tests/testthat/_snaps/tb_subset.md

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

you can subset on drecno, age, meddra_id

Code
  tb_subset(wd_in = paste0(wd_in, "/"), wd_out = paste0(wd_in, "/",
    "subset_drecno", "/"), subset_var = "drecno", sv_selection = sv_selection_drecno)
Message

  -- tb_subset() -----------------------------------------------------------------
  i Subsetting VigiBase tables.
  ====>-------------------------- percent, seconds | Reading source tables 
  =========>--------------------- percent, seconds | Picking subset 
  ==============>---------------- percent, seconds | Collect case list 
  ===============>--------------- percent, seconds | Collect drug list 
  ==================>------------ percent, seconds | Apply case level subset 
  ========================>------ percent, seconds | Apply drug level subset 
  ==============================> percent, seconds | Done 
  v Subset successful

  i percent, seconds | Number of rows in subset
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2

Code
  tb_subset(wd_in = paste0(wd_in, "/"), wd_out = paste0(wd_in, "/",
    "subset_drecno_item", "/"), subset_var = "drecno", sv_selection = sv_selection_drecno_item)
Message

  -- tb_subset() -----------------------------------------------------------------
  i Subsetting VigiBase tables.
  ====>-------------------------- percent, seconds | Reading source tables 
  =========>--------------------- percent, seconds | Picking subset 
  ==============>---------------- percent, seconds | Collect case list 
  ===============>--------------- percent, seconds | Collect drug list 
  ==================>------------ percent, seconds | Apply case level subset 
  ========================>------ percent, seconds | Apply drug level subset 
  ==============================> percent, seconds | Done 
  v Subset successful

  i percent, seconds | Number of rows in subset
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3

Code
  tb_subset(wd_in = paste0(wd_in, "/"), wd_out = paste0(wd_in, "/", "subset_age",
    "/"), subset_var = "age", sv_selection = c(7, 8))
Message

  -- tb_subset() -----------------------------------------------------------------
  i Subsetting VigiBase tables.
  ====>-------------------------- percent, seconds | Reading source tables 
  =========>--------------------- percent, seconds | Picking subset 
  ==============>---------------- percent, seconds | Collect case list 
  ===============>--------------- percent, seconds | Collect drug list 
  ==================>------------ percent, seconds | Apply case level subset 
  ========================>------ percent, seconds | Apply drug level subset 
  ==============================> percent, seconds | Done 
  v Subset successful

  i percent, seconds | Number of rows in subset
  > percent, seconds | 1
  > percent, seconds | 1
  > percent, seconds | 1
  > percent, seconds | 1
  > percent, seconds | 1
  > percent, seconds | 1
  > percent, seconds | 1
  > percent, seconds | 1

Code
  tb_subset(wd_in = paste0(wd_in, "/"), wd_out = paste0(wd_in, "/",
    "subset_meddraid", "/"), subset_var = "meddra_id", sv_selection = sv_selection_mid)
Message

  -- tb_subset() -----------------------------------------------------------------
  i Subsetting VigiBase tables.
  ====>-------------------------- percent, seconds | Reading source tables 
  =========>--------------------- percent, seconds | Picking subset 
  ==============>---------------- percent, seconds | Collect case list 
  ===============>--------------- percent, seconds | Collect drug list 
  ==================>------------ percent, seconds | Apply case level subset 
  ========================>------ percent, seconds | Apply drug level subset 
  ==============================> percent, seconds | Done 
  v Subset successful

  i percent, seconds | Number of rows in subset
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2

you can keep suspdup

Code
  tb_subset(wd_in = paste0(wd_in, "/"), wd_out = paste0(wd_in, "/",
    "subset_age_suspdup", "/"), subset_var = "age", sv_selection = c(7, 8),
  rm_suspdup = FALSE)
Message

  -- tb_subset() -----------------------------------------------------------------
  i Subsetting VigiBase tables.
  ====>-------------------------- percent, seconds | Reading source tables 
  =========>--------------------- percent, seconds | Picking subset 
  ==============>---------------- percent, seconds | Collect case list 
  ===============>--------------- percent, seconds | Collect drug list 
  ==================>------------ percent, seconds | Apply case level subset 
  ========================>------ percent, seconds | Apply drug level subset 
  ==============================> percent, seconds | Done 
  v Subset successful

  i percent, seconds | Number of rows in subset
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 1
  > percent, seconds | 3
  > percent, seconds | 3
  > percent, seconds | 3

Code
  tb_subset(wd_in = paste0(wd_in, "/"), wd_out = paste0(wd_in, "/", "subset_age",
    "/"), subset_var = "age", sv_selection = c(7, 8), rm_suspdup = TRUE)
Message

  -- tb_subset() -----------------------------------------------------------------
  i Subsetting VigiBase tables.
  ====>-------------------------- percent, seconds | Reading source tables 
  =========>--------------------- percent, seconds | Picking subset 
  ==============>---------------- percent, seconds | Collect case list 
  ===============>--------------- percent, seconds | Collect drug list 
  ==================>------------ percent, seconds | Apply case level subset 
  ========================>------ percent, seconds | Apply drug level subset 
  ==============================> percent, seconds | Done 
  v Subset successful

  i percent, seconds | Number of rows in subset
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2

alternative syntaxes work

Code
  tb_subset(wd_in = wd_in, wd_out = paste0(wd_in, "/", "subset_age"), subset_var = "age",
  sv_selection = c(7, 8))
Message

  -- tb_subset() -----------------------------------------------------------------
  i Subsetting VigiBase tables.
  ====>-------------------------- percent, seconds | Reading source tables 
  =========>--------------------- percent, seconds | Picking subset 
  ==============>---------------- percent, seconds | Collect case list 
  ===============>--------------- percent, seconds | Collect drug list 
  ==================>------------ percent, seconds | Apply case level subset 
  ========================>------ percent, seconds | Apply drug level subset 
  ==============================> percent, seconds | Done 
  v Subset successful

  i percent, seconds | Number of rows in subset
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2
  > percent, seconds | 2

error if no wd_in

Code
  tb_subset(wd_in = "that_dir_doesnt_exist", sv_selection = list(a = c(1, 2)))
Condition <no_dir>
  Error in `tb_subset()`:
  ! `wd_in` must exist.
  x "that_dir_doesnt_exist" does not exist.

printing error no dir [plain]

Code
  error_dir_exists("wd_in", "/wrong_path/")
Condition
  Error:
  ! `wd_in` must exist.
  x "/wrong_path/" does not exist.

printing error no dir [ansi]

Code
  error_dir_exists("wd_in", "/wrong_path/")
Condition
  [1m[33mError[39m:[22m
  [1m[22m[33m![39m `wd_in` must exist.
  [31mx[39m [34m"/wrong_path/"[39m does not exist.

printing error no dir [unicode]

Code
  error_dir_exists("wd_in", "/wrong_path/")
Condition
  Error:
  ! `wd_in` must exist.
  ✖ "/wrong_path/" does not exist.

printing error no dir [fancy]

Code
  error_dir_exists("wd_in", "/wrong_path/")
Condition
  [1m[33mError[39m:[22m
  [1m[22m[33m![39m `wd_in` must exist.
  [31m✖[39m [34m"/wrong_path/"[39m does not exist.

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