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Collapse Survival Outcomes to One Row per Subject

Source: R/surv_helpers.R
surv_subject_truth.Rd

Turns right-censored or counting-process (start/stop) survival outcomes into the one-row-per-subject, right-censored truth that yardstick's survival metrics require.

Usage

surv_subject_truth(truth, subject_id = NULL)

Arguments

truth

A [survival::Surv()] object: `Surv(time, event)` or `Surv(start, stop, event)`.

subject_id

Subject identifiers, one per element of `truth`. Required for counting-process data; for right-censored data each row is its own subject when `subject_id` is `NULL`.

Value

A tibble with one row per subject, sorted by `subject_id`: `.subject_id`, `.entry` (start of the first interval; 0 for right-censored data), and `.truth`, a right-censored `Surv` object.

Details

For counting-process data, a subject's time is the stop time of their last interval and their event status is the status of that interval. Rows are checked first: within a subject, intervals must not overlap, and an event may only occur in the last interval (recurrent events are not supported).

See also

[censoring_km()], [graf_weights()], [add_graf_weights()]

Examples

if (requireNamespace("survival", quietly = TRUE)) {
  long <- data.frame(
    subject_id = c(1, 1, 2, 3, 3),
    tstart = c(0, 5, 0, 0, 4),
    tstop = c(5, 9, 6, 4, 10),
    status = c(0, 1, 0, 0, 0)
  )
  surv_subject_truth(
    survival::Surv(long$tstart, long$tstop, long$status),
    subject_id = long$subject_id
  )
}
#> # A tibble: 3 × 3
#>   .subject_id .entry .truth
#>         <dbl>  <dbl> <Surv>
#> 1           1      0     9 
#> 2           2      0     6+
#> 3           3      0    10+