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Add DRUG column(s) to a dataset (tidyverse syntax)

Source: R/add_drug.R
add_drug.Rd

[Stable] Creates drug columns. in vigibase datasets (demo, link, adr, but also drug).

Usage

add_drug(
  .data,
  d_code,
  d_names = names(d_code),
  repbasis = "sci",
  method = c("DrecNo", "MedicinalProd_Id"),
  drug_data,
  data_type = deprecated()
)

Arguments

.data

The dataset used to identify individual reports (usually, it is demo)

d_code

A named list of drug codes (DrecNos or MPI). See Details.

d_names

A character vector. Names for drug columns (must be the same length as d_code), default to names(d_code)

repbasis

Suspect, interacting and/or concomitant. Type initial of those you wish to select ("s" for suspect, "c" for concomitant and "i" for interacting ; default to all, e.g. "sci").

method

A character string. The type of drug code (DrecNo or MedicinalProd_Id). See details.

drug_data

A data.frame containing the drug data (usually, it is drug)

data_type

[Deprecated]. Data_type is now detected internally.

Value

A dataset with the new drug columns. Each element of d_names will add a column with the same name in .data. The value can be 0 (the corresponding drug is absent) or 1 (the drug is present in the case if .data is demo or adr, or "this row correspond to this drug", if .data is drug or link).

Details

d_code is a named list containing drug codes. Either drug record numbers (e.g., from get_drecno()), or medicinalprod_ids (e.g., from get_atc_code()). Default method is to DrecNos.

Argument repbasis

Drugs can be reported according to one of three reputation bases:

  • s for suspect

  • c for concomitant

  • i for interacting

in the occurrence of the adverse drug reaction. To study only one of these reputation basis, type only the corresponding letter in repbasis, e.g. "s" for suspects, or "si" for suspect or interacting.

You can add drug identification to a demo, link, adr or even drug dataset.(in this latter case, you must provide adr twice, as .data and drug_data)

See also

add_adr(), get_drecno(), get_atc_code()

Examples

# create a nivolumab column in demo_

d_sel_names <- list(nivolumab = "nivolumab")

d_drecno <- get_drecno(d_sel_names,
                        mp = mp_)
#> 
#> ── get_drecno() ────────────────────────────────────────────────────────────────
#> 
#> ── `d_sel`: Matching drugs ──
#> 
#> ── ✔ Matched drugs 
#> 
#> → `nivolumab`: "nivolumab" and "ipilimumab;nivolumab"
#> 
#> ℹ Set `verbose` to FALSE to suppress this section.
#> 
#> ────────────────────────────────────────────────────────────────────────────────
demo_ <-
  add_drug(
    .data = demo_,
    d_code = d_drecno,
    method = "DrecNo",
    repbasis = "sci",
    drug_data = drug_
  )
#> ℹ `.data` detected as `demo` table.

# remember to assign the result to your actual demo dataset

# do you want to work only with cases where nivolumab was a "suspected" drug?
# change argument repbasis to "s"

demo_ <-
  add_drug(
    .data = demo_,
    d_code = d_drecno,
    d_names = "nivolumab_suspected",
    method = "DrecNo",
    repbasis = "s",
    drug_data = drug_
  )
#> ℹ `.data` detected as `demo` table.

check_dm(demo_, cols = c("nivolumab", "nivolumab_suspected"))
#>                     [,1]
#> nivolumab            225
#> nivolumab_suspected  214