On Feb 22, 2012, at 7:47 PM, David Winsemius wrote:
>
> On Feb 22, 2012, at 6:59 PM, niloo javan wrote:
>
>> hi
>> I have a problem with Median in Survival.
>> when I use
>> S1=survfit(Surv(Time,Status))
>> the result shows the median but I cannot use it as numeric!
>> S1$median in Null
>
> That does not look like a formula.
Yeah, the OP is missing the '~ 1' part:
survfit(Surv(Time, Status) ~ 1, data = ...)
>
> Furthermore I do not think there is an element in a survfit.object named
> 'median'. (It's certainly not documented on the help pages.) Objects are
> passed to their print methods and the `print.survfit` function passes off its
> data argument first to `survmean`, then to `pfun`, then to `minmin` which
> does the job of calculating a median, which print.survfit then prints (as a
> side-effect using `cat`), but never stores in a returned object.
>
> Is this is homework?
Perhaps, but the information is available from ?summary.survfit, where the
Value section indicates that the returned object includes a 'table' component:
> summary(survfit(Surv(futime, fustat) ~ 1, data = ovarian))$table
records n.max n.start events median 0.95LCL 0.95UCL
26 26 26 12 638 464 NA
> RES <- summary(survfit(Surv(futime, fustat) ~ 1, data = ovarian))$table
> RES["median"]
median
638
> RES["0.95LCL"]
0.95LCL
464
> RES["0.95UCL"]
0.95UCL
NA
This will be a matrix rather than a vector, if the analysis consists of RHS
covariates:
> summary(survfit(Surv(futime, fustat) ~ rx, data = ovarian))$table
records n.max n.start events median 0.95LCL 0.95UCL
rx=1 13 13 13 7 638 268 NA
rx=2 13 13 13 5 NA 475 NA
...
> RES[, "median"]
rx=1 rx=2
638 NA
If memory serves, the 'table' component was added about three years ago, as
previously, one would have to use capture.output() on the result of explicitly
using print.survfit() and then parse the textual results to get the median and
CI's. It was one of those 'infelicities' in using these functions where the
print method included code to calculate new values, rather than simply printing
the results derived in the core function.
HTH,
Marc Schwartz
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