optimalSurvivalCutoff {psichomics} | R Documentation

## Calculate optimal data cutoff that best separates survival curves

### Description

Uses `stats::optim` with the Brent method to test multiple cutoffs and to find the minimum log-rank p-value.

### Usage

    optimalSurvivalCutoff(
      clinical,
      data,
      censoring,
      event,
      timeStart,
      timeStop = NULL,
      followup = "days_to_last_followup",
      session = NULL,
      filter = TRUE,
      survTime = NULL,
      lower = NULL,
      upper = NULL
    )

### Arguments

`clinical` | Data frame: clinical data
`data` | Numeric: data values
`censoring` | Character: censor using `left`, `right`, `interval` or `interval2`
`event` | Character: name of column containing time of the event of interest
`timeStart` | Character: name of column containing starting time of the interval or follow up time
`timeStop` | Character: name of column containing ending time of the interval (only relevant for interval censoring)
`followup` | Character: name of column containing follow up time
`session` | Shiny session (only used for the visual interface)
`filter` | Boolean or numeric: elements to use (all are used by default)
`survTime` | `survTime` object: times to follow up, time start, time stop and event (optional)
`lower, upper` | Bounds in which to search (if `NULL`, bounds are set to `lower = 0` and `upper = 1` if all data values are within that interval; otherwise, `lower = min(data, na.rm = TRUE)` and `upper = max(data, na.rm = TRUE)`)

### Value

List containing the optimal cutoff (`par`) and the corresponding p-value (`value`)

### See Also

Other functions to analyse survival: `assignValuePerSubject()`, `getAttributesTime()`, `labelBasedOnCutoff()`, `plotSurvivalCurves()`, `plotSurvivalPvaluesByCutoff()`, `processSurvTerms()`, `survdiffTerms()`, `survfit.survTerms()`, `testSurvival()`

### Examples

    clinical <- read.table(text = "2549   NA ii  female
                                    840   NA i   female
                                     NA 1204 iv    male
                                     NA  383 iv  female
                                   1293   NA iii   male
                                     NA 1355 ii    male")
    names(clinical) <- c("patient.days_to_last_followup",
                         "patient.days_to_death",
                         "patient.stage_event.pathologic_stage",
                         "patient.gender")
    timeStart  <- "days_to_death"
    event      <- "days_to_death"

    psi <- c(0.1, 0.2, 0.9, 1, 0.2, 0.6)
    opt <- optimalSurvivalCutoff(clinical, psi, "right", event, timeStart)

[Package psichomics version 1.12.1 Index]