consider moving startDateColumn to omopgenerics

[edward-burn]

@catalamarti seems more like a function for omopgenerics? https://darwin-eu-dev.github.io/PatientProfiles/reference/startDateColumn.html

[edward-burn]

Similarly

• https://darwin-eu-dev.github.io/PatientProfiles/reference/standardConceptIdColumn.html
• https://darwin-eu-dev.github.io/PatientProfiles/reference/sourceConceptIdColumn.html
• https://darwin-eu-dev.github.io/PatientProfiles/reference/variableTypes.html

[catalamarti]

should we have a vocab or sth similar package? @edward-burn I would agree it is not the place in pp but maybe neither in og? @edward-burn

[edward-burn]

I would have thought omopgenerics because it seems a useful function for CDMConnector, CodelistGenerator, and PatientProfiles. Similar with the others (except variableTypes) in that they are related to the definition of the omop cdm

[catalamarti]

create a set of functions vocabulary based

[ilovemane]

@catalamarti shall I re export of those functions ed mention above or just copy over?

[catalamarti]

• To check where this function is used
• We would go for new argument in omopColumns if onlyRequired can be deprecated

[ilovemane]

This function is not used in anywhere.

[catalamarti]

• omopColumn

vs

• startDateColumn
• endDateColumn
• standardConceptColumn
• sourceConceptColumn

[catalamarti]

# OPTION 1
startDateColumn <- function(table) {
  omopColumn(table = table, field = "start_date")
}

omopColumn <- function(table, field, call = parent.frame()) {
  # initial checks
  assertChoice(table, optionsTable, call = call)

  # internal dataset
  fields$name[fields$table == table & fields$type == field]
}

# OPTION 2
omopColumn <- function(table, field) {
  # initial checks
  assertChoice(table, optionsTable)
  assertChoice(field, c("start_date", "end_date", ...))

  # internal dataset
  fields$name[fields$table == table & fields$type == field]
}