Feature request: fill in CONCEPT NAME, DOMAIN ID etc. without database connection

[SulevR]

Currently, when one is creating conceptset via cs(), it has to use getConceptSetDetails() afterwards to fill in the concept names and domain_id-s of the conceptset. This is inconvenient when you do not have direct access to OMOP database.

However, you may have the vocabulary in the R project as CSV files or just as R object. Then, it would be very helpful if I could just update conceptset object after creating it via cs() or even while creating it by providing the corresponding names and domains as variables.

[SulevR]

In case you have the concept_name and domain_id in the data frame CONCEPT, you can use the following code for updating conceptset:

for (i in seq_along(conceptset@Expression)) {
    cid <- conceptset@Expression[[i]]@Concept@concept_id
    info <- CONCEPT %>% filter(concept_id == cid)

    if (nrow(info) == 1) {
      conceptset@Expression[[i]]@Concept@concept_name <- info$concept_name
      conceptset@Expression[[i]]@Concept@domain_id <- info$domain_id
    }
  }

But for sure, it would be better if it could be done via a proper function.

[mdlavallee92]

You can fork the package and make a PR targeting the develop branch with your desired function and tag me for review.

I am curious, how are you using the concept set? Typically, you need a connection to an OMOP CDM to execute the sql that is linked to the Capr object via circe. But maybe there is a use case with just concept sets that I am missing.