Re: [R] Survival analysis: ERROR: Time and status are different lengths

2015-12-04 Thread Therneau, Terry M., Ph.D. 
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-requ...@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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Re: [R] Survival analysis: ERROR: Time and status are different lengths

2015-12-04 Thread Marleen Hamoen 
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. :

> 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$linear.predictors will be shorter than the original data set,
> and the printout will have a note about "...deleted due to missing".
>
> The simplest solution to this is to set
>   options(na.action="na.exclude")
> before doing the fit.  Then predict(fit) and resid(fit) will return
> vectors of the same length as the input data, containing NA in the
> appropriate positions.  The default na.action of "na.omit" leaves missing
> out of both the fit and the residuals.
>
> (Unfortunately, only a few modeling functions in R pay attention to the
> difference between these two na.action options.)
>
> Terry Therneau
>
>
>
> On 12/04/2015 05:00 AM, r-help-requ...@r-project.org wrote:
>
>> Hi,
>>
>> I am fitting an AFT model assuming a Weibull distribution and I would like
>> to check the residuals compared to the Kaplan Meier residuals, but when I
>> try to create the Kaplan Meier residuals I get an error: Time and status
>> are different lengths.
>>
>> I am using the following script:
>>
>> # Fitting the AFT model
>> fit.weib <- survreg(Surv(TimeDeath, event) ~ age + sex + mutation +
>> ventilation + BM1 + BM2, data = DF, dist = "weibull")
>> fits <- fit.weib$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,
>>
>

[[alternative HTML version deleted]]

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[R] Survival analysis: ERROR: Time and status are different lengths

2015-12-03 Thread Marleen Hamoen 
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,

M

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.