R help - Dec 2015 - Survival analysis: ERROR: Time and status are different lengths

Hi Terry,

I already suspected it had something to do with missing values in one of
the covariates. I couldn't get the na.action="na.exclude" to work
(perhaps
this is because I am relatively unexperienced with R), but I managed to
solve the problem by using the following command with
"complete.cases":

DF <- with(DF,DF[complete.cases(TimeDeath, event, age, sex, mutation,
ventilation, BM1, BM2), ])

Thank you very much for your help!


2015-12-04 15:02 GMT+01:00 Therneau, Terry M., Ph.D. <therneau at
mayo.edu>:
> I expect that reading the result of print(fit.weib) will answer your
> question.  If there were any missing values in the data set, then the
> fit.weib$linear.predictors will be shorter than the original data set,
> and the printout will have a note about "...deleted due to
missing".
>
> The simplest solution to this is to set
>   options(na.action="na.exclude")
> before doing the fit.  Then predict(fit) and resid(fit) will return
> vectors of the same length as the input data, containing NA in the
> appropriate positions.  The default na.action of "na.omit" leaves
missing
> out of both the fit and the residuals.
>
> (Unfortunately, only a few modeling functions in R pay attention to the
> difference between these two na.action options.)
>
> Terry Therneau
>
>
>
> On 12/04/2015 05:00 AM, r-help-request at r-project.org wrote:
>
>> Hi,
>>
>> I am fitting an AFT model assuming a Weibull distribution and I would
like
>> to check the residuals compared to the Kaplan Meier residuals, but when
I
>> try to create the Kaplan Meier residuals I get an error: Time and
status
>> are different lengths.
>>
>> I am using the following script:
>>
>> # Fitting the AFT model
>> fit.weib <- survreg(Surv(TimeDeath, event) ~ age + sex + mutation +
>> ventilation + BM1 + BM2, data = DF, dist = "weibull")
>> fits <- fit.weib$linear.predictors
>> resids <- (fit.weib$y[, 1] - fits)/fit.weib$scale
>> resKM <- survfit(Surv(resids, event) ~ 1, data = DF)
>>
>> I get the error from the last line of the script.
>>
>> I tried some things that didn't work and I was wondering if anyone
could
>> help me.
>> If you need more information please let me know.
>>
>> Thanks in advance,
>>
>
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