| 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) optimalPSIcutoff(clinical, psi, censoring, event, timeStart, timeStop = NULL, followup = "days_to_last_followup", session = NULL, filter = TRUE, survTime = NULL)
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 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, they will be automatically set to 0 and 1 if all data values are within that interval; otherwise, they will be set to the minimum and maximum values of data) |
psi |
Numeric: PSI values to test against the cutoff |
List containg the optimal cutoff (par) and the corresponding
p-value (value)
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)