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Outcome descriptive

Source: R/desc_outcome.R
desc_outcome.Rd

[Experimental] Compute outcome description over a set of adr and drugs.

Usage

desc_outcome(.data, drug_s = "drug1", adr_s = "adr1")

Arguments

.data,

An adr data.table. See adr_

drug_s

A character vector, the drug column(s)

adr_s

A character vector, the adverse drug reaction column(s).

Value

A data.table with one row per drug-adr pair.

  • drug_s and adr_s, same as input

  • n_cas, number of cases for each category

  • out_label, the worst outcome for this drug-adr pair

Details

You need an adr data.table. Be careful that you cannot directly filter adr data.table on drugs! You first have to add drug columns to adr, with add_drug(). The function reports the worst outcome into consideration for a given case, if many are reported. Outcomes, from best to worst are:

  • Recovered/resolved

  • Recovering/resolving

  • Recovered/resolved with sequelae

  • Not recovered/not resolved

  • Fatal

  • Died- unrelated to reaction

  • Died- reaction may be contributory

See vignette("descriptive") for more details.

See also

adr_, add_drug(), add_adr()

Examples


adr_ <-
  adr_ |>
  add_drug(
    d_code = ex_$d_groups_drecno,
    drug_data = drug_
  ) |>
  add_adr(
    a_code = ex_$a_llt,
    adr_data = adr_
  )
#> ℹ `.data` detected as `adr` table.
#> ℹ `.data` detected as `adr` table.

desc_outcome(
  adr_,
  drug_s = "pd1",
  adr_s = "a_colitis"
  )
#> # A tibble: 6 × 4
#>   drug_s adr_s     n_cas out_label                       
#>   <chr>  <chr>     <int> <chr>                           
#> 1 pd1    a_colitis    13 Unknown                         
#> 2 pd1    a_colitis    39 Recovered/resolved              
#> 3 pd1    a_colitis    17 Recovering/resolving            
#> 4 pd1    a_colitis     1 Recovered/resolved with sequelae
#> 5 pd1    a_colitis    10 Not recovered/not resolved      
#> 6 pd1    a_colitis     3 Fatal                           

# you can vectorize over multiple adrs and drugs

desc_outcome(
  adr_,
  drug_s = c("pd1", "pdl1"),
  adr_s = c("a_colitis", "a_pneumonitis")
  )
#> # A tibble: 18 × 4
#>    drug_s adr_s         n_cas out_label                       
#>    <chr>  <chr>         <int> <chr>                           
#>  1 pd1    a_colitis        13 Unknown                         
#>  2 pd1    a_colitis        39 Recovered/resolved              
#>  3 pd1    a_colitis        17 Recovering/resolving            
#>  4 pd1    a_colitis         1 Recovered/resolved with sequelae
#>  5 pd1    a_colitis        10 Not recovered/not resolved      
#>  6 pd1    a_colitis         3 Fatal                           
#>  7 pdl1   a_colitis         5 Unknown                         
#>  8 pdl1   a_colitis         7 Recovered/resolved              
#>  9 pdl1   a_colitis         6 Not recovered/not resolved      
#> 10 pd1    a_pneumonitis    18 Unknown                         
#> 11 pd1    a_pneumonitis    33 Recovered/resolved              
#> 12 pd1    a_pneumonitis    16 Recovering/resolving            
#> 13 pd1    a_pneumonitis     2 Recovered/resolved with sequelae
#> 14 pd1    a_pneumonitis    16 Not recovered/not resolved      
#> 15 pd1    a_pneumonitis    12 Fatal                           
#> 16 pdl1   a_pneumonitis     4 Unknown                         
#> 17 pdl1   a_pneumonitis     1 Recovering/resolving            
#> 18 pdl1   a_pneumonitis     1 Fatal