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.
# #### 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)
)