Package: Rdiagnosislist 1.5.1

Anoop D. Shah

Rdiagnosislist: Manipulate SNOMED CT Diagnosis Lists

Functions and methods for manipulating 'SNOMED CT' concepts. The package contains functions for loading the 'SNOMED CT' release into a convenient R environment, selecting 'SNOMED CT' concepts using regular expressions, and navigating the 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table of concepts IDs with descriptions. The package can be used to construct sets of 'SNOMED CT' concepts for research (<doi:10.1093/jamia/ocac158>). For more information about 'SNOMED CT' visit <https://www.snomed.org/>.

Authors:Anoop D. Shah [aut, cre]

Rdiagnosislist_1.5.1.tar.gz
Rdiagnosislist_1.5.1.zip(r-4.7)Rdiagnosislist_1.5.1.zip(r-4.6)Rdiagnosislist_1.5.1.zip(r-4.5)
Rdiagnosislist_1.5.1.tgz(r-4.6-any)Rdiagnosislist_1.5.1.tgz(r-4.5-any)
Rdiagnosislist_1.5.1.tar.gz(r-4.7-any)Rdiagnosislist_1.5.1.tar.gz(r-4.6-any)
Rdiagnosislist_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rdiagnosislist/json (API)

# Install 'Rdiagnosislist' in R:
install.packages('Rdiagnosislist', repos = c('https://anoopshah.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/anoopshah/rdiagnosislist/issues

Datasets:
  • CONCEPT - Sample concept table from SNOMED CT dictionary
  • DESCRIPTION - Sample description table from SNOMED CT dictionary
  • EXTENDEDMAP - Sample extended map table from SNOMED CT dictionary
  • HISTORY - Sample history substitution table from SNOMED CT dictionary
  • MANUAL_SYNONYMS - Sample manual synonym table to assist in creation of concept database
  • QUERY - Sample query table from SNOMED CT dictionary
  • READMAPS - Sample mappings from Read to SNOMED CT
  • REFSET - Sample refset table from SNOMED CT dictionary
  • RELATIONSHIP - Sample relationship tables from SNOMED CT dictionary
  • SIMPLEMAP - Sample SIMPLE map table from SNOMED CT dictionary
  • STATEDRELATIONSHIP - Sample relationship tables from SNOMED CT dictionary

On CRAN:

Conda:

7.39 score 13 stars 26 scripts 101 downloads 47 exports 22 dependencies

Last updated from:b729eb852d. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE148
source / vignettesOK190
linux-release-x86_64NOTE191
macos-release-arm64NOTE201
macos-oldrel-arm64NOTE197
windows-develNOTE113
windows-releaseNOTE101
windows-oldrelNOTE112
wasm-releaseOK102

Exports:acronymsaddComposeLookupToCDBaddInactiveConceptsaddWordnetancestorsas.SNOMEDcodelistas.SNOMEDconceptattrConceptbatchDecomposeblacklist_almost_all_except_diseasesblacklist_vague_findingschildrencomposecontractSNOMEDcreateCDBcreateTransitivedecomposedescendantsdescriptiondownloadOrphanetdownloadWordnetexclude_irrelevant_findingsexpandSNOMEDexportexportMiADECDBexportSNOMEDenvirgetMapsgetRefsetgetSNOMEDhasAttributeshtmlCodelistHierarchyinactiveIncludedintersectis.SNOMEDcodelistis.SNOMEDconceptloadREADMAPSloadSNOMEDparentsrelatedConceptssampleSNOMEDsemanticTypesetdiffshowCodelistHierarchysimplifySNOMEDcodelistSNOMEDconceptunion

Dependencies:bitbit64cellrangerclicpp11crayondata.tablegluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readxlrematchrlangtibbleutf8vctrs

Converting and creating codelists
Searching for and using inactive concepts in SNOMED CT | Creating SNOMED CT codelists from scratch | Converting Read codelists to SNOMED CT | HTML codelist for this example | More information
Rendered fromconvertingAndCreatingCodelists.Rmdusingknitr::rmarkdown

Last update: 2025-01-28
Started: 2022-02-11

Converting concept database for natural language processing
Creating a concept database for MiADE and MedCAT | SNOMED CT concept decomposition | More information
Rendered fromcreatingConceptDatabaseForNLP.Rmdusingknitr::rmarkdown

Last update: 2025-01-28
Started: 2024-10-21

Using Rdiagnosislist functions with custom hierarchies
Rendered fromcustomHierarchy.Rmdusingknitr::rmarkdown

Last update: 2025-01-28
Started: 2021-12-09

Using SNOMED dictionaries and codelists
Basic introduction to SNOMED CT | Loading the SNOMED CT dictionaries | Using R environments | SNOMED CT concepts IDs in R | Set operations using SNOMEDconcept | Using relationships between SNOMED CT concepts | Attributes of SNOMED CT concepts | SNOMED CT codelists | 'History of' SNOMED CT concepts | SNOMED CT simple refsets | Mapping between SNOMED CT and ICD-10 and OPCS4 | Mapping between SNOMED CT and Read Clinical Terminology | More information
Rendered fromSNOMEDcodelists.Rmdusingknitr::rmarkdown

Last update: 2025-01-28
Started: 2020-10-22

Readme and manuals

Help Manual

Help pageTopics
Extract acronyms stated in the description of SNOMED CT conceptsacronyms
Add composition lookups to CDBaddComposeLookupToCDB
Add inactive concepts to a SNOMEDcodelist or SNOMEDconcept vectoraddInactiveConcepts
Use WordNet to assist concept database creationaddWordnet
Return the SNOMED CT concept IDs for a set of termsas.data.frame.SNOMEDconcept as.integer64.SNOMEDconcept as.SNOMEDconcept SNOMEDconcept
Retrieve all attributes of a set of SNOMED CT conceptsattrConcept
Creates a set of lookups for SNOMED compositionbatchDecompose
Concatenate vectors of SNOMED CT conceptsc.SNOMEDconcept
Select more specific SNOMED CT concepts based on attributescompose
Creates an environment containing CDB filescreateCDB
Create indices for tables in a SNOMED environmentcreateSNOMEDindices
Create a transitive closure table for is-a relationships for faster ancestor / descendant lookupscreateTransitive
Decomposition of meaning of a finding or disorder SNOMED CT conceptdecompose
Obtain descriptions for a set of SNOMED CT termsdescription
Download Orphanet to assist with adding synonyms for rare diseasesdownloadOrphanet
Download WordNet to assist concept database creationdownloadWordnet
Sample inclusion, exclusion and blacklist sets for a MiADE CDBblacklist_almost_all_except_diseases blacklist_vague_findings exclude_irrelevant_findings
Expand or contract a SNOMEDcodelistcontractSNOMED expandSNOMED showCodelistHierarchy
Export a SNOMEDcodelistexport export.SNOMEDcodelist
Exports CDB files for MedCAT / MiADEexportMiADECDB
Export a SNOMED environment to a folderexportSNOMEDenvir
Obtain Read 2, CTV3, ICD-10 and OPCS4 maps for SNOMED CT conceptsgetMaps
Retrieves a Refset from the REFSET tablegetRefset
Retrieves SNOMED CT dictionary from the global environmentgetSNOMED
Whether SNOMED CT concepts have particular attributeshasAttributes
Sample history substitution table from SNOMED CT dictionaryHISTORY
Export a SNOMEDcodelist hierarchy to HTMLhtmlCodelistHierarchy
Check if inactive terms are included in SNOMED CT dictionaryinactiveIncluded
Check if an object is a SNOMEDcodelistis.SNOMEDcodelist
Check if an object is a SNOMEDconceptis.SNOMEDconcept
Load mappings from Read to SNOMED CT into an R data.tableloadREADMAPS
Load SNOMED CT files from a folder(s) into R data.table objectsloadSNOMED
Sample manual synonym table to assist in creation of concept databaseMANUAL_SYNONYMS
Ancestors and descendants of SNOMED CT conceptsancestors children descendants parents
Display a SNOMEDcodelist on screenprint.SNOMEDcodelist
Display a SNOMEDconcept object with descriptionsprint.SNOMEDconcept
Print method for output of 'decompose' functionprint.SNOMEDfindings
Sample query table from SNOMED CT dictionaryQUERY
Sample mappings from Read to SNOMED CTREADMAPS
Obtain related concepts for a set of SNOMED CT conceptsrelatedConcepts
Sample SNOMED CT dictionarysampleSNOMED
Retrieves semantic types using the text 'tag' in the descriptionsemanticType
Retrieves closest single ancestor within a given set of SNOMED CT conceptssimplify
Sample concept table from SNOMED CT dictionaryCONCEPT SNOMED_CONCEPT
Sample description table from SNOMED CT dictionaryDESCRIPTION SNOMED_DESCRIPTION
Sample extended map table from SNOMED CT dictionaryEXTENDEDMAP SNOMED_EXTENDEDMAP
Sample refset table from SNOMED CT dictionaryREFSET SNOMED_REFSET
Sample relationship tables from SNOMED CT dictionaryRELATIONSHIP SNOMED_RELATIONSHIP SNOMED_STATEDRELATIONSHIP STATEDRELATIONSHIP
Sample SIMPLE map table from SNOMED CT dictionarySIMPLEMAP SNOMED_SIMPLEMAP
Convert a data.frame to a SNOMEDcodelist objectas.SNOMEDcodelist SNOMEDcodelist
Set operations for SNOMEDconcept vectorsintersect intersect.default intersect.SNOMEDconcept setdiff setdiff.default setdiff.SNOMEDconcept union union.default union.SNOMEDconcept
Unique vector of SNOMED CT conceptsunique.SNOMEDconcept