Extract of subset of Vigibase

Create a subset of the VigiBase ECL datasets

Usage

tb_subset(
  wd_in,
  wd_out,
  subset_var = c("drecno", "medprod_id", "meddra_id", "age"),
  sv_selection,
  rm_suspdup = TRUE
)

Arguments

wd_in

Source directory pathway (character)

wd_out

Output directory pathway (character)

subset_var

One of "drecno", "medprod_id", "meddra_id", "age"

sv_selection

A named list or a vector containing the appropriate ids (according to the method, see details)

rm_suspdup

A logical. Should suspected duplicates be removed? TRUE by default

Value

Parquet files in the output directory. All files from a vigibase ECL main folder are returned subsetted (including suspectedduplicates).

Details

You must select a subset variable with subset_var and provide an appropriate list according to this variable in sv_selection. Available subset_var :

• drecno will use Drug Record Number (DrecNo), from WHO Drug, and will subset from drug (see get_drecno()).

• medprod_id will use MedicinalProd_Id, also from drug. May be useful if requesting from ATC classes. (see get_atc_code()).

• meddra_id will use MedDRA_Id, subset from adr. (see get_llt_soc() or See get_llt_smq()).

• age will use AgeGroup from demo. See below.

Age groups ids are as follows:

• 1 0 - 27 days

• 2 28 days to 23 months

• 3 2 - 11 years

• 4 12 - 17 years

• 5 18 - 44 years

• 6 45 - 64 years

• 7 65 - 74 years

• 8 >= 75 years

• 9 Unknown

Example: To work with patients aged 18 to 74, provide c(5, 6, 7) as sv_selection.

Use dt_parquet() to load the tables afterward.

See also

get_drecno(), get_atc_code(), get_llt_soc(), get_llt_smq(), dt_parquet()

Examples

if (FALSE) { # interactive()

# --- technical steps ---- #

wd_in <- paste0(tempdir(), "/", "tbsubsetex")
dir.create(wd_in)
create_ex_main_pq(wd_in)

# Select a subset_var and corresponding data

# Subset on adr colitis codes

adr_llt <-
 list(
   colitis = "Colitis"
   ) |>
   get_llt_soc(term_level = "pt", meddra_, verbose = FALSE)

wd_out <- paste0(wd_in, "/", "colitis_subset", "/")

tb_subset(wd_in, wd_out,
          subset_var = "meddra_id",
          sv_selection = adr_llt)

# Subset on drug codes

 d_drecno <-
   list(
    ipi = "ipilimumab") |>
    get_drecno(mp = mp_, verbose = FALSE)

wd_out <- paste0(wd_in, "/", "nivolumab_subset", "/")

tb_subset(wd_in, wd_out,
          subset_var = "drecno",
          sv_selection = d_drecno)

 # Subset on age > 65 year-old

 sv_selection <-
    c(7, 8)

wd_out <- paste0(wd_in, "/", "more_than_65_subset", "/")

tb_subset(wd_in, wd_out,
          subset_var = "age",
          sv_selection = sv_selection)

unlink(wd_in, recursive = TRUE)
}