Rdiagnosislist1.4.0 package

Manipulate SNOMED CT Diagnosis Lists

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

attrConcept

Retrieve all attributes of a set of SNOMED CT concepts

batchDecompose

Creates a set of lookups for SNOMED composition

c.SNOMEDconcept

Concatenate vectors of SNOMED CT concepts

compose

Select more specific SNOMED CT concepts based on attributes

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 an...

decompose

Decomposition of meaning of a finding or disorder SNOMED CT concept

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

exportMiADECDB

Exports CDB files for MedCAT / MiADE

exportSNOMEDenvir

Export a SNOMED environment to a folder

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

htmlCodelistHierarchy

Export a SNOMEDcodelist hierarchy to HTML

inactiveIncluded

Check if inactive terms are included in SNOMED CT dictionary

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

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

Rdiagnosislist-package

Rdiagnosislist: A package for manipulating SNOMED CT diagnosis lists

relatedConcepts

Obtain related concepts for a set of SNOMED CT concepts

sampleSNOMED

Sample SNOMED CT dictionary

semanticType

Retrieves semantic types using the text 'tag' in the description

simplify

Retrieves closest single ancestor within a given set of SNOMED CT conc...

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

SNOMEDcodelist

Convert a data.frame to a SNOMEDcodelist object

SNOMEDconcept

Return the SNOMED CT concept IDs for a set of terms

union.SNOMEDconcept

Set operations for SNOMEDconcept vectors

unique.SNOMEDconcept

Unique vector of SNOMED CT concepts

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/>.

  • Maintainer: Anoop D. Shah
  • License: GPL-3
  • Last published: 2025-01-29