Package: Rdiagnosislist 1.3

Anoop 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. For more information about 'SNOMED CT' visit <https://www.snomed.org/>.

Authors:Anoop Shah [aut, cre]

Rdiagnosislist_1.3.tar.gz
Rdiagnosislist_1.3.tar.gz(r-4.5-noble)Rdiagnosislist_1.3.tar.gz(r-4.4-noble)
Rdiagnosislist_1.3.tgz(r-4.4-emscripten)Rdiagnosislist_1.3.tgz(r-4.3-emscripten)
Rdiagnosislist.pdf |Rdiagnosislist.html✨
Rdiagnosislist/json (API)
NEWS

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

Peer review:

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

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.56 score 1 stars 18 scripts 659 downloads 47 exports 23 dependencies

Last updated 2 months agofrom:4b0c878d86. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 28 2024
R-4.5-linuxOKNov 28 2024

Exports:acronymsaddInactiveConceptsaddWordnetancestorsas.SNOMEDcodelistas.SNOMEDconceptattrConceptbatchDecomposeblacklist_almost_all_except_diseasesblacklist_vague_findingschildrencomposecontractSNOMEDcreateCDBcreateComposeLookupcreateTransitivedecomposedescendantsdescriptiondownloadOrphanetdownloadWordnetexclude_irrelevant_findingsexpandSNOMEDexportexportMiADECDBexportSNOMEDenvirgetMapsgetRefsetgetSNOMEDhasAttributeshtmlCodelistHierarchyinactiveIncludedintersectis.SNOMEDcodelistis.SNOMEDconceptloadREADMAPSloadSNOMEDparentsrelatedConceptssampleSNOMEDsemanticTypesetdiffshowCodelistHierarchysimplifySNOMEDcodelistSNOMEDconceptunion

Dependencies:bitbit64cellrangerclicpp11crayondata.tablefansigluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readxlrematchrlangtibbleutf8vctrs

Converting and creating codelists

Anoop Shah

Rendered fromconvertingAndCreatingCodelists.Rmdusingknitr::rmarkdownon Nov 28 2024.

Last update: 2023-04-18
Started: 2023-04-18

Converting concept database for natural language processing

Anoop Shah

Rendered fromcreatingConceptDatabaseForNLP.Rmdusingknitr::rmarkdownon Nov 28 2024.

Last update: 2024-10-28
Started: 2024-10-28

Using Rdiagnosislist functions with custom hierarchies

Anoop Shah

Rendered fromcustomHierarchy.Rmdusingknitr::rmarkdownon Nov 28 2024.

Last update: 2023-04-18
Started: 2023-04-18

Using SNOMED dictionaries and codelists

Anoop Shah

Rendered fromSNOMEDcodelists.Rmdusingknitr::rmarkdownon Nov 28 2024.

Last update: 2023-04-18
Started: 2021-07-19

Readme and manuals

Help Manual

Help pageTopics
Extract acronyms stated in the description of SNOMED CT conceptsacronyms
Add inactive concepts to a SNOMEDcodelist or SNOMEDconcept vectoraddInactiveConcepts
Use WordNet to assist concept database creationaddWordnet
Returns 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
Creates a set of lookups for SNOMED compositioncreateComposeLookup
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