R: Manipulate SNOMED CT Diagnosis Lists

# Manipulate SNOMED CT Diagnosis Lists

## Documentation for package ‘Rdiagnosislist’ version 1.5.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

acronyms | Extract acronyms stated in the description of SNOMED CT concepts
addComposeLookupToCDB | Add composition lookups to CDB
addInactiveConcepts | Add inactive concepts to a SNOMEDcodelist or SNOMEDconcept vector
addWordnet | Use WordNet to assist concept database creation
ancestors | Ancestors and descendants of SNOMED CT concepts
as.data.frame.SNOMEDconcept | Return the SNOMED CT concept IDs for a set of terms
as.integer64.SNOMEDconcept | Return the SNOMED CT concept IDs for a set of terms
as.SNOMEDcodelist | Convert a data.frame to a SNOMEDcodelist object
as.SNOMEDconcept | Return the SNOMED CT concept IDs for a set of terms
attrConcept | Retrieve all attributes of a set of SNOMED CT concepts
batchDecompose | Creates a set of lookups for SNOMED composition
blacklist_almost_all_except_diseases | Sample inclusion, exclusion and blacklist sets for a MiADE CDB
blacklist_vague_findings | Sample inclusion, exclusion and blacklist sets for a MiADE CDB
c.SNOMEDconcept | Concatenate vectors of SNOMED CT concepts
children | Ancestors and descendants of SNOMED CT concepts
compose | Select more specific SNOMED CT concepts based on attributes
CONCEPT | Sample concept table from SNOMED CT dictionary
contractSNOMED | Expand or contract a SNOMEDcodelist
createCDB | Creates an environment containing CDB files
createSNOMEDindices | Create indices for tables in a SNOMED environment
createTransitive | Create a transitive closure table for is-a relationships for faster ancestor / descendant lookups
decompose | Decomposition of meaning of a finding or disorder SNOMED CT concept
descendants | Ancestors and descendants of SNOMED CT concepts
DESCRIPTION | Sample description table from SNOMED CT dictionary
description | Obtain descriptions for a set of SNOMED CT terms
downloadOrphanet | Download Orphanet to assist with adding synonyms for rare diseases
downloadWordnet | Download WordNet to assist concept database creation
exclude_irrelevant_findings | Sample inclusion, exclusion and blacklist sets for a MiADE CDB
expandSNOMED | Expand or contract a SNOMEDcodelist
export | Export a SNOMEDcodelist
export.SNOMEDcodelist | Export a SNOMEDcodelist
exportMiADECDB | Exports CDB files for MedCAT / MiADE
exportSNOMEDenvir | Export a SNOMED environment to a folder
EXTENDEDMAP | Sample extended map table from SNOMED CT dictionary
getMaps | Obtain Read 2, CTV3, ICD-10 and OPCS4 maps for SNOMED CT concepts
getRefset | Retrieves a Refset from the REFSET table
getSNOMED | Retrieves SNOMED CT dictionary from the global environment
hasAttributes | Whether SNOMED CT concepts have particular attributes
HISTORY | Sample history substitution table from SNOMED CT dictionary
htmlCodelistHierarchy | Export a SNOMEDcodelist hierarchy to HTML
inactiveIncluded | Check if inactive terms are included in SNOMED CT dictionary
intersect | Set operations for SNOMEDconcept vectors
intersect.default | Set operations for SNOMEDconcept vectors
intersect.SNOMEDconcept | Set operations for SNOMEDconcept vectors
is.SNOMEDcodelist | Check if an object is a SNOMEDcodelist
is.SNOMEDconcept | Check if an object is a SNOMEDconcept
loadREADMAPS | Load mappings from Read to SNOMED CT into an R data.table
loadSNOMED | Load SNOMED CT files from a folder(s) into R data.table objects
MANUAL_SYNONYMS | Sample manual synonym table to assist in creation of concept database
parents | Ancestors and descendants of SNOMED CT concepts
print.SNOMEDcodelist | Display a SNOMEDcodelist on screen
print.SNOMEDconcept | Display a SNOMEDconcept object with descriptions
print.SNOMEDfindings | Print method for output of 'decompose' function
QUERY | Sample query table from SNOMED CT dictionary
READMAPS | Sample mappings from Read to SNOMED CT
REFSET | Sample refset table from SNOMED CT dictionary
relatedConcepts | Obtain related concepts for a set of SNOMED CT concepts
RELATIONSHIP | Sample relationship tables from SNOMED CT dictionary
sampleSNOMED | Sample SNOMED CT dictionary
semanticType | Retrieves semantic types using the text 'tag' in the description
setdiff | Set operations for SNOMEDconcept vectors
setdiff.default | Set operations for SNOMEDconcept vectors
setdiff.SNOMEDconcept | Set operations for SNOMEDconcept vectors
showCodelistHierarchy | Expand or contract a SNOMEDcodelist
SIMPLEMAP | Sample SIMPLE map table from SNOMED CT dictionary
simplify | Retrieves closest single ancestor within a given set of SNOMED CT concepts
SNOMEDcodelist | Convert a data.frame to a SNOMEDcodelist object
SNOMEDconcept | Return the SNOMED CT concept IDs for a set of terms
SNOMED_CONCEPT | Sample concept table from SNOMED CT dictionary
SNOMED_DESCRIPTION | Sample description table from SNOMED CT dictionary
SNOMED_EXTENDEDMAP | Sample extended map table from SNOMED CT dictionary
SNOMED_REFSET | Sample refset table from SNOMED CT dictionary
SNOMED_RELATIONSHIP | Sample relationship tables from SNOMED CT dictionary
SNOMED_SIMPLEMAP | Sample SIMPLE map table from SNOMED CT dictionary
SNOMED_STATEDRELATIONSHIP | Sample relationship tables from SNOMED CT dictionary
STATEDRELATIONSHIP | Sample relationship tables from SNOMED CT dictionary
union | Set operations for SNOMEDconcept vectors
union.default | Set operations for SNOMEDconcept vectors
union.SNOMEDconcept | Set operations for SNOMEDconcept vectors
unique.SNOMEDconcept | Unique vector of SNOMED CT concepts