Routes

Run the route check

All possible routes can be seen in athena. https://athena.ohdsi.org/search-terms/terms?vocabulary=SNOMED&invalidReason=Valid&domain=Route&page=1&pageSize=15&query=

library(DrugExposureDiagnostics)
library(dplyr)
#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
#>   object 'type_sum.accel' not found
library(DT)

# acetaminophen concept id is 1125315
acetaminophen <- 1125315
cdm <- mockDrugExposure()
acetaminophen_checks <- executeChecks(
  cdm = cdm,
  ingredients = acetaminophen,
  checks = "route"
)

Route Overall

This shows the routes of the drug records summarised on ingredient level.

datatable(acetaminophen_checks$drugRoutesOverall,
  rownames = FALSE
)

Column	Description
ingredient_concept_id	Concept ID of ingredient.
ingredient	Name of drug ingredient.
route_concept_id	Concept ID of route
route_type	Concept name for route
n_records	Number of records for ingredient concept. If n_records is the same as n_sample this means that there are more records but the number was cut at the pre-specified sample number for efficiency reasons.
n_sample	The pre-specified maximum sample. If n_records is smaller than the sample it means that sampling was ignored because the total number of records was already too small.
n_person	Number of individuals.
result_obscured	TRUE if count has been suppressed due to being below the minimum cell count, otherwise FALSE.

Route by drug concept

This shows the route of the drug records on the drug concept level. The tables are identical to the overall just including two more columns at the beginning.

Column	Description
drug_concept_id	ID of the drug concept.
drug	Name of the drug concept.

datatable(acetaminophen_checks$drugRoutesByConcept,
  rownames = FALSE
)