darwin-eu / darwin-eu/DrugUtilisation
How to add route information to cohort?
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Description
Hi,
I was wondering what is the best way to add route information to a cohort?
```r
j01c_desc <- getATCCodes(cdm = cdm,
level = "ATC 3rd",
name = "BETA-LACTAM ANTIBACTERIALS, PENICILLINS",
type = "codelist")
cdm <- generateDrugUtilisationCohortSet(
cdm = cdm,
name = "beta_lactam_penicillins_exposures",
conceptSet = j01c_desc,
gapEra = 0,
daysPrescribed = TRUE,
numberExposures = TRUE
)
```
At this point the rows have been collapsed down to subject_id, start_date, end_date, so I can't join it back to drug exposure to get the route.
I can do it manually like this:
```r
cdm$drug_exposure %>%
inner_join(
cdm$visit_occurrence %>%
filter(visit_concept_id %in% c(9201, 262)),
by = join_by("visit_occurrence_id", within(drug_exposure_start_date, drug_exposure_end_date, visit_start_date, visit_end_date))
) %>%
left_join(
cdm$concept %>%
select(
route_concept_id = concept_id,
route_name = concept_name
),
by = "route_concept_id"
) %>%
filter(drug_concept_id %in% j01c_desc$J01C_beta_lactam_antibacterials_penicillins ) %>%
group_by(route_name) %>%
summarise(n_persons = n_distinct(person_id.x),
n_visits = n_distinct(visit_occurrence_id))
```
But ideally I would like to include this per row in the cohort and then use CohortCharacteristics::summariseCharacteristics & tableCharacteristics to summarize this along with other variables. I also have multiple cohorts (based on j01c_desc, j01d_desc, j01e_desc etc.)
Any advice would be appreciated,
Thank you!
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