add_adr: Add ADR column(s) to a dataset

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

Add ADR column(s) to a dataset

Description

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

Usage

add_adr(
  .data,
  a_code,
  a_names = names(a_code),
  adr_data,
  data_type = deprecated()
)

Arguments

.data	The dataset to update (demo, link, drug, adr).
a_code	A named list of low level terms codes (llt_codes).
a_names	A character vector. Names for adr columns (must be the same length as adr_list), default to names(a_code)
adr_data	A data.frame containing the adr data (usually, it is adr)
data_type	. Data_type is now detected internally.

Details

Low-level term codes are the preferred level of requesting in Vigibase extract case level since they capture all possible codes for a given Preferred Term. Collect low-level terms with get_llt_soc() and get_llt_smq(). You can add adr identification to a demo, a link, drug or even an adr dataset (in this latter case, you must provide adr twice, as .data and adr_data). Column names of these dataset should not have been modified from the original vigibase dataset (as created with tb_vigibase()).

Value

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

See Also

add_drug(), get_llt_soc(), get_llt_smq()

Examples

# create adr_colitis, adr_embolism and adr_pneumonitis columns in demo

# be careful, this example may overwrite your own demo dataset
demo <- demo_

a_pt_sel <- ex_$pt_sel


adr <- adr_

a_llt <-
  get_llt_soc(
  term_sel = a_pt_sel,
  term_level = "pt",
  meddra = meddra_
  )

demo <-
  demo |>
    add_adr(
      a_code = a_llt,
      adr_data = adr
    )

demo |>
  check_dm(names(a_pt_sel))

vigicaen documentation built on April 3, 2025, 8:55 p.m.