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Create main VigiBase ECL tables

Source: R/tb_vigibase.R
tb_vigibase.Rd

[Stable] Transform VigiBase .txt files to .parquet files.

Usage

tb_vigibase(
  path_base,
  path_sub,
  force = FALSE,
  rm_suspdup = TRUE,
  overwrite_existing_tables = FALSE
)

Arguments

path_base

Character string, a directory containing vigibase txt tables. It is also the output directory.

path_sub

Character string, a directory containing subsidiary tables.

force

Logical, to be passed to cli::cli_progress_update(). Used for internal purposes.

rm_suspdup

Logical, should suspected duplicates (from SUSPECTEDDUPLICATES.txt) be removed from main tables? Default is TRUE. Set to FALSE to keep all cases, including suspected duplicates.

overwrite_existing_tables

Logical, should existing parquet tables be overwritten? Default is FALSE.

Value

  • .parquet files of all main tables into the path_base directory: demo, adr, drug, link, ind, out, srce, followup, and the suspdup (suspected duplicates) table. Check ?demo_ for more information on the tables.

  • The link table is augmented with tto_mean and range, to analyze time to onset according to WHo's recommendations (see vignette("descriptive").

  • .parquet files of all other subsidiary tables into the path_sub directory: AgeGroup, Dechallenge, Dechallenge2, Frequency, Gender, Notifier, Outcome, Rechallenge, Rechallenge2, Region, RepBasis, ReportType, RouteOfAdm, Seriousness, and SizeUnit.

.parquet files into the path_base directory (including suspected duplicates tables). Some columns are returned as integer (UMCReportId, Drug_Id, MedicinalProd_Id, Adr_Id, MedDRA_Id), and some columns as numeric (TimeToOnsetMin, TimeToOnsetMax) All other columns are character.

Details

Vigibase Extract Case Level is delivered as zipped text files, that you should transform to a more efficient format. Parquet format from arrow has many advantages: It works with out-of-memory data, which makes it possible to process Vigibase tables on a computer with not-so-much RAM. It is also lightweighted and standard across different langages. The function also creates variables in each table. The suspectedduplicates table will be added to the base directory. Use dt_parquet() to load the tables afterward.

The argument overwrite_existing_tables is especially useful if the function crashes or is interrupted: it allows you to resume the process without rebuilding tables that were already successfully created. If set to FALSE (the default), the function will skip the construction of any .parquet tables that already exist, so you do not have to start from scratch after a failure. Set to TRUE to force rebuilding all tables.

See also

tb_who(), tb_meddra(), tb_subset(), dt_parquet()

Examples

if (FALSE) { # interactive()

# --- Set up example source files ---- ####

path_base <- paste0(tempdir(), "/", "main", "/")

path_sub  <- paste0(tempdir(), "/", "sub",  "/")

dir.create(path_base)
dir.create(path_sub)

create_ex_main_txt(path_base)
create_ex_sub_txt(path_sub)

 # ---- Running tb_vigibase

 tb_vigibase(path_base = path_base,
        path_sub  = path_sub)

 # Clear temporary files when you're done
 unlink(path_base, recursive = TRUE)
 unlink(path_sub, recursive = TRUE)
}