Package: vigicaen 2.0.0.9000

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]

vigicaen_2.0.0.9000.tar.gz
vigicaen_2.0.0.9000.zip(r-4.7)vigicaen_2.0.0.9000.zip(r-4.6)vigicaen_2.0.0.9000.zip(r-4.5)
vigicaen_2.0.0.9000.tgz(r-4.6-any)vigicaen_2.0.0.9000.tgz(r-4.5-any)
vigicaen_2.0.0.9000.tar.gz(r-4.7-any)vigicaen_2.0.0.9000.tar.gz(r-4.6-any)
vigicaen_2.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
vigicaen/json (API)

# 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/docs 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

6.59 score 3 stars 12 scripts 254 downloads 39 exports 35 dependencies

Last updated from:bf50ee2ebb. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK234
source / vignettesOK225
linux-release-x86_64OK240
macos-release-arm64OK170
macos-oldrel-arm64OK173
windows-develOK251
windows-releaseOK207
windows-oldrelOK205
wasm-releaseOK124

Exports:add_adradd_deathadd_doseadd_drugadd_fupadd_indadd_seriouscffcheck_dmcompute_disprocompute_interactioncompute_or_modcreate_ex_main_csvcreate_ex_main_pqcreate_ex_meddra_asccreate_ex_sub_csvcreate_ex_sub_pqcreate_ex_who_csvdesc_contdesc_dchdesc_facvardesc_outcomedesc_rchdesc_ttodt_parquetextract_ttoget_atc_codeget_drecnoget_llt_smqget_llt_socic_tailnice_pscreen_adrscreen_drugtb_meddratb_subsettb_vigibasetb_whovigi_routine

Dependencies:arrowassertthatbitbit64clicpp11data.tabledplyrfarvergenericsggplot2gluegridExtragtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Basic Workflow
Introduction | Objectives | Reminder of Database Structure | Step 0: Load Packages | Build tables from source files | Collecting IDs | Data management | Drugs | Principle | Step 1: Load the tables | Step 2: Choose drugs of Interest | Step 3: Identify drug codes | Steps 4 and 5: add_drug() function | Step 6: Check your data management | Step 2 and 3 variant: ATC classes | Step 4 and 5 variant: Suspect, concomitant, interacting | Create multiple drug columns | Drug groups | Adverse drug reactions | Principles | Step 2: Choose events of interest | Step 3: Identify event codes | Steps 4 and 5: add_adr() function | Other variables | Indications | Age | Sex | Using case_when() | Seriousness, death | Disproportionality | Univariate analysis | Disproportionality metrics | Advanced modelling, multivariate analysis | Extract Odds-Ratio with compute_or_mod() | Conclusion
Rendered frombasic_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-06-26
Started: 2023-01-03

Descriptive
Introduction | Objectives | Prerequisite | Demo data: counts of drugs, adrs, case characteristics | Step 0: Load packages | Step 1: Load datasets and add drug and adr columns | desc_facvar() | Multi-level variables | Binary variables | Logical variables | Exporting raw values | Grouping several levels of a variable | Explicit categorical variables | Other arguments of desc_facvar() | Drug data: drug screening | Adr data: adr screening and evolution of adverse events | Adr screening | Outcome | Step 1: Data management of adr with add_drug and add_adr | Step 2: desc_outcome() function | Link data: time to onset, dechallenge, rechallenge | Step 1: Load the datasets | Step 2: Add drug and adr columns | Learn the content of link | Identify drugs and adverse events | Time to onset | Dechallenge | Rechallenge
Rendered fromdescriptive.Rmdusingknitr::rmarkdown

Last update: 2026-06-26
Started: 2024-02-15

Data management and disproportionality
Main (data management and disproportionality) script template | Paths | Demo | Link | Basic models | Basic descriptive
Rendered fromtemplate_main.Rmdusingknitr::rmarkdown

Last update: 2026-06-26
Started: 2025-01-27

Getting started
Purpose | Overview | Deploy tables | Folder and files | Table builders (tb_* functions) | Outputs | Loading tables into R | Working on a computer with low specifications | Subsetting tables | Handling interruptions and resuming table creation
Rendered fromgetting_started.Rmdusingknitr::rmarkdown

Last update: 2026-03-26
Started: 2025-01-27

Dictionary
Dictionary script template
Rendered fromtemplate_dictionary.Rmdusingknitr::rmarkdown

Last update: 2025-11-05
Started: 2025-01-27

Routine pharmacovigilance
Motivation | The whole game | Load tables | Identify drug and reaction of interest | Select the drug and reaction | Collect IDs of drug and reaction | Use vigi_routine() | Add your own case time to onset | Customize the graph | Exporting your results | Advanced options: suspect_only and d_code_2 | Example: Dual drug analysis
Rendered fromroutine_pharmacovigilance.Rmdusingknitr::rmarkdown

Last update: 2025-10-31
Started: 2024-11-25

Routine
Rendered fromtemplate_routine.Rmdusingknitr::rmarkdown

Last update: 2025-10-31
Started: 2025-02-04

Interactions
Introduction | Additive interactions | Multivariate analysis | Subgroup comparisons | Statistical interactions | Logistic regression model | Bayesian Information Component, compute_interaction()
Rendered frominteractions.Rmdusingknitr::rmarkdown

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

Readme and manuals

Help Manual

Help pageTopics
Add adverse drug reaction column(s) to a datasetadd_adr
Add drug dose column(s) to a dataset, in milligram per dayadd_dose
Add drug column(s) to a datasetadd_drug
Add indication column(s) to a datasetadd_ind
Add outcome columns to a datasetadd_death add_fup add_outcomes add_serious
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_csv create_ex_main_pq create_ex_meddra_asc create_ex_sub_csv create_ex_sub_pq create_ex_who_csv
Data of immune checkpoint inhibitors.adr_ demo_ drug_ followup_ ind_ link_ out_ srce_
Summarise continuous variablesdesc_cont
Dechallenge descriptivedesc_dch
Summarise categorical variablesdesc_facvar
Outcome descriptivedesc_outcome
Rechallenge descriptivedesc_rch
Time to onset descriptivedesc_tto
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 Record_Idget_drecno
Get low level term codes from SMQsget_llt_smq
Get low level term codes from soc classificationget_llt_soc
Credibility interval limits for the information componentic_tail
Sample of MedDRAmeddra_ 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 VigiBase ECL tablestb_vigibase
Create WHO tablestb_who
Display routine pharmacovigilance summaryvigi_routine