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

From: Charles C. Berry <cberry_at_tajo.ucsd.edu>
Date: Tue, 4 Dec 2007 16:54:26 -0800

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
>

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
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>> PLEASE do read the posting guide
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>> 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

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