---
title: "Routine"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{template_routine}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

This very short vignette contains a condensed script, based on
`vignette("routine_pharmacovigilance")`.

You are strongly advised to check it out before using this one.

```{r 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"
)
```
