I am new to coding and to R. Currently working with package relsurv. For this I would like to calculate the relative survival at certain timepoints.
I am using the following to assess RS at five years:
rcurve2 <- rs.surv(Surv(time_days17/365.241,event_17)~1+
ratetable(age = age_diagnosis*365.241, sex = sex,
year = year_diagnosis_days), data = survdata, ratetable = swepop,
method="ederer1",conf.int=0.95,type="kaplan-meier",
add.times = 5*365.241)
summary(rcurve2)
However, I get the same result in my summary output regardless of what number I put after add.times ie for all event/cenasoring points (see below)
time n.risk n.event survival std.err lower 95% CI upper 95% CI
0.205 177 1 0.9944 0.00562 0.9834 1.005
0.627 176 1 0.9888 0.00792 0.9734 1.004
0.742 175 1 0.9831 0.00968 0.9644 1.002
0.827 174 1 0.9775 0.01114 0.9559 1.000
0.849 173 1 0.9718 0.01242 0.9478 0.996
0.947 172 1 0.9662 0.01356 0.9400 0.993
...cont.
I am clearly not getting it right! Would be grateful for your help!
A very good question!
When adding "imaginary" times using add.times, they are automatically censored, and wont show up with the summary() function. To see your added times set censored = TRUE:
summary(rcurve2, censored = TRUE)
You should now find your added time in the list that follows.
Using built in data with the relsurv package
data(slopop)
data(rdata)
#note the last argument add.times=1000
rcurve2 <- rs.surv(Surv(time,cens)~sex+ratetable(age=age*365.241, sex=sex,
year=year), ratetable=slopop, data=rdata, add.times = 1000)
When using summary(rcurve2) the time 1000 wont show up:
>summary(rcurve2)
[...]
973 200 1 0.792 0.03081 0.734 0.855
994 199 1 0.790 0.03103 0.732 0.854
1002 198 1 0.783 0.03183 0.723 0.848
[...]
BUT using summary(rcurve2, censored=TRUE) it will!
>summary(rcurve2, censored=TRUE)
[...]
973 200 1 0.792 0.03081 0.734 0.855
994 199 1 0.790 0.03103 0.732 0.854
1000 198 0 0.791 0.03106 0.732 0.854
1002 198 1 0.783 0.03183 0.723 0.848
[...]