dictionary.inspect {opalr}

Inspect the dictionary of a tibble

Description

Inspect the data dictionary, checking for inconsistencies. Error is raised when the identifiers column cannot be found.

Usage

dictionary.inspect(tibble, id.name = "id", warn = TRUE)

Arguments

tibble

Tibble to be inspected.

id.name

The name of the column representing the entity identifiers. Default is 'id'.

warn

Print warning messages. Default is TRUE.

Value

TRUE if inspection is successful, FALSE otherwise.

Examples

## Not run: 
# prepare datasets of visits, several visits for one patient
visits <- tibble::tribble(
~id, ~patient_id, ~sex, ~visit_date,
1, 1, "M", as.Date("2020-01-01"),
2, 2, "F", as.Date("2020-01-02"),
3, 3, "M", as.Date("2020-01-03"),
4, 3, "M", as.Date("2020-01-04"))

o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org")

# save visits dataset
opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE)

# get visit and make it a dataset of patients 
patients <- opal.table_get(o, "RSRC", "visits", id.name = "id")
# set dataset IDs
patients$visit_id <- patients$id
patients$id <- patients$patient_id
patients$patient_id <- NULL
patients

# save patients dataset, there should be a warning that some variables are not repeatable
# while there are patients with multiple data lines
opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE)

opal.logout(o)

## End(Not run)