[R] Another correction WAS: Re: predict error for survreg with natural splines

[Charles C. Berry]

On Tue, 4 Dec 2007, Charles C. Berry wrote:

> On Tue, 4 Dec 2007, Charles C. Berry wrote:
>
>> 
>>
>>  I think coxph() leaves safe prediction off by default. You need to turn it
>>  on.
>
>
> Sorry for the misdirection, I see now that you are describing survreg() not 
> coxph().
>
> But even coxph() seems to barf on this.
>
> A possible workaround:
>
>>  n <- data.frame(age=c(65,rep(mean(ovarian$age)), 10))
>>  predict(s, newdata=n)[-1]
> [1] -0.4182318 -1.9911592

This was wrong. It is not invariant to the choice of the discarded value.

I guess it is time to study up on safe prediction. It is obvious I am 
missing something.

Sorry again,

Chuck

>> 
>
> Chuck
>
>
>>
>>  See
>>
>>   ?predict.coxph
>>
>>  Chuck
>>
>>  On Wed, 5 Dec 2007, Gad Abraham wrote:
>> 
>> >   Hi,
>> > 
>> >   The following error looks like a bug to me but perhaps someone can shed
>> >   light on it:
>> > 
>> > >   library(splines)
>> > >   library(survival)
>> > >   s <- survreg(Surv(futime, fustat) ~ ns(age, knots=c(50, 60)),
>> >   data=ovarian)
>> > >   n <- data.frame(age=rep(mean(ovarian$age), 10))
>> > >   predict(s, newdata=n)
>> >   Error in qr.default(t(const)) :
>> >     NA/NaN/Inf in foreign function call (arg 1)
>> > 
>> >   Thanks,
>> >   Gad
>> > 
>> > 
>> > 
>> > >   sessionInfo()
>> >   R version 2.6.1 (2007-11-26)
>> >   i486-pc-linux-gnu
>> > 
>> >   locale:
>> >   LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;
>> >   LC_COLLATE=en_AU.UTF-8;LC_MONETARY=en_AU.UTF-8;LC_MESSAGES=en_AU.UTF-8;
>> >   LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;
>> >   LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C
>> > 
>> >   attached base packages:
>> >   [1] splines   stats     graphics  grDevices utils     datasets  methods
>> >   [8] base
>> > 
>> >   other attached packages:
>> >   [1] survival_2.34
>> > 
>> >   loaded via a namespace (and not attached):
>> >   [1] rcompgen_0.1-17
>> > 
>> > 
>> > 
>> >   --
>> >   Gad Abraham
>> >   Department of Mathematics and Statistics
>> >   The University of Melbourne
>> >   Parkville 3010, Victoria, Australia
>> >   email: g.abraham at ms.unimelb.edu.au
>> >   web: http://www.ms.unimelb.edu.au/~gabraham
>> > 
>> >   ______________________________________________
>> >   R-help at r-project.org mailing list
>> >   https://stat.ethz.ch/mailman/listinfo/r-help
>> >   PLEASE do read the posting guide
>> >   http://www.R-project.org/posting-guide.html
>> >   and provide commented, minimal, self-contained, reproducible code.
>> > 
>>
>>  Charles C. Berry                            (858) 534-2098
>>                                             Dept of Family/Preventive
>>  Medicine
>>  E mailto:cberry at tajo.ucsd.edu	            UC San Diego
>>  http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>> 
>> 
>> 
>
> Charles C. Berry                            (858) 534-2098
>                                            Dept of Family/Preventive 
> Medicine
> E mailto:cberry at tajo.ucsd.edu	            UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>
>
>
>

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901