Thank you David. It is my understanding that using survit below I get the
median predicted survival. I actually was looking for the mean. I can't
seem to find in the documentation how to get that.
options(na.action=na.exclude) # retain NA in predictions
fit <- coxph(Surv(time, status) ~ age + ph.ecog, lung)
pred <- survfit(fit, newdata=lung)
head(pred)
Thanks again,
Axel.
On Sat, Jul 5, 2014 at 1:54 PM, David Winsemius
wrote:
>
> On Jul 5, 2014, at 5:28 AM, Axel Urbiz wrote:
>
> Dear R users,
>>
>> My apologies for the simple question, as I'm starting to learn the
>> concepts
>> behind the Cox PH model. I was just experimenting with the survival and
>> rms
>> packages for this.
>>
>> I'm simply trying to obtain the expected survival time (as opposed to the
>> probability of survival at a given time t).
>>
>
> What does "expected survival time" actually mean? Do you want the median
> survival time?
>
>
> I can't seem to find an option
>> from the "type" argument in the predict methods from coxph{survival} or
>> cph{rms} that will give me expected survival times.
>>
>> library(rms)
>> options(na.action=na.exclude) # retain NA in predictions
>> fit <- coxph(Surv(time, status) ~ age + ph.ecog, lung)
>> fit2 <- cph(Surv(time, status) ~ age + ph.ecog, lung)
>> head(predict(fit,type="lp"))
>> head(predict(fit2,type="lp"))
>>
>
> `predict` will return the results of the regression, i.e. the log-hazard
> ratios for each term in the RHS of the formula. What you want (as described
> in the Index for the survival package) is either `survfit` or `survexp`.
>
> require(survival)
> help(pack=survival)
> ?survfit
> ?survexp
> ?summary.survfit
> ?quantile.survfit # to get the median
> ?print.summary.survfit
>
> require(rms)
> help(pack=rms)
>
> The rms-package also adds a `survfit.cph` function but I have found the
> `survest` function also provides useful added features, beyond those
> offered by survfit
>
>
>>
>> Thank you.
>>
>> Regards,
>> Axel.
>>
>> [[alternative HTML version deleted]]
>>
>
> This is a plain text mailing list.
>
> --
>
> David Winsemius, MD
> Alameda, CA, USA
>
>
[[alternative HTML version deleted]]