CodelistGenerator (version 4.1.0)

associatedRelationshipIds: Get all relationships types that exist in the OMOP vocabulary concept_relationship table for a given set of concepts in a codelist.

Description

Get all relationships types that exist in the OMOP vocabulary concept_relationship table for a given set of concepts in a codelist.

Usage

associatedRelationshipIds(
  x,
  cdm,
  standardConcept1 = c("Standard", "Non-standard", "Classification"),
  standardConcept2 = c("Standard", "Non-standard", "Classification"),
  domains1 = NULL,
  domains2 = NULL
)

Value

A character vector with unique concept relationship values.

Arguments

x

A codelist, codelist_with_details, or a concept_set. See newCodelist(), newCodelistWithDetails(), newConceptSetExpression() functions for more details.

cdm

A cdm reference to an OMOP CDM dataset. If data is held within a database, the vocabulary tables should be in the same schema as the clinical tables (person, observation period, and so on).

standardConcept1

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

standardConcept2

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

domains1

Character vector with one or more of the OMOP CDM domain. If NULL, all domains are considered.

domains2

Character vector with one or more of the OMOP CDM domain. If NULL, all domains are considered.

Examples

# \donttest{
library(CodelistGenerator)
library(omock)

# Create CDM object
cdm <- mockCdmReference()

# Create codelist
codelist <- newCodelist(list("codes1" = c(8479L, 4117795L, 44022939L),
                             "codes2" = c(8480L, 8600L, 8481L, 4189167L, 40371897L)))

# You can optionally restrict to only relationships between concepts that are
# "Standard" and "Non-standard". For example:
relationships <- associatedRelationshipIds(x = codelist,
                                           cdm = cdm,
                                           standardConcept1 = "Standard",
                                           standardConcept2 = "Non-standard")
relationships

# It returns the relationships between concepts where:
#  - concept_id_1 is 'Standard'
#  - concept_id_2 is 'Non-standard'
# Similarly, we can obtain the relationships restricting by domain:
relationships <- associatedRelationshipIds(x = codelist,
                                           cdm = cdm,
                                           domains1 = c("Drug", "Condition"),
                                           domains2 = c("Drug", "Condition"))
relationships
# }