tests/testthat/_snaps/add_drug.md

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

works with drecnos, regular names for demo and drug

Code
  demo_n <- add_drug(demo, d_code = d_drecno, method = "DrecNo", repbasis = "sci",
    drug_data = drug)
Message
  i `.data` detected as `demo` table.

Code
  demo_a <- dplyr::collect(add_drug(arrow::as_arrow_table(demo), d_code = d_drecno,
  method = "DrecNo", repbasis = "sci", drug_data = arrow::as_arrow_table(drug)))
Message
  i `.data` detected as `demo` table.

works with irregular names for demo and drug

Code
  dema <- add_drug(dema, d_code = d_drecno, method = "DrecNo", repbasis = "sci",
    drug_data = druga)
Message
  i `.data` detected as `demo` table.

works with mpi_list

Code
  demo <- add_drug(demo_, d_code = mpi, method = "MedicinalProd_Id", repbasis = "sci",
    drug_data = drug_)
Message
  i `.data` detected as `demo` table.

Code
  demo_a <- add_drug(arrow::as_arrow_table(demo_), d_code = mpi, method = "MedicinalProd_Id",
  repbasis = "sci", drug_data = arrow::as_arrow_table(drug_))
Message
  i `.data` detected as `demo` table.

selecting only s, c, i works and provide less cases than sci altogether

Code
  res_each <- purrr::map(bas, function(repbasis_) add_drug(demo_, d_code = d_drecno,
    method = "DrecNo", repbasis = repbasis_, drug_data = drug_))
Message
  i `.data` detected as `demo` table.
  i `.data` detected as `demo` table.
  i `.data` detected as `demo` table.

Code
  res_each_a <- purrr::map(bas, function(repbasis_) dplyr::collect(add_drug(
    arrow::as_arrow_table(demo_), d_code = d_drecno, method = "DrecNo", repbasis = repbasis_,
    drug_data = arrow::as_arrow_table(drug_))))
Message
  i `.data` detected as `demo` table.
  i `.data` detected as `demo` table.
  i `.data` detected as `demo` table.

Code
  res_all <- add_drug(demo_, d_code = d_drecno, method = "DrecNo", repbasis = "sci",
    drug_data = drug_)
Message
  i `.data` detected as `demo` table.

Code
  res_all_a <- dplyr::collect(add_drug(arrow::as_arrow_table(demo_), d_code = d_drecno,
  method = "DrecNo", repbasis = "sci", drug_data = arrow::as_arrow_table(drug_)))
Message
  i `.data` detected as `demo` table.

works with link and drug data, drug identification is Drug_Id wise, not UMCReportId wise

Code
  link_test <- add_drug(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), d_code = d_drecno_test, drug_data = drug_test)
Message
  i `.data` detected as `link` table.

Code
  link_test_a <- dplyr::collect(add_drug(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)), d_code = d_drecno_test,
  drug_data = arrow::as_arrow_table(drug_test)))
Message
  i `.data` detected as `link` table.

Code
  drug_output_test <- add_drug(drug_test, d_code = d_drecno_test, drug_data = drug_test)
Message
  i `.data` detected as `drug` table.

Code
  drug_output_test_a <- dplyr::collect(add_drug(arrow::as_arrow_table(drug_test),
  d_code = d_drecno_test, drug_data = arrow::as_arrow_table(drug_test)))
Message
  i `.data` detected as `drug` table.

works with adr data, drug identification is UMCReportId wise

Code
  adr_test <- add_drug(data.table(UMCReportId = c(1, 1, 2, 2, 3), Adr_Id = c(
    "a1_adr1", "a2_adr4", "a3_adr2", "a4_adr4", "a5_adr2"), MedDRA_Id = c(1e+05,
    20000, 30000, 40000, 50000), Outcome = c(1, 2, 3, 2, 2)), d_code = d_drecno_test,
  drug_data = drug_test)
Message
  i `.data` detected as `adr` table.

Code
  adr_test_a <- dplyr::collect(add_drug(arrow::as_arrow_table(data.table(
    UMCReportId = c(1, 1, 2, 2, 3), Adr_Id = c("a1_adr1", "a2_adr4", "a3_adr2",
      "a4_adr4", "a5_adr2"), MedDRA_Id = c(1e+05, 20000, 30000, 40000, 50000),
    Outcome = c(1, 2, 3, 2, 2))), d_code = d_drecno_test, drug_data = arrow::as_arrow_table(
    drug_test)))
Message
  i `.data` detected as `adr` table.

handle ambiguous names in .data

Code
  res <- add_drug(demo_test, d_code = d_drecno_test, method = "DrecNo", repbasis = "sci",
    drug_data = drug_test)
Message
  i `.data` detected as `demo` table.

Code
  res_a <- dplyr::collect(add_drug(arrow::as_arrow_table(demo_test), d_code = d_drecno_test,
  method = "DrecNo", repbasis = "sci", drug_data = arrow::as_arrow_table(
    drug_test)))
Message
  i `.data` detected as `demo` table.

you can choose output column names with d_names

Code
  res <- add_drug(demo_test, d_code = d_drecno_test, d_names = changed_names,
    method = "DrecNo", repbasis = "sci", drug_data = drug_test)
Message
  i `.data` detected as `demo` table.

Code
  res_a <- add_drug(arrow::as_arrow_table(demo_test), d_code = d_drecno_test,
  d_names = changed_names, method = "DrecNo", repbasis = "sci", drug_data = arrow::as_arrow_table(
    drug_test))
Message
  i `.data` detected as `demo` table.

you can use arrow/parquet format

Code
  res <- add_drug(demo_parquet, d_code = d_drecno_test, method = "DrecNo",
    repbasis = "sci", drug_data = drug_parquet)
Message
  i `.data` detected as `demo` table.

Code
  res_a <- add_drug(demo_test, d_code = d_drecno_test, method = "DrecNo",
    repbasis = "sci", drug_data = drug_test)
Message
  i `.data` detected as `demo` table.

Providing data_type arg raises deprecation warn

Code
  r1 <- add_drug(demo_, d_code = ex_$d_drecno, method = "DrecNo", drug_data = drug_,
  data_type = "demo")
Condition
  Warning:
  The `data_type` argument of `add_drug()` is deprecated as of vigicaen 0.14.1.
  i data_type is now internally detected
Message
  i `.data` detected as `demo` table.

drug_data should be a valid drug type data

Code
  add_drug(demo_, d_code = ex_$d_drecno, method = "DrecNo", drug_data = adr_,
  data_type = "demo")
Condition
  Error in `add_drug()`:
  ! `drug_data` must be a `drug` table.
  x Missing columns: DrecNo, MedicinalProd_Id, and Drug_Id
  > Supply a `drug` table to `drug_data`. See ?drug_.

vigicaen documentation built on April 3, 2025, 8:55 p.m.