version 1.4.0\n", "time": 1738139407 }, "_maintainer": { "name": "Anoop D. Shah", "email": "anoop@doctors.org.uk", "orcid": "0000-0002-8907-5724" }, "_registered": true, "_dependencies": [ { "package": "readxl", "role": "Depends" }, { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "data.table", "version": ">= 1.12.8", "role": "Imports" }, { "package": "bit64", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 142, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rdiagnosislist" }, "_searchresults": 21, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/Rdiagnosislist.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.2", "date": "2021-07-19" }, { "version": "1.0", "date": "2021-11-28" }, { "version": "1.2", "date": "2023-04-18" }, { "version": "1.3", "date": "2024-10-28" }, { "version": "1.4.0", "date": "2025-01-29" } ], "_exports": [ "acronyms", "addComposeLookupToCDB", "addInactiveConcepts", "addWordnet", "ancestors", "as.SNOMEDcodelist", "as.SNOMEDconcept", "attrConcept", "batchDecompose", "blacklist_almost_all_except_diseases", "blacklist_vague_findings", "children", "compose", "contractSNOMED", "createCDB", "createTransitive", "decompose", "descendants", "description", "downloadOrphanet", "downloadWordnet", "exclude_irrelevant_findings", "expandSNOMED", "export", "exportMiADECDB", "exportSNOMEDenvir", "getMaps", "getRefset", "getSNOMED", "hasAttributes", "htmlCodelistHierarchy", "inactiveIncluded", "intersect", "is.SNOMEDcodelist", "is.SNOMEDconcept", "loadREADMAPS", "loadSNOMED", "parents", "relatedConcepts", "sampleSNOMED", "semanticType", "setdiff", "showCodelistHierarchy", "simplify", "SNOMEDcodelist", "SNOMEDconcept", "union" ], "_datasets": [ { "name": "CONCEPT", "title": "Sample concept table from SNOMED CT dictionary", "object": "CONCEPT", "class": [ "data.table", "data.frame" ], "fields": [ "id", "effectiveTime", "active", "moduleId", "definitionStatusId" ], "rows": 509, "table": true, "tojson": true }, { "name": "DESCRIPTION", "title": "Sample description table from SNOMED CT dictionary", "object": "DESCRIPTION", "class": [ "data.table", "data.frame" ], "fields": [ "id", "effectiveTime", "active", "moduleId", "conceptId", "languageCode", "typeId", "term", "caseSignificanceId" ], "rows": 1596, "table": true, "tojson": true }, { "name": "EXTENDEDMAP", "title": "Sample extended map table from SNOMED CT dictionary", "object": "EXTENDEDMAP", "class": [ "data.table", "data.frame" ], "fields": [ "effectiveTime", "active", "moduleId", "refsetId", "referencedComponentId", "mapGroup", "mapPriority", "mapRule", "mapAdvice", "mapTarget", "mapCategoryId", "mapBlock" ], "rows": 915, "table": true, "tojson": true }, { "name": "HISTORY", "title": "Sample history substitution table from SNOMED CT dictionary", "object": "HISTORY", "class": [ "data.table", "data.frame" ], "fields": [ "OLDCONCEPTID", "OLDCONCEPTSTATUS", "NEWCONCEPTID", "NEWCONCEPTSTATUS", "PATH", "ISAMBIGUOUS", "ITERATIONS", "OLDCONCEPTFSN", "OLDCONCEPTFSN_TAGCOUNT", "NEWCONCEPTFSN", "NEWCONCEPTFSN_STATUS", "TLH_IDENTICALFLAG", "FSN_TAGLESSIDENTICALFLAG", "FSN_TAGIDENTICALFLAG" ], "rows": 199, "table": true, "tojson": true }, { "name": "MANUAL_SYNONYMS", "title": "Sample manual synonym table to assist in creation of concept database", "object": "MANUAL_SYNONYMS", "class": [ "data.frame" ], "fields": [ "synonym", "snomed", "bidirectional" ], "rows": 317, "table": true, "tojson": true }, { "name": "QUERY", "title": "Sample query table from SNOMED CT dictionary", "object": "QUERY", "class": [ "data.table", "data.frame" ], "fields": [ "supertypeId", "subtypeId", "provenance" ], "rows": 1767, "table": true, "tojson": true }, { "name": "READMAPS", "title": "Sample mappings from Read to SNOMED CT", "object": "READMAPS", "class": [ "data.table", "data.frame" ], "fields": [ "conceptId", "read2_code", "read2_term", "ctv3_concept", "ctv3_termid" ], "rows": 124, "table": true, "tojson": true }, { "name": "REFSET", "title": "Sample refset table from SNOMED CT dictionary", "object": "REFSET", "class": [ "data.table", "data.frame" ], "fields": [ "effectiveTime", "active", "moduleId", "refsetId", "referencedComponentId" ], "rows": 428, "table": true, "tojson": true }, { "name": "RELATIONSHIP", "title": "Sample relationship tables from SNOMED CT dictionary", "object": "RELATIONSHIP", "class": [ "data.table", "data.frame" ], "fields": [ "id", "effectiveTime", "active", "moduleId", "sourceId", "destinationId", "relationshipGroup", "typeId", "characteristicTypeId", "modifierId" ], "rows": 1915, "table": true, "tojson": true }, { "name": "SIMPLEMAP", "title": "Sample SIMPLE map table from SNOMED CT dictionary", "object": "SIMPLEMAP", "class": [ "data.table", "data.frame" ], "fields": [ "effectiveTime", "active", "moduleId", "refsetId", "referencedComponentId", "mapTarget" ], "rows": 124, "table": true, "tojson": true }, { "name": "STATEDRELATIONSHIP", "title": "Sample relationship tables from SNOMED CT dictionary", "object": "STATEDRELATIONSHIP", "class": [ "data.table", "data.frame" ], "fields": [ "id", "effectiveTime", "active", "moduleId", "sourceId", "destinationId", "relationshipGroup", "typeId", "characteristicTypeId", "modifierId" ], "rows": 329, "table": true, "tojson": true } ], "_help": [ { "page": "acronyms", "title": "Extract acronyms stated in the description of SNOMED CT concepts", "topics": [ "acronyms" ] }, { "page": "addComposeLookupToCDB", "title": "Add composition lookups to CDB", "concept": [ "CDB functions" ], "topics": [ "addComposeLookupToCDB" ] }, { "page": "addInactiveConcepts", "title": "Add inactive concepts to a SNOMEDcodelist or SNOMEDconcept vector", "concept": [ "SNOMEDcodelist functions" ], "topics": [ "addInactiveConcepts" ] }, { "page": "addWordnet", "title": "Use WordNet to assist concept database creation", "concept": [ "CDB functions" ], "topics": [ "addWordnet" ] }, { "page": "SNOMEDconcept", "title": "Return the SNOMED CT concept IDs for a set of terms", "concept": [ "SNOMEDconcept functions" ], "topics": [ "as.data.frame.SNOMEDconcept", "as.integer64.SNOMEDconcept", "as.SNOMEDconcept", "SNOMEDconcept" ] }, { "page": "attrConcept", "title": "Retrieve all attributes of a set of SNOMED CT concepts", "topics": [ "attrConcept" ] }, { "page": "batchDecompose", "title": "Creates a set of lookups for SNOMED composition", "concept": [ "CDB functions" ], "topics": [ "batchDecompose" ] }, { "page": "c.SNOMEDconcept", "title": "Concatenate vectors of SNOMED CT concepts", "concept": [ "SNOMEDconcept functions" ], "topics": [ "c.SNOMEDconcept" ] }, { "page": "compose", "title": "Select more specific SNOMED CT concepts based on attributes", "topics": [ "compose" ] }, { "page": "createCDB", "title": "Creates an environment containing CDB files", "concept": [ "CDB functions" ], "topics": [ "createCDB" ] }, { "page": "createSNOMEDindices", "title": "Create indices for tables in a SNOMED environment", "topics": [ "createSNOMEDindices" ] }, { "page": "createTransitive", "title": "Create a transitive closure table for is-a relationships for faster ancestor / descendant lookups", "topics": [ "createTransitive" ] }, { "page": "decompose", "title": "Decomposition of meaning of a finding or disorder SNOMED CT concept", "topics": [ "decompose" ] }, { "page": "description", "title": "Obtain descriptions for a set of SNOMED CT terms", "topics": [ "description" ] }, { "page": "downloadOrphanet", "title": "Download Orphanet to assist with adding synonyms for rare diseases", "concept": [ "CDB functions" ], "topics": [ "downloadOrphanet" ] }, { "page": "downloadWordnet", "title": "Download WordNet to assist concept database creation", "concept": [ "CDB functions" ], "topics": [ "downloadWordnet" ] }, { "page": "exclude_irrelevant_findings", "title": "Sample inclusion, exclusion and blacklist sets for a MiADE CDB", "concept": [ "MiADE functions" ], "topics": [ "blacklist_almost_all_except_diseases", "blacklist_vague_findings", "exclude_irrelevant_findings" ] }, { "page": "expandSNOMED", "title": "Expand or contract a SNOMEDcodelist", "concept": [ "SNOMEDcodelist functions" ], "topics": [ "contractSNOMED", "expandSNOMED", "showCodelistHierarchy" ] }, { "page": "export", "title": "Export a SNOMEDcodelist", "concept": [ "SNOMEDcodelist functions" ], "topics": [ "export", "export.SNOMEDcodelist" ] }, { "page": "exportMiADECDB", "title": "Exports CDB files for MedCAT / MiADE", "concept": [ "MiADE functions" ], "topics": [ "exportMiADECDB" ] }, { "page": "exportSNOMEDenvir", "title": "Export a SNOMED environment to a folder", "topics": [ "exportSNOMEDenvir" ] }, { "page": "getMaps", "title": "Obtain Read 2, CTV3, ICD-10 and OPCS4 maps for SNOMED CT concepts", "topics": [ "getMaps" ] }, { "page": "getRefset", "title": "Retrieves a Refset from the REFSET table", "topics": [ "getRefset" ] }, { "page": "getSNOMED", "title": "Retrieves SNOMED CT dictionary from the global environment", "topics": [ "getSNOMED" ] }, { "page": "hasAttributes", "title": "Whether SNOMED CT concepts have particular attributes", "topics": [ "hasAttributes" ] }, { "page": "HISTORY", "title": "Sample history substitution table from SNOMED CT dictionary", "concept": [ "SNOMEDsample", "sampleSNOMED" ], "topics": [ "HISTORY" ] }, { "page": "htmlCodelistHierarchy", "title": "Export a SNOMEDcodelist hierarchy to HTML", "topics": [ "htmlCodelistHierarchy" ] }, { "page": "inactiveIncluded", "title": "Check if inactive terms are included in SNOMED CT dictionary", "topics": [ "inactiveIncluded" ] }, { "page": "is.SNOMEDcodelist", "title": "Check if an object is a SNOMEDcodelist", "concept": [ "SNOMEDcodelist functions" ], "topics": [ "is.SNOMEDcodelist" ] }, { "page": "is.SNOMEDconcept", "title": "Check if an object is a SNOMEDconcept", "concept": [ "SNOMEDconcept functions" ], "topics": [ "is.SNOMEDconcept" ] }, { "page": "loadREADMAPS", "title": "Load mappings from Read to SNOMED CT into an R data.table", "topics": [ "loadREADMAPS" ] }, { "page": "loadSNOMED", "title": "Load SNOMED CT files from a folder(s) into R data.table objects", "topics": [ "loadSNOMED" ] }, { "page": "MANUAL_SYNONYMS", "title": "Sample manual synonym table to assist in creation of concept database", "topics": [ "MANUAL_SYNONYMS" ] }, { "page": "parents", "title": "Ancestors and descendants of SNOMED CT concepts", "topics": [ "ancestors", "children", "descendants", "parents" ] }, { "page": "print.SNOMEDcodelist", "title": "Display a SNOMEDcodelist on screen", "concept": [ "SNOMEDcodelist functions" ], "topics": [ "print.SNOMEDcodelist" ] }, { "page": "print.SNOMEDconcept", "title": "Display a SNOMEDconcept object with descriptions", "concept": [ "SNOMEDconcept functions" ], "topics": [ "print.SNOMEDconcept" ] }, { "page": "print.SNOMEDfindings", "title": "Print method for output of 'decompose' function", "topics": [ "print.SNOMEDfindings" ] }, { "page": "QUERY", "title": "Sample query table from SNOMED CT dictionary", "concept": [ "SNOMEDsample" ], "topics": [ "QUERY" ] }, { "page": "READMAPS", "title": "Sample mappings from Read to SNOMED CT", "concept": [ "sampleSNOMED" ], "topics": [ "READMAPS" ] }, { "page": "relatedConcepts", "title": "Obtain related concepts for a set of SNOMED CT concepts", "topics": [ "relatedConcepts" ] }, { "page": "sampleSNOMED", "title": "Sample SNOMED CT dictionary", "concept": [ "sampleSNOMED" ], "topics": [ "sampleSNOMED" ] }, { "page": "semanticType", "title": "Retrieves semantic types using the text 'tag' in the description", "topics": [ "semanticType" ] }, { "page": "simplify", "title": "Retrieves closest single ancestor within a given set of SNOMED CT concepts", "topics": [ "simplify" ] }, { "page": "SNOMED_CONCEPT", "title": "Sample concept table from SNOMED CT dictionary", "concept": [ "sampleSNOMED" ], "topics": [ "CONCEPT", "SNOMED_CONCEPT" ] }, { "page": "SNOMED_DESCRIPTION", "title": "Sample description table from SNOMED CT dictionary", "concept": [ "sampleSNOMED" ], "topics": [ "DESCRIPTION", "SNOMED_DESCRIPTION" ] }, { "page": "SNOMED_EXTENDEDMAP", "title": "Sample extended map table from SNOMED CT dictionary", "concept": [ "sampleSNOMED" ], "topics": [ "EXTENDEDMAP", "SNOMED_EXTENDEDMAP" ] }, { "page": "SNOMED_REFSET", "title": "Sample refset table from SNOMED CT dictionary", "concept": [ "sampleSNOMED" ], "topics": [ "REFSET", "SNOMED_REFSET" ] }, { "page": "SNOMED_RELATIONSHIP", "title": "Sample relationship tables from SNOMED CT dictionary", "concept": [ "SNOMEDsample", "sampleSNOMED" ], "topics": [ "RELATIONSHIP", "SNOMED_RELATIONSHIP", "SNOMED_STATEDRELATIONSHIP", "STATEDRELATIONSHIP" ] }, { "page": "SNOMED_SIMPLEMAP", "title": "Sample SIMPLE map table from SNOMED CT dictionary", "concept": [ "sampleSNOMED" ], "topics": [ "SIMPLEMAP", "SNOMED_SIMPLEMAP" ] }, { "page": "SNOMEDcodelist", "title": "Convert a data.frame to a SNOMEDcodelist object", "concept": [ "SNOMEDcodelist functions" ], "topics": [ "as.SNOMEDcodelist", "SNOMEDcodelist" ] }, { "page": "union.SNOMEDconcept", "title": "Set operations for SNOMEDconcept vectors", "concept": [ "SNOMEDconcept functions" ], "topics": [ "intersect", "intersect.default", "intersect.SNOMEDconcept", "setdiff", "setdiff.default", "setdiff.SNOMEDconcept", "union", "union.default", "union.SNOMEDconcept" ] }, { "page": "unique.SNOMEDconcept", "title": "Unique vector of SNOMED CT concepts", "concept": [ "SNOMEDconcept functions" ], 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