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Rdiagnosislist

This is an R package for using the SNOMED CT hierarchy and manipulating lists of SNOMED CT codes.

It includes functions for loading a SNOMED CT distribution into an R environment, searching for concepts by regular expression search, finding attributes of concepts, navigating the hierarchy, and handling lists of SNOMED CT concepts.

This is an open source package licensed under GPL V3.

The stable version is available on CRAN: https://cran.r-project.org/web/packages/Rdiagnosislist/index.html

This GitHub repository contains the development version.

For feedback or suggestions, please contact Anoop Shah (anoop@doctors.org.uk).

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Version

Install

install.packages('Rdiagnosislist')

Monthly Downloads

289

Version

1.4.0

License

GPL-3

Maintainer

Anoop Shah

Last Published

January 29th, 2025

Functions in Rdiagnosislist (1.4.0)

addInactiveConcepts

Add inactive concepts to a SNOMEDcodelist or SNOMEDconcept vector

Decomposition of meaning of a finding or disorder SNOMED CT concept

Select more specific SNOMED CT concepts based on attributes

createTransitive

Create a transitive closure table for is-a relationships for faster ancestor / descendant lookups

createSNOMEDindices

Create indices for tables in a SNOMED environment

Obtain descriptions for a set of SNOMED CT terms

Whether SNOMED CT concepts have particular attributes

htmlCodelistHierarchy

Export a SNOMEDcodelist hierarchy to HTML

print.SNOMEDconcept

Display a SNOMEDconcept object with descriptions

exportSNOMEDenvir

Export a SNOMED environment to a folder

Obtain Read 2, CTV3, ICD-10 and OPCS4 maps for SNOMED CT concepts

print.SNOMEDcodelist

Display a SNOMEDcodelist on screen

Retrieves a Refset from the REFSET table

Retrieves SNOMED CT dictionary from the global environment

print.SNOMEDfindings

Print method for output of 'decompose' function

inactiveIncluded

Check if inactive terms are included in SNOMED CT dictionary

is.SNOMEDcodelist

Check if an object is a SNOMEDcodelist

Sample SNOMED CT dictionary

Creates an environment containing CDB files

Expand or contract a SNOMEDcodelist

exclude_irrelevant_findings

Sample inclusion, exclusion and blacklist sets for a MiADE CDB

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

relatedConcepts

Obtain related concepts for a set of SNOMED CT concepts

is.SNOMEDconcept

Check if an object is a SNOMEDconcept

unique.SNOMEDconcept

Unique vector of SNOMED CT concepts

Retrieves closest single ancestor within a given set of SNOMED CT concepts

union.SNOMEDconcept

Set operations for SNOMEDconcept vectors

Load mappings from Read to SNOMED CT into an R data.table

Exports CDB files for MedCAT / MiADE

Ancestors and descendants of SNOMED CT concepts

downloadWordnet

Download WordNet to assist concept database creation

Load SNOMED CT files from a folder(s) into R data.table objects

Export a SNOMEDcodelist

Convert a data.frame to a SNOMEDcodelist object

downloadOrphanet

Download Orphanet to assist with adding synonyms for rare diseases

Sample query table from SNOMED CT dictionary

as.data.frame.SNOMEDconcept

Return the SNOMED CT concept IDs for a set of terms

Retrieve all attributes of a set of SNOMED CT concepts

addComposeLookupToCDB

Add composition lookups to CDB

Creates a set of lookups for SNOMED composition

Use WordNet to assist concept database creation

Extract acronyms stated in the description of SNOMED CT concepts

c.SNOMEDconcept

Concatenate vectors of SNOMED CT concepts

Sample concept table from SNOMED CT dictionary

SNOMED_SIMPLEMAP

Sample SIMPLE map table from SNOMED CT dictionary

MANUAL_SYNONYMS

Sample manual synonym table to assist in creation of concept database

Sample history substitution table from SNOMED CT dictionary

SNOMED_RELATIONSHIP

Sample relationship tables from SNOMED CT dictionary

Sample mappings from Read to SNOMED CT

SNOMED_DESCRIPTION

Sample description table from SNOMED CT dictionary

Rdiagnosislist-package

Rdiagnosislist: A package for manipulating SNOMED CT diagnosis lists

SNOMED_EXTENDEDMAP

Sample extended map table from SNOMED CT dictionary

Sample refset table from SNOMED CT dictionary