# Routine

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.

    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"
    )