codes_to_std_concepts: Retrieve standard concept IDs for a set of codes

In baileych/ohdsi-argos: Affordances for Retrieval of General OHDSI Stuff

Description

Given a set of codes drawn from one or more terminologies in the OHDSI vocabulary, return the corresponding standard concept IDs, names, and vocabularies.

Usage

codes_to_std_concepts(codes, vocabulary = NA, src = ohdsi_default_src())

Arguments

codes	The source codes to map. This may be a simple character vector, in which case the vocabulary parameter is required, or a data frame, in which case the concept_code column provides the source code and the vocabulary_id column supplies the vocabulary.
vocabulary	A character vector listing the vocabulary(ies) from which the source codes are drawn
src	The src through which the connection to the OHDSI vocabularies is made, if different from ohdsi_default_src().

Details

N.B. A source code may map to more than one standard concept.

Because the source and standard terms have similar attributes, the return value disambiguates them by using different names:

src_concept_code

The code passed into the function.

src_vocabulary_id

The name of the terminology from which to the souce code was drawn, also passed into the function.

std_concept_code

The code for the corresponding standard concept in its own terminology (e.g. RxNorm)

std_vocabulary_id

The name of the terminology from which the standard concept was drawn.

std_concept_name

The human-readable description of the standard term, as defined by the terminology from which it was drawn.

std_concept_id

The OHDSI internal ID for the standard concept; this is what you use when looking up the term in OHDSI databases

Value

A tbl object containing information about the standard concepts, as described.

Examples

## Not run: 
codes_to_std_concepts(c('282.61', '282.62', '282.41', '282.42'),
                      vocabulary = 'ICD9CM')

## End(Not run)

baileych/ohdsi-argos documentation built on Dec. 1, 2019, 12:41 p.m.