I am following THIS guide on how to create a survival analysis in R.
The instructions say, "Each row is a subject. An event (death) is indicated if the variable outcome is 1, in which case time indicates the time of death. An outcome of 0 refers to no event (censored data), in which case time is the time of censoring.".
However, I have datasets which have no censored rows as all events were deaths but when I produce my figure my samples are shaded as if censored.
This is the code I have been running:
#TWO GROUP KAPLAN-MEIER CURVE
#read in file
ATCC <- read.csv("ATCCsample.csv")
head(ATCC )
#Surv beeded to convert the data to a format used by package
ATCCSurv <- Surv(time = ATCC$OverallSurvivalDays, event = ATCC$status)
#Survfit used to calculate survival curve
ATCCKM <- survfit(ATCCSurv ~ Subtype, data = ATCC , type="kaplan-meier")
#plot curve
ggsurvplot(ATCCKM, conf.int = TRUE, pval = FALSE, risk.table = FALSE,
legend.labs=c("ATCC 1", "ATCC 2"),
legend.title = "Subtype",
censor.shape = "|", censor.size = 4,
palette=c("firebrick", "goldenrod1"),
xlab = "Time since inoculation (days)",
ylab = "Proportion surviving")
I have tried playing around with the "censor.size" but it doesn't look any different whether I change it to 0 or 20. It produces the same figure.
Is there something wrong with the code I am using? In THIS data set, each row only has a 1, and those still alive by day 7 I left blank (did not input 1 or 0).
