decompose: Decomposition of meaning of a finding or disorder SNOMED CT...

In anoopshah/Rdiagnosislist: Manipulate SNOMED CT Diagnosis Lists

Decomposition of meaning of a finding or disorder SNOMED CT concept

Description

Decomposes a SNOMED CT term into separate components according to the SNOMED CT information model and text parsing. Each term may have a number of possible decompositions. Requires a CDB environment created by createCDB.

Usage

decompose(
  conceptIds,
  diagnosis_text = NULL,
  CDB,
  SNOMED = getSNOMED(),
  noisy = FALSE,
  omit_unmatched = TRUE
)

Arguments

conceptIds	vector of SNOMED CT concepts to decompose
diagnosis_text	vector of SNOMED CT terms (or in theory any text that has the same meaning as the SNOMED CT concept). If NULL, decompositions are created for all SNOMED CT synonyms of the concepts.
CDB	an environment containing CDB files, as created by createCDB
SNOMED	an environment containing the SNOMED CT dictionary
noisy	whether to output messages (for debugging)
omit_unmatched	whether to omit rows in which some attributes could not be matched to SNOMED CT concepts

Value

a SNOMEDfinding objects, which is a data.table with columns rootId (integer64), with (integer64), due_to (integer64), after (integer64), without (integer64), body_site (integer64), severity (integer64), stage (integer64), laterality (integer64), roottext (character), partId (integer64), other_conceptId (character, a string of SNOMED CT concept IDs separated by spaces), origId (integer64)

Examples

## Not run: 
miniCDB <- createCDB(SNOMED = sampleSNOMED())
D <- decompose(as.SNOMEDconcept('Cor pulmonale',
  SNOMED = sampleSNOMED()), CDB = miniCDB, SNOMED = sampleSNOMED())

## End(Not run)

# -------------------------------------------------------
# 83291003 | Cor pulmonale (disorder)
# -------------------------------------------------------
# Root : 367363000 | Right ventricular failure (disorder)
# - Due to : 19829001 | Disorder of lung (disorder)

anoopshah/Rdiagnosislist documentation built on March 29, 2025, 10:46 a.m.