NEWS

Rdiagnosislist 1.3 (2024-10-28)

Ensure that 'description' returns a 'type' column if there are 0 rows and include_synonyms = TRUE
Ensure that 'description' returns only one Fully Specified Name per concept, and 'semanticType' returns only a single result per concept

New function 'createTransitive' to generate a transitive closure table containing all ancestor-descendant pairs. This makes subsequent ancestor / descendant searches quicker
Revised ancestor and descendant functions to be able to use a transitive closure table
New function 'addInactiveConcepts' to add inactive concepts to codelists, using the history and query tables
New functions 'createCDB' and 'createMiADECDB' to generate a concept database and lookups for named entity recognition
New function 'createDisambiguationTrainer' to use longer SNOMED CT terms to create texts to help train disambiguation of short terms.
New functions 'decompose', 'batchDecompose' and 'createComposeLookup' to create a lookup table for composition of SNOMED CT concepts
New function 'compose' to select a detailed SNOMED CT concept based on a general concept and separate concepts for attributes such as body site

as.integer64.SNOMEDconcept now allows additional optional arguments, like the generic as.integer64 function

loadSNOMED also optionally loads history and query tables from a SNOMED CT distribution
New function addInactiveConcepts to add inactive concepts to codelists, using the history and query tables

Showing a concept description caused an error if there were multiple descriptions for a concept and duplicate concepts in the SNOMEDconcept vector
SNOMEDcodelist timestamps were set to the user-supplied date instead of the system time
Error on exporting SNOMEDcodelists with single row maps that had NULL values. Instead the NULLs are now zero-length character vectors, which can be exported correctly with fwrite.
Ensure that SNOMED environment is passed from htmlCodelistHierarchy to showCodelistHierarchy
Corrected bug in hasAttribute when SNOMED RELATIONSHIP table contains duplicate source-type-destination triples (e.g. if some are inactive)

New vignette 'customHierarchy.Rmd' explaining how to create a custom SNOMED-like database to enable the hierarchical view
Vignette shows how to obtain 'History of' terms for phenotyping algorithms

New getMaps function to map a codelist to another terminology system
New htmlCodelistHierarchy function to create an interactive HTML file to explore a codelist
SNOMED CT simple reference sets included in the SNOMED environment, with new function getRefset
Function to load a mapping table from the NHS Digital data migration pack (loadREADMAPS), for mapping to Read V2 and CTV3

SNOMEDcodelist S3 data type has been redesigned to include metadata as well as accommodate different formats of codelists
SNOMEDcodelist no longer includes descendants by default
SNOMED environment now includes mapping tables and simple refsets
Updated method of displaying SNOMED CT codelists