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Add outcome columns to a dataset

Source: R/add_outcomes.R
add_outcomes.Rd

[Experimental] add_death(), add_serious(), and add_fup() create outcome columns in a vigibase dataset (typically demo), using data from the out and followup tables. These functions handle both in-memory and out-of-memory (Arrow) tables.

Usage

add_death(.data, out_data, col_name = "death")

add_serious(.data, out_data, col_name = "serious")

add_fup(.data, fup_data, col_name = "fup")

Arguments

.data

The dataset to update (usually demo).

out_data

A data.frame containing the outcome data (usually out).

col_name

A character string. Name of the new column. Defaults to "death", "serious", or "fup" respectively.

fup_data

A data.frame containing the follow-up data (usually followup).

Value

A dataset with the new outcome column.

Details

  • add_death() adds a column indicating whether the case resulted in death (i.e., Seriousness == "1" in the out table). Cases with no outcome data are coded NA. Cases with outcome data but no death are coded 0. Cases with death are coded 1.

  • add_serious() adds a column indicating whether the case was serious (i.e., Serious == "Y" in the out table). Cases with no outcome data are coded NA. Cases with outcome data but not serious are coded 0. Serious cases are coded 1.

  • add_fup() adds a column indicating whether the case has a follow-up (i.e., UMCReportId appears in the followup table). Cases with a follow-up are coded 1. Others are coded 0.

See also

add_drug(), add_adr()

Examples

demo <- demo_
out  <- out_

demo <- add_death(demo, out_data = out)
#> ℹ `.data` detected as `demo` table.
demo <- add_serious(demo, out_data = out)
#> ℹ `.data` detected as `demo` table.

followup <- followup_

demo <- add_fup(demo, fup_data = followup)
#> ℹ `.data` detected as `demo` table.

desc_facvar(demo, c("death", "serious", "fup"))
#> # A tibble: 6 × 4
#>   var     level value         n_avail
#>   <chr>   <chr> <chr>           <int>
#> 1 death   0     612/747 (82%)     747
#> 2 death   1     135/747 (18%)     747
#> 3 serious 0     181/747 (24%)     747
#> 4 serious 1     566/747 (76%)     747
#> 5 fup     0     458/750 (61%)     750
#> 6 fup     1     292/750 (39%)     750