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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"
)

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.