processSurvTerms {psichomics} | R Documentation

## Process survival curves terms to calculate survival curves

### Description

Process survival curves terms to calculate survival curves

### Usage

    processSurvTerms(
      clinical,
      censoring,
      event,
      timeStart,
      timeStop = NULL,
      group = NULL,
      formulaStr = NULL,
      coxph = FALSE,
      scale = "days",
      followup = "days_to_last_followup",
      survTime = NULL
    )

### Arguments

`clinical` | Data frame: clinical data
`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)
`group` | Character: group relative to each subject
`formulaStr` | Character: formula to use
`coxph` | Boolean: fit a Cox proportional hazards regression model?
`scale` | Character: rescale the survival time to `days`, `weeks`, `months` or `years`
`followup` | Character: name of column containing follow up time
`survTime` | `survTime` object: times to follow up, time start, time stop and event (optional)

### Details

The `event` time is only used to determine whether the event has occurred (`1`) or not (`0`) in case of missing values.

If `survTime = NULL`, survival times are obtained from the clinical dataset according to the names given in `timeStart`, `timeStop`, `event` and `followup`. This may become quite slow when used in a loop. If the aforementioned variables are constant, consider running `getAttributesTime()` outside the loop and using its output via the `survTime` argument of this function (see Examples).

### Value

A list with a `formula` object and a data frame with terms needed to calculate survival curves

### See Also

Other functions to analyse survival: `assignValuePerSubject()`, `getAttributesTime()`, `labelBasedOnCutoff()`, `optimalSurvivalCutoff()`, `plotSurvivalCurves()`, `plotSurvivalPvaluesByCutoff()`, `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"
    formulaStr <- "patient.stage_event.pathologic_stage + patient.gender"
    survTerms  <- processSurvTerms(clinical, censoring="right", event, timeStart,
                                   formulaStr=formulaStr)

    # If running multiple times, consider calculating survTime only once
    survTime <- getAttributesTime(clinical, event, timeStart)
    for (i in seq(5)) {
      survTerms <- processSurvTerms(clinical, censoring="right", event,
                                    timeStart, formulaStr=formulaStr,
                                    survTime=survTime)
    }

[Package psichomics version 1.14.1 Index]