Package: vigicaen 0.15.6

Charles Dolladille

vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

Perform the analysis of the World Health Organization (WHO) Pharmacovigilance database 'VigiBase' (Extract Case Level version), <https://who-umc.org/> e.g., load data, perform data management, disproportionality analysis, and descriptive statistics. Intended for pharmacovigilance routine use or studies. This package is NOT supported nor reflect the opinion of the WHO, or the Uppsala Monitoring Centre. Disproportionality methods are described by Norén et al (2013) <doi:10.1177/0962280211403604>.

Authors:Charles Dolladille [aut, cre], Basile Chrétien [aut], Universite de Caen Normandie [cph], Unite de pharmaco-epidemiologie [cph]

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vigicaen.pdf |vigicaen.html✨
vigicaen/json (API)
NEWS

# Install 'vigicaen' in R:
install.packages('vigicaen', repos = c('https://pharmacologie-caen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pharmacologie-caen/vigicaen/issues

Pkgdown site:https://pharmacologie-caen.github.io

Datasets:
  • adr_ - Data of immune checkpoint inhibitors.
  • demo_ - Data of immune checkpoint inhibitors.
  • drug_ - Data of immune checkpoint inhibitors.
  • ex_ - Data for the immune checkpoint inhibitors example
  • followup_ - Data of immune checkpoint inhibitors.
  • ind_ - Data of immune checkpoint inhibitors.
  • link_ - Data of immune checkpoint inhibitors.
  • meddra_ - Sample of Meddra.
  • mp_ - Sample of WHODrug
  • out_ - Data of immune checkpoint inhibitors.
  • smq_content_ - Sample of Meddra.
  • smq_list_ - Sample of Meddra.
  • smq_list_content_ - Sample of Meddra.
  • srce_ - Data of immune checkpoint inhibitors.
  • thg_ - Sample of WHODrug

On CRAN:

Conda:

datamanagementpharmacovigilance

6.27 score 1 stars 11 scripts 214 downloads 34 exports 45 dependencies

Last updated 2 hours agofrom:2a1519ef33. Checks:7 OK, 2 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 13 2025
R-4.5-winOKMar 13 2025
R-4.5-macOKMar 13 2025
R-4.5-linuxOKMar 13 2025
R-4.4-winOKMar 13 2025
R-4.4-macOKMar 13 2025
R-4.4-linuxOKMar 13 2025
R-4.3-winWARNINGMar 13 2025
R-4.3-macWARNINGMar 13 2025

Exports:add_adradd_drugcffcheck_dmcompute_disprocompute_interactioncompute_or_modcreate_ex_main_pqcreate_ex_main_txtcreate_ex_meddra_asccreate_ex_sub_txtcreate_ex_who_txtdesc_contdesc_dchdesc_facvardesc_outcomedesc_rchdesc_ttodt_fstdt_parquetextract_ttoget_atc_codeget_drecnoget_llt_smqget_llt_socic_tailnice_pscreen_adrscreen_drugtb_meddratb_subsettb_vigibasetb_whovigi_routine

Dependencies:arrowassertthatbitbit64clicolorspacecpp11data.tabledplyrfansifarverfstfstcoregenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Basic Workflow

Rendered frombasic_workflow.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-02-04
Started: 2023-01-03

Descriptive

Rendered fromdescriptive.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-03-09
Started: 2024-02-15

Getting started

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-02-14
Started: 2025-01-27

Interactions

Rendered frominteractions.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-02-04
Started: 2025-01-27

Routine pharmacovigilance

Rendered fromroutine_pharmacovigilance.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-03-12
Started: 2024-11-25

Dictionary

Rendered fromtemplate_dictionary.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-02-04
Started: 2025-01-27

Data management and disproportionality

Rendered fromtemplate_main.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-03-09
Started: 2025-01-27

Routine

Rendered fromtemplate_routine.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2025-02-04
Started: 2025-02-04

Readme and manuals

Help Manual

Help pageTopics
Add ADR column(s) to a datasetadd_adr
Add DRUG column(s) to a dataset (tidyverse syntax)add_drug
Fast formatting of numberscff
Check binary variablescheck_dm
Compute disproportionalitycompute_dispro
Compute interaction disproportionalitycompute_interaction
Compute (r)OR from a model summarycompute_or_mod
Example source tables for VigiBase and MedDRAcreate_example_tables create_ex_main_pq create_ex_main_txt create_ex_meddra_asc create_ex_sub_txt create_ex_who_txt
Data of immune checkpoint inhibitors.adr_ demo_ drug_ followup_ ind_ link_ out_ srce_
Summarize continuous variablesdesc_cont
Dechallenge descriptivedesc_dch
Summarise categorical variablesdesc_facvar
Outcome descriptivedesc_outcome
Rechallenge descriptivedesc_rch
Time to onset descriptivedesc_tto
Read fst and convert to data.tabledt_fst
Read parquet and convert to data.tabledt_parquet
Data for the immune checkpoint inhibitors exampleex_
Time to onset extractionextract_tto
Get ATC codes (DrecNos or MPIs)get_atc_code
Get DrecNo from drug names or MedicinalProd_Idget_drecno
Extract low level terms from SMQsget_llt_smq
Extract low level terms from soc classificationget_llt_soc
Credibility interval limits for the information componentic_tail
Sample of Meddra.meddra_ smq_content_ smq_list_ smq_list_content_
Sample of WHODrugmp_ thg_
Nice printing of p-valuesnice_p
Screening of Adverse Drug Reactionsscreen_adr
Screening of Drugsscreen_drug
Create MedDRA tablestb_meddra
Extract of subset of Vigibasetb_subset
Create main VigiBase ECL tablestb_vigibase
Create main WHO tablestb_who
Pharmacovigilance routine functionvigi_routine