tb_vigibase {vigicaen} | R Documentation |
Create main VigiBase ECL tables
Description
Transform VigiBase .txt
files to .parquet files.
Usage
tb_vigibase(path_base, path_sub, force = 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 |
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.
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
andrange
, to analyze time to onset according to WHo's recommendations (seevignette("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
.
See Also
tb_who()
, tb_meddra()
, tb_subset()
, dt_parquet()
Examples
# --- 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)