Why does the survival probability of the survival package return 0% at the end of the time horizon when there are survivors in the dataset?

Question

I've just started using the survival and survminer packages in R and am trying to understand its output. In the code below I create a dataframe with the first 12 rows of my actual dataset, as representative of the issue/question. In this representative data:

• ID = unique identifier for each element
• time = survival time for the element in months where value > 0 means death (the month that death occurs) and value = 0 means no death (right censored) during the study period
• status = the element's censoring status where 1=censored and 2=dead
• node = one of the variables associated with each element where I try to assess its association with the probability of death

Running length(which(testDF$status == 2))/nrow(testDF) shows a death rate of 66.67% with this data, but the survival probability curves shown in the image below end at 0%. Should they not be ending at 66.67% at least for the average of all the data? What am I doing wrong here or am I misinterpreting survival probability?

Code:

library(ggplot2)
library(survival)
library(survminer)

testDF <- data.frame(
  ID = 1:12,
  time = c(0,34,0,12,12,21,0,0,39,11,13,26),
  status = c(1,2,1,2,2,2,1,1,2,2,2,2),
  node = c("C","C","B","A","C","C","B","C","B","C","A","B")
)

fit <- survfit(Surv(time, status) ~ node, data = testDF)

ggsurvplot(fit,
           pval = TRUE, 
           conf.int = TRUE,
           linetype = "strata",
           surv.median.line = "hv",
           ggtheme = theme_bw()
           )

# percentage of deaths
length(which(testDF$status == 2))/nrow(testDF)

Modifying the OP above to reflect accepted solution:

Revised dataframe to reflect paulduf solution to correctly represent censored data (in my data, no deaths within the 40 month study is "censored"), with commented revised graphic beneath:

testDF <- data.frame(
  ID = 1:12,
  time = c(40,34,40,12,12,21,40,40,39,11,13,26), # 40 month study window (0's for no death changed to 40)
  status = c(0,1,0,1,1,1,0,0,1,1,1,1), # 0 = censored, 1 = death
  node = c("C","C","B","A","C","C","B","C","B","C","A","B")
)

# percentage of deaths summary
length(which(testDF$status == 0))/nrow(testDF)
length(which(testDF$status == 0 & testDF$node == "A"))/length(which(testDF$node == "A"))
length(which(testDF$status == 0 & testDF$node == "B"))/length(which(testDF$node == "B"))
length(which(testDF$status == 0 & testDF$node == "C"))/length(which(testDF$node == "C"))

In the plot confidence intervals are removed for enhanced clarity:

Answer 1

• time = survival time for the element in months where value > 0 means death (the month that death occurs) and value = 0 means no death (right censored) during the study period
• status = the element's censoring status where 1=censored and 2=dead

The data you entered in the model is corrupted. The setting of "value=0" for a censored observation is the cause of the "bug". The information that death did not occur for an individual within the study period is already contained in status. Set time=T where T is the observation time (end of study date - enrollment date) and you should see the expected behaviour.

As Henry noticed,

Your censored values (all with time 0) do not seem to have affected the graph or the fit

I think indeed if you write the math you see they have no influence so the model is not fitted on the data you expect.