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Add ADR column(s) to a dataset

Source: R/add_adr.R
add_adr.Rd

[Stable]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

[Deprecated]. Data_type is now detected internally.

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).

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()).

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_
  )
#> 
#> ── get_llt_soc() ───────────────────────────────────────────────────────────────
#> 
#> ── ✔ Matched reactions at `pt` level (number of codes) ──
#> 
#> → `colitis`: "Autoimmune colitis (1)", "Colitis (25)", "Colitis microscopic
#>   (3)", "Diarrhoea (53)", "Diarrhoea haemorrhagic (8)", "Duodenitis (5)",
#>   "Enteritis (8)", "Enterocolitis (4)", "Enterocolitis haemorrhagic (10)", and
#>   "Ulcerative gastritis (1)"
#> → `pneumonitis`: "Organising pneumonia (9)" and "Pneumonitis (6)"
#> 
#> ℹ Set `verbose` to FALSE to suppress this section.
#> 

demo <-
  demo |>
    add_adr(
      a_code = a_llt,
      adr_data = adr
    )
#> ℹ `.data` detected as `demo` table.

demo |>
  check_dm(names(a_pt_sel))
#>             [,1]
#> colitis      104
#> pneumonitis  103