# Dictionary

# Dictionary script template

You may want to organize your research folder using small scripts, each designed for a part of your analysis plan.

Inspired from Reproducible Research in R

- /folder
- ../data
- ../scripts
- ../etc.

The dictionary might be located in scripts, under the name “dict.R”.

- ../scripts/00_dict.R

If you haven’t, visit `vignette("getting_started")` and `vignette("basic_workflow")` for details on what this template does.

    library(vigicaen)
    library(rlang)
    library(dplyr)

    # #### PATHS #### ####

    path_who    <- "../vigibase_ecl/who" # adapt to your own

    path_meddra <- "../meddra"

    # #### IMPORT #### ####

    # ---- Datasets ---- ####

    mp     <- dt_parquet(path_who, "mp")

    thg    <- dt_parquet(path_who, "thg")

    meddra <- dt_parquet(path_meddra, "meddra_hierarchy")

    smq_list <- dt_parquet(path_meddra, "meddra_smq_list")

    smq_content <- dt_parquet(path_meddra, "meddra_smq_content")

    # #### Drug definitions #### ####

    d_sel <-
      list(
        nivolumab = "nivolumab", # use lower case
        ici = c("nivolumab", "pembrolizumab")
      )

    # ---- ID collector

    d_drecno <-
      d_sel |>
      get_drecno(
        mp = mp
      )

    # #### ATC definitions #### ####

    atc_sel <-
      list(l03 = "L03") # ATC code

    # ---- ID collector

    atc_drecno <-
      atc_sel |>
      get_atc_code(
        mp = mp,
        thg_data = thg
      )

    # #### ADR definitions #### ####

    # adr selection, matching meddra case

    # ---- SOC definition

    pt_sel <-
      list(
        hepatitis = c("Hepatitis", "Budd-Chiari syndrome"),
        hyponatremia = c("Pneumonitis")
      )

    hlt_sel <-
      list(
        conduction = "Diarrhoea (excl infective)"
      )

    # ---- SMQ definition

    smq_sel <-
      list(
        hta = "Ischaemic heart disease (SMQ)"
      )

    # ---- ID collectors

    a_llt <-
      c(
        get_llt_soc(pt_sel,
                    term_level = "pt",
                    meddra = meddra),
        get_llt_soc(hlt_sel,
                    term_level = "hlt",
                    meddra),
        get_llt_smq(smq_sel,
                    smq_scope =  "narrow",
                    smq_list,
                    smq_content)
      )

    # ---- Set indication terms ---- ####

    i_list <-
     list(
       melanoma = c("Malignant melanoma", "Metastatic malignant melanoma"),
       lung_cancer = c("Non-small cell lung cancer", "Lung adenocarcinoma")
       )