Kaplan Meier for Annual Survival with Staggered Entry

Question

I am carrying out survival analysis for two populations of mammals. The data available is GPS collar data: date collared, date of death or date of end of study. I am using the non-parametric Kaplan Meier estimator in R to create survival curves. And I am using a log-rank test to compare between the survival curves of my two study sites. The data I used was number of days that each individual was collared (or alive) and whether or not they were alive at the end of the study.

I have two concerns with what I have done so far.

I haven't managed to find code to analaysis specifically for annual survival. To display annual survival I shortened the x-axis to 365 days. I worry that 1) this is not correct and 2) that my log-rank test only tests for differences between the 2 complete curves, and not between just one year.

Additionally, I found a paper (Pollock et al, 1989) which modified the Kaplan Meier estimator (originally for medical trials) to allow for a staggered entry design, useful for collaring studies. I have two study sites. At one study site all jackals were collared on the same day. For the other study site the jackals were collared over a range of dates. I followed a tutorial online and their data did share the same study start date. I am looking for annual survival, and not survival at a set point in time ie end of a specific season or at a specific event, and so I am unsure if the Pollock version would be more approporiate to use or not?

I did not use the Cox-proportional hazard because we have no covariates

Answer 1

I'm not sure if you are still looking, but generally you might try to use survival package and:

output<-summary(survfit(Surv(as.numeric(enter, exit), event)~(as.factor(year)), conf.type = "log-log", data=data)).

From your output you can extract year (output$strata) and survival values (output$surv) and SE and CI components (output$std.err, output$lower, output$upper)