optimalSurvivalCutoff {psichomics} | R Documentation |
Uses stats::optim
with the Brent method to test multiple cutoffs and
to find the minimum log-rank p-value.
optimalSurvivalCutoff( clinical, data, censoring, event, timeStart, timeStop = NULL, followup = "days_to_last_followup", session = NULL, filter = TRUE, survTime = NULL, lower = NULL, upper = NULL )
clinical |
Data frame: clinical data |
data |
Numeric: data values |
censoring |
Character: censor using |
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 |
|
lower, upper |
Bounds in which to search (if |
List containing the optimal cutoff (par
) and the corresponding
p-value (value
)
Other functions to analyse survival:
assignValuePerSubject()
,
getAttributesTime()
,
labelBasedOnCutoff()
,
plotSurvivalCurves()
,
plotSurvivalPvaluesByCutoff()
,
processSurvTerms()
,
survdiffTerms()
,
survfit.survTerms()
,
testSurvival()
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)