tests/testthat/_snaps/get_drecno.md

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

get drecno of single drug, or combination allowed

Code
  d_drecno_res <- get_drecno(d_sel = d_sel_names, mp = mp_, allow_combination = FALSE,
    method = "drug_name", show_all = FALSE)
Condition
  Warning:
  The `show_all` argument of `get_drecno()` is deprecated as of vigicaen 0.14.1.
  i Unmatching DrecNos or MedicinalProd_Ids will be shown by default.
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `nivolumab`: "nivolumab"
  > `ipilimumab`: "ipilimumab"
  > `nivo_ipi`: "nivolumab" and "ipilimumab"

  i Set `verbose` to FALSE to suppress this section.

  --------------------------------------------------------------------------------

Code
  d_drecno_res_comb <- get_drecno(d_sel = d_sel_names, mp = mp_,
    allow_combination = TRUE, method = "drug_name", show_all = FALSE)
Condition
  Warning:
  The `show_all` argument of `get_drecno()` is deprecated as of vigicaen 0.14.1.
  i Unmatching DrecNos or MedicinalProd_Ids will be shown by default.
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `nivolumab`: "nivolumab" and "ipilimumab;nivolumab"
  > `ipilimumab`: "ipilimumab" and "ipilimumab;nivolumab"
  > `nivo_ipi`: "nivolumab", "ipilimumab;nivolumab", and "ipilimumab"

  i Set `verbose` to FALSE to suppress this section.

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(list(a = "paracetamol"), allow_combination = TRUE, mp = mp_,
  verbose = TRUE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `a`: "chlorphenamine;guaifenesin;paracetamol;pseudoephedrine;tipepidine", "cinnamomum spp.;ephedra spp.;glycyrrhiza spp.;paeonia spp.;paracetamol;pueraria spp.;zingiber officinale;ziziphus spp.", "eperisone;paracetamol", "guaifenesin;paracetamol;pseudoephedrine", "caffeine;chlorphenamine;guaifenesin;methylephedrine;paracetamol;phenylephrine", "ascorbic acid;chlorphenamine;cloperastine;coptis spp.;lysozyme;methylephedrine;paracetamol;platycodon grandiflorus", "cetirizine;paracetamol;phenylephrine;zinc", "chlorphenamine;cloperastine;lysozyme;paracetamol", "allobarbital;codeine;paracetamol;salicylamide", "atropine;codeine;papaverine;paracetamol", "codeine;paracetamol;pentobarbital", "amobarbital;caffeine;codeine;paracetamol", "amobarbital;caffeine;codeine;octibenzonium bromide;paracetamol", "amobarbital;caffeine;codeine;dihydroergotamine;paracetamol", "caffeine;codeine;meprobamate;paracetamol", "codeine;meprobamate;paracetamol", "caffeine;codeine;paracetamol;phenazone;prothipendyl", "codeine;methaqualone;paracetamol", ..., "atropa bella-donna;caffeine;dihydrocodeine;diphenylpyraline;guaifenesin;methylephedrine;noscapine;paracetamol", and "ascorbic acid;caffeine;chlorphenamine;dextromethorphan;guaifenesin;herbal nos;paracetamol;pseudoephedrine"

  i Set `verbose` to FALSE to suppress this section.

  --------------------------------------------------------------------------------

d_sel has inappropriate structure

Code
  get_drecno(drug1, mp_, verbose = FALSE)
Condition
  Error in `get_drecno()`:
  ! `d_sel` items must all be of type character or numeric.
  i Nested `lists` are not allowed.
  > Supply a named list of character or numeric vectors to `d_sel`. See ?ex_.

show_all is deprecated

Code
  r1 <- expect_warning(get_drecno(drug1, mp_, show_all = TRUE, verbose = FALSE),
  "deprecated")

non WHO names raise appropriate warnings

Code
  expect_warning(r1 <- get_drecno(drug1, mp_, verbose = FALSE),
  "Switch to .* WHO names.")
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs are not WHO name

  ! Not WHO name | i WHO name

  * In `atra`:
    * ! "all-trans retinoic acid" | i tretinoin

  --------------------------------------------------------------------------------

Code
  expect_warning(r1 <- get_drecno(drug2, mp_, verbose = FALSE),
  "Switch to .* WHO names.")
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs are not WHO name

  ! Not WHO name | i WHO name

  * In `doli`:
    * ! "doliprane" | i paracetamol

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(drug3, mp_, verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs were not found

  * In `medi`: x "medicament"

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(drug4, mp_, verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs were not found

  * In `doli`: x "paracetam"

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(drug5, mp_, verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs were not found

  * In `att`: x "antithrombin"

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(drug6, mp_, verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs were not found

  * In `medi`: x "medicament" and "medicament2"
  * In `medi2`: x "autremedic"

  --------------------------------------------------------------------------------

Code
  expect_warning(r1 <- get_drecno(drug7, mp_, allow_combination = TRUE, verbose = FALSE),
  "Switch to .* WHO names.")
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs are not WHO name

  ! Not WHO name | i WHO name

  * In `notwho`:
    * ! "all-trans retinoic acid" | i tretinoin
    * ! "doliprane" | i paracetamol
  * In `notwho2`:
    * ! "doliprane" | i paracetamol

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(drug7, mp_, allow_combination = FALSE, verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- ! Some drugs are not WHO name

  ! Not WHO name | i WHO name

  * In `notwho`:
    * ! "all-trans retinoic acid" | i tretinoin
    * ! "doliprane" | i paracetamol
  * In `notwho2`:
    * ! "doliprane" | i paracetamol

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(drug8, mp_, verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Checking names --

  ! names of `d_sel` were lowered and trimed

  * `Medi` > `medi`

  -- `d_sel`: Matching drugs --

  -- ! Some drugs were not found

  * In `medi`: x "medicament" and "medicament2"

  -- ! Some drugs are not WHO name

  ! Not WHO name | i WHO name

  * In `mix`:
    * ! "all-trans retinoic acid" | i tretinoin
    * ! "keytruda" | i pembrolizumab
  * In `notwho2`:
    * ! "doliprane" | i paracetamol

Condition
  Warning:
  You might have missed combinations.
  > Switch to i WHO names.
Message
  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(drug8, mp_, allow_combination = FALSE, verbose = TRUE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Checking names --

  ! names of `d_sel` were lowered and trimed

  * `Medi` > `medi`

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `medi`: "enalapril"
  > `mix`: "enalaprilat" and "enalapril"
  > `notwho2`: x No match
  > `who`: "nivolumab"

  i Set `verbose` to FALSE to suppress this section.

  -- ! Some drugs were not found

  * In `medi`: x "medicament" and "medicament2"

  -- ! Some drugs are not WHO name

  ! Not WHO name | i WHO name

  * In `mix`:
    * ! "all-trans retinoic acid" | i tretinoin
    * ! "keytruda" | i pembrolizumab
  * In `notwho2`:
    * ! "doliprane" | i paracetamol

  --------------------------------------------------------------------------------

Code
  expect_warning(r1 <- get_drecno(drug8, mp_, allow_combination = TRUE, verbose = TRUE),
  "Switch to .* WHO names.")
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Checking names --

  ! names of `d_sel` were lowered and trimed

  * `Medi` > `medi`

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `medi`: "enalapril", "enalapril;folic acid", and "captopril;enalapril"
  > `mix`: "enalaprilat", "enalapril", "enalapril;folic acid", and "captopril;enalapril"
  > `notwho2`: x No match
  > `who`: "nivolumab" and "ipilimumab;nivolumab"

  i Set `verbose` to FALSE to suppress this section.

  -- ! Some drugs were not found

  * In `medi`: x "medicament" and "medicament2"

  -- ! Some drugs are not WHO name

  ! Not WHO name | i WHO name

  * In `mix`:
    * ! "all-trans retinoic acid" | i tretinoin
    * ! "keytruda" | i pembrolizumab
  * In `notwho2`:
    * ! "doliprane" | i paracetamol

  --------------------------------------------------------------------------------

works for mpi_list as well

Code
  r1 <- get_drecno(mpi, mp_, method = "mpi_list", allow_combination = FALSE,
    verbose = TRUE)
Message

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `para`: "paracetamol"

  i Set `verbose` to FALSE to suppress this section.

verbose works

Code
  r_verbose_1 <- get_drecno(d_one, mp = mp_, method = "drug_name",
    allow_combination = FALSE, verbose = TRUE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `set1`: "enalapril"

  i Set `verbose` to FALSE to suppress this section.

  --------------------------------------------------------------------------------

Code
  r_verbose_2 <- get_drecno(d_one, mp = mp_, method = "drug_name",
    allow_combination = TRUE, verbose = TRUE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `set1`: "nivolumab" and "ipilimumab;nivolumab"

  i Set `verbose` to FALSE to suppress this section.

  --------------------------------------------------------------------------------

Code
  r_insp2 <- get_drecno(d_sel = d_min, mp = mp_, method = "drug_name",
    allow_combination = TRUE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `set1`: "ipilimumab", "ipilimumab;nivolumab", and "nivolumab"

  i Set `verbose` to FALSE to suppress this section.

  --------------------------------------------------------------------------------

Code
  r_insp3 <- get_drecno(mpi, mp_, method = "mpi_list", verbose = TRUE,
    allow_combination = FALSE)
Message

  -- `d_sel`: Matching drugs --

  -- v Matched drugs

  > `set1`: "enalapril"

  i Set `verbose` to FALSE to suppress this section.

inspect and show_all are deprecated

Code
  r_inspect <- expect_warning(get_drecno(d_one, mp = mp_, method = "drug_name",
    allow_combination = FALSE, inspect = TRUE, verbose = FALSE), "deprecated")

Code
  r_inspect <- expect_warning(get_drecno(d_one, mp = mp_, method = "drug_name",
    allow_combination = FALSE, show_all = TRUE, verbose = FALSE), "deprecated")

names of d_sel were tolower-ed and trimed warning

Code
  r1 <- get_drecno(d_sel = d_sel_names, mp = mp_, allow_combination = TRUE,
    method = "drug_name", verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Checking names --

  ! names of `d_sel` were lowered and trimed

  * `Nivolumab` > `nivolumab`
  * `Ipilimumab` > `ipilimumab`
  * `Nivo_ipi` > `nivo_ipi`

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(d_sel = d_sel_long, mp = mp_, allow_combination = TRUE,
    method = "drug_name", verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Checking names --

  ! names of `d_sel` were lowered and trimed

  * `Drug1` > `drug1`
  * `Drug2` > `drug2`
  * `Drug3` > `drug3`
  * `Drug4` > `drug4`
  * `Drug5` > `drug5`
  * ...
  * i Showing first 5 only

  --------------------------------------------------------------------------------

Code
  r1 <- get_drecno(d_sel = d_sel_mix, mp = mp_, allow_combination = TRUE, method = "drug_name",
    verbose = FALSE)
Message

  -- get_drecno() ----------------------------------------------------------------

  -- `d_sel`: Checking names --

  ! names of `d_sel` were lowered and trimed

  * `Drug2` > `drug2`

  --------------------------------------------------------------------------------

ambiguous drug name format is ok [plain]

Code
  find_drug_and_check_exist("triatec", vigicaen:::find_combination, mp = mp_)
Condition
  Error in `find_drug_and_check_exist()`:
  ! Drug name must match a single drug.
  x Ambiguous name: "triatec"
  ! Matches: ramipril, caffeine;codeine;paracetamol, and ramipril;bis.
  i Please provide WHO name.

ambiguous drug name format is ok [ansi]

Code
  find_drug_and_check_exist("triatec", vigicaen:::find_combination, mp = mp_)
Condition
  [1m[33mError[39m in `find_drug_and_check_exist()`:[22m
  [1m[22m[33m![39m Drug name must match a single drug.
  [31mx[39m Ambiguous name: [34m"triatec"[39m
  [33m![39m Matches: ramipril, caffeine;codeine;paracetamol, and ramipril;bis.
  [36mi[39m Please provide WHO name.

ambiguous drug name format is ok [unicode]

Code
  find_drug_and_check_exist("triatec", vigicaen:::find_combination, mp = mp_)
Condition
  Error in `find_drug_and_check_exist()`:
  ! Drug name must match a single drug.
  ✖ Ambiguous name: "triatec"
  ⚠ Matches: ramipril, caffeine;codeine;paracetamol, and ramipril;bis.
  ℹ Please provide WHO name.

ambiguous drug name format is ok [fancy]

Code
  find_drug_and_check_exist("triatec", vigicaen:::find_combination, mp = mp_)
Condition
  [1m[33mError[39m in `find_drug_and_check_exist()`:[22m
  [1m[22m[33m![39m Drug name must match a single drug.
  [31m✖[39m Ambiguous name: [34m"triatec"[39m
  [33m⚠[39m Matches: ramipril, caffeine;codeine;paracetamol, and ramipril;bis.
  [36mℹ[39m Please provide WHO name.

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