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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

The dictionary might be located in scripts, under the name “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)
  )

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.