Get DrecNo from drug names or MedicinalProd_Id

Collect Drug Record Numbers associated to one or more drugs.

Usage

get_drecno(
  d_sel,
  mp,
  allow_combination = TRUE,
  method = c("drug_name", "mpi_list"),
  verbose = TRUE,
  show_all = deprecated(),
  inspect = deprecated()
)

Arguments

d_sel: A named list. Selection of drug names or medicinalprod_id. See details
mp: A modified MP data.table. See mp_
allow_combination: A logical. Should fixed associations including the drug of interest be retrieved? See details.
method: Should DrecNo be found from drug names or from MedicinalProd_Id?
verbose: A logical. Allows you to see matching drug names in the console. Turn to FALSE once you've checked the matching.
show_all: Use verbose instead.
inspect: Use verbose instead.

Value

A named list of integers. DrecNos.

Details

get_drecno() is an ID collector function. Collected IDs can be used to create drug columns in datasets like demo, link, etc. (see vignette("basic_workflow"))

Argument `verbose`

The verbose argument is here to let you check the result of get_drecno(). This is an important step in your project setup: You must ensure that the drugs you are looking for are correctly matched.

Argument `d_sel`

d_sel must be a named list of character vectors. To learn why, see vignette("basic_workflow"). Names of d_sel are automatically lowered and trimed.

Matching drugs

With "drug_name" method, either exact match or perl regex match can be used. The latter is built upon lookarounds to ensure that a string does not match to composite drug names including the string, i.e. trastuzumab emtasine for trastuzumab, or close names like alitretinoin when looking for tretinoin.

Exact match is used for "mpi_list" method.

Choosing a method

"drug_name" let you work with drug names. It's likely to be the appropriate method in most of the cases.

"mpi_list" is used when you have a list of MedicinalProd_Ids. A drug can have multiple MedicinalProd_Ids, corresponding to different packagings. The MedicinalProd_Id matching is typically used to identify DrecNo(s) contained in an ATC class (extracted from thg), since not all MPI of drugs are present in thg (explanations in get_atc_code()).

WHO names

WHO names are attributed to drugs by... the WHO. A drug only has one WHO name, but can have multiple international nonproprietary names (e.g. "tretinoin" and "all-trans retinoic acid").

You should use WHO names to ensure proper identification of drugs and DrecNos, especially if you work with combinations.

Argument `allow_combination`

Fixed associations of drugs refers to specialty containing more than one active ingredient (for example, acetylsalicylic acid and clopidogrel). In VigiLyze, the default is NOT to account for these fixed associations. For example, when you call "acetylsalicylic acid" in VigiLyze, you don't have the cases reported with the fixed-association "acetylsalicylic acid; clopidogrel" unless the substances were distinctly coded by the reporter. Here, the default is to find a drug even if it is prescribed in a fixed association. Importantly, when retrieving fixed-association drugs, the non-of-interest drug alone drecno is not found, hence the cases related to this drug will not be added to those of the drug of interest.

Examples

if (FALSE) { # interactive()

# ## Get drecnos for a list a drugs. Check spelling and use WHO name,
# in lowercase

d_sel_names <- list(
  nivolumab = "nivolumab",
  ipilimumab = "ipilimumab",
  nivo_ipi = c("nivolumab", "ipilimumab")
  )

# Read mp with get_drecno(), to identify drugs without combinations

# Take the time to read the matching drugs. Did you forget a drug?

d_drecno <-
  get_drecno(d_sel_names,
             mp = mp_,
             allow_combination = FALSE,
             method = "drug_name")
d_drecno

# And DrecNos of drugs allowing for combinations

d_drecno <-
  get_drecno(d_sel = d_sel_names,
             mp = mp_,
             allow_combination = TRUE,
             method = "drug_name")
d_drecno
}