add_adr.md
In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

works with regular names for demo and adr

Code
  demo <- demo %>% add_adr(a_code = ex_$a_llt, a_names = a_names, adr_data = adr)
Message
  i `.data` detected as `demo` table.

Code
  demo_a <- dplyr::collect(add_adr(arrow::as_arrow_table(demo), a_code = ex_$
  a_llt, a_names = a_names, adr_data = arrow::as_arrow_table(adr)))
Message
  i `.data` detected as `demo` table.

works with irregular names for demo and adr

Code
  dema <- dema %>% add_adr(a_code = ex_$a_llt, a_names = a_names, adr_data = adra)
Message
  i `.data` detected as `demo` table.

Code
  dema_a <- dplyr::collect(add_adr(arrow::as_arrow_table(dema), a_code = ex_$
  a_llt, a_names = a_names, adr_data = arrow::as_arrow_table(adra)))
Message
  i `.data` detected as `demo` table.

works with link data, adr identification is Adr_Id wise, not UMCReportId wise

Code
  link_test <- data.table(Drug_Id = c("d1_ici1", "d2_ici2", "d3_ici3", "d4_ici1",
    "d5_ici1"), Adr_Id = c("a1_adr1", "a2_adr4", "a3_adr2", "a4_adr4", "a5_adr2"),
  UMCReportId = c(1, 1, 2, 2, 3), Dechallenge1 = NA, TimeToOnsetMin = NA) %>%
    add_adr(a_code = adr_list_test, adr_data = adr_test)
Message
  i `.data` detected as `link` table.

Code
  link_test_a <- dplyr::collect(add_adr(arrow::as_arrow_table(data.table(Drug_Id = c(
    "d1_ici1", "d2_ici2", "d3_ici3", "d4_ici1", "d5_ici1"), Adr_Id = c("a1_adr1",
    "a2_adr4", "a3_adr2", "a4_adr4", "a5_adr2"), UMCReportId = c(1, 1, 2, 2, 3),
  Dechallenge1 = NA, TimeToOnsetMin = NA)), a_code = adr_list_test, adr_data = arrow::as_arrow_table(
    adr_test)))
Message
  i `.data` detected as `link` table.

works with adr data as the .data argument

Code
  adr_try <- add_adr(adr_test, a_code = adr_list_test, adr_data = adr_test)
Message
  i `.data` detected as `adr` table.

Code
  adr_try_a <- dplyr::collect(add_adr(arrow::as_arrow_table(adr_test), a_code = adr_list_test,
  adr_data = arrow::as_arrow_table(adr_test)))
Message
  i `.data` detected as `adr` table.

works with drug data as the .data argument

Code
  drug_try <- add_adr(drug_test, a_code = adr_list_test, adr_data = adr_test)
Message
  i `.data` detected as `drug` table.

Code
  drug_try_a <- dplyr::collect(add_adr(arrow::as_arrow_table(drug_test), a_code = adr_list_test,
  adr_data = arrow::as_arrow_table(adr_test)))
Message
  i `.data` detected as `drug` table.

handle ambiguous names in .data

Code
  res <- demo_test %>% add_adr(a_code = adr_list_test, adr_data = adr_test)
Message
  i `.data` detected as `demo` table.

Code
  res_a <- dplyr::collect(add_adr(arrow::as_arrow_table(demo_test), a_code = adr_list_test,
  adr_data = arrow::as_arrow_table(adr_test)))
Message
  i `.data` detected as `demo` table.

Providing data_type arg raises deprecation warn

Code
  r1 <- add_adr(demo_, a_code = ex_$a_llt, adr_data = adr_, data_type = "demo")
Condition
  Warning:
  The `data_type` argument of `add_adr()` is deprecated as of vigicaen 0.14.1.
  i data_type is now internally detected
Message
  i `.data` detected as `demo` table.

adr_data should be a valid adr type data

Code
  add_adr(demo_, a_code = ex_$a_llt, adr_data = drug_)
Condition
  Error in `add_adr()`:
  ! `adr_data` must be an `adr` table.
  x Missing columns: Adr_Id, MedDRA_Id, and Outcome
  > Supply an `adr` table to `adr_data`. See ?adr_.