processSurvTerms {psichomics} | R Documentation |
Process survival curves terms to calculate survival curves
processSurvTerms(clinical, censoring, event, timeStart, timeStop = NULL, group = NULL, formulaStr = NULL, coxph = FALSE, scale = "days", followup = "days_to_last_followup", survTime = NULL)
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 patient |
formulaStr |
Character: formula to use |
coxph |
Boolean: fit a Cox proportional hazards regression model? FALSE by default |
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) |
If survTime
is NULL, the survival times will be fetch from the
clinical dataset according to the names given in timeStart
,
timeStop
, event
and followup
. This can became quite slow
when using the function in a for loop. If these variables are constant,
consider running the function getAttributesTime
to retrieve the
time of such columns once and hand the result to the survTime
argument
of this function.
A list with a formula
object and a data frame with terms
needed to calculate survival curves
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)