Add a nomenclature pack to RDaggregator

This function analyzes the nomenclature pack files and saves them internally in an R-friendly format.

Usage

add_nomenclature_pack(
  zip_filepath,
  default = FALSE,
  force = FALSE,
  destdir = tools::R_user_dir("RDaggregator", "data")
)

Arguments

zip_filepath

The location of the .zip file containing the nomenclature pack.

default

If TRUE, set the added pack as default.

force

If TRUE, adds the pack even if an identical version was internally found.

destdir

The destination directory, in which the processed data will be saved.

Details

Orphanet publishes the nomenclature pack on a yearly basis, and is deployed in different language versions. The different nomenclature pack versions are available here. They must be downloaded locally and uncompressed to be added to RDaggregator.

The uncompressed Orphanet nomenclature pack contains a set of .xml and .xlsx files for coding, including the nomenclature file (e.g. ORPHAnomenclature_fr_2023.xml) and a set of more than 30 classifications (usually contained in Classifications folder).

The nomenclature file contains for each ORPHAcode the associated properties, like their associated label (and synonyms), status (active or not), classification levels (group of disorder, disorder or subtype of disorder), and redirections to another ORPHAcode (for deprecated or obsolete only).

Each classification contains numerous from/to relationships between clinical entities, depicting the global Orphanet classification system.

Once added, the nomenclature pack will appear among the available options through the RDaggregator_options() interface. It can also be manually set using the built-in options() function and the "nomenclature_version" name.

See also

RDaggregator_options() to switch from a pack to another, load_nomenclature(), load_raw_nomenclature(), load_classifications(), load_synonyms(), load_redirections() to load the data added through this function.