inst/doc/template_routine.R

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----full_script, eval = FALSE------------------------------------------------
# 
# library(vigicaen)
# 
# # ---- Set paths ---- ####
# 
# path_base   <- "~/vigibase/main/"
# path_who    <- "~/vigibase/who/"
# path_meddra <- "~/meddra/"
# 
# # ---- Load data ---- ####
# 
# demo <- dt_parquet(path_base, "demo", in_memory = FALSE)
# drug <- dt_parquet(path_base, "drug", in_memory = FALSE)
# adr  <- dt_parquet(path_base, "adr",  in_memory = FALSE)
# link <- dt_parquet(path_base, "link", in_memory = FALSE)
# 
# mp <- dt_parquet(path_who,  "mp")
# meddra   <- dt_parquet(path_meddra, "meddra")
# 
# # ---- Select drug and adverse drug reaction ---- ####
# 
# d_sel <- list(
#   nivolumab = "nivolumab"
# )
# 
# a_sel <- list(
#   # this is a High Level Term. Could be any term level instead.
#   colitis = "Colitis (excl infective)"
# )
# 
# # ---- Collect drug and adr IDs ---- ####
# 
# d_code <-
#   get_drecno(d_sel, mp = mp)
# 
# a_code <-
#   get_llt_soc(a_sel,
#               term_level = "hlt",
#               meddra = meddra)
# 
# # see also get_atc_code() and get_llt_smq()
# 
# # ---- Run vigi_routine() ---- ####
# 
# # Change case_tto for your own case time to onset
# 
# # Change export_to to an appropriate path on your computer
# 
# # install.packages("svglite") # run this line if you want to use .svg
# 
# vigi_routine(
#   case_tto  = 150,
#   demo_data = demo,
#   drug_data = drug,
#   adr_data  = adr,
#   link_data = link,
#   d_code    = d_code,
#   a_code    = a_code,
#   d_label   = "Nivolumab",
#   a_label   = "Colitis (HLT)",
#   vigibase_version = "September 2024",
#   export_to = "~/vigicaen_graph.svg"
# )