[R] Error using newdata argument in survfit
Hanke, Alex
HankeA at mar.dfo-mpo.gc.ca
Thu Jun 16 16:49:58 CEST 2005
Thanks to Thomas, Brain and Ales,
Whose advice led me to the solution. I actually had a second problem
preventing Thomas' solution :
survfit(fit,list(Week=c(15,15),LagAOO=c(0,0),Prior.f=factor(c(1,2),levels=1:
5)))
from working. In the model statement I create a factor from Prior.f via
factor(Prior.f). Rather one should predefine the factor variable
Prior.f<-factor(Prior.f) and use that term in the model and then Thomas'
solution works fine.
Alex
-----Original Message-----
From: Thomas Lumley [mailto:tlumley at u.washington.edu]
Sent: June 16, 2005 11:00 AM
To: Hanke, Alex
Cc: 'r-help at stat.math.ethz.ch'
Subject: Re: [R] Error using newdata argument in survfit
On Thu, 16 Jun 2005, Hanke, Alex wrote:
> Hi Brian,
> The factor Prior.f has 5 levels (1,2,3,4,5) which coxph deals with by
> creating 4 dummy variables coded with 1 or zero. That's what I see when I
> look at fit$x.
> fit$x[1:5,]
> Week LagAOO factor(Prior.f)2 factor(Prior.f)3 factor(Prior.f)4
> 31 22 0 0 0 0
> 32 22 0 0 0 0
> 33 22 2 0 0 0
> 34 22 3 0 0 0
> 35 22 2 0 0 0
> factor(Prior.f)5
> 31 0
> 32 0
> 33 0
> 34 0
> 35 0
> I have played with the formula a bit adding a term at a time and then
> checking to see if I can produce the survival curves for pseudo cohorts. I
> get as far as the Prior.f term and am successful if I treat it as a
> continuous variable. If I introduce it as a factor and assume it wants
four
> dummy variables as above I get the variable lengths error. If I represent
> the term with one variable:
> survfit(fit,list(Week=c(15,15),LagAOO=c(0,0),Prior.f=c(1,2)))
> I get:
> Error in x2 %*% coef : non-conformable arguments
Yes, but it wants a factor with *5* levels. Try
survfit(fit,list(Week=c(15,15),LagAOO=c(0,0),Prior.f=factor(c(1,2),levels=1:
5)))
-thomas
> Which is a nice change but still short of knowing what is going on.
> Regards
> Alex
>
> -----Original Message-----
> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
> Sent: June 15, 2005 4:24 PM
> To: Hanke, Alex
> Cc: 'r-help at stat.math.ethz.ch'
> Subject: Re: [R] Error using newdata argument in survfit
>
> You appear to have a coding for prior.f in newdata rather than the factor
> itself.
>
> It's a bit hard to be sure when we don't have data8 to compare with.
>
> On Wed, 15 Jun 2005, Hanke, Alex wrote:
>
>> Dear R-helpers,
>> To get curves for a pseudo cohort other than the one centered at the mean
> of
>> the covariates, I have been trying to use the newdata argument to survfit
>> with no success. Here is my model statement, the newdata and the ensuing
>> error. What am I doing wrong?
>>
>>> summary(fit)
>> Call:
>> coxph(formula = Surv(Start, Stop, Event, type = "counting") ~
>> Week + LagAOO + Prior.f + cluster(interaction(Station, Year)),
>> data = data8, method = "breslow", x = T, y = T)
>>
>> n= 1878
>> coef exp(coef) se(coef) robust se z p
>> Week 0.00582 1.01 0.0323 0.0239 0.244 8.1e-01
>> LagAOO 0.71929 2.05 0.1238 0.1215 5.918 3.3e-09
>> Prior.f2 0.12927 1.14 0.4402 0.4025 0.321 7.5e-01
>> Prior.f3 0.79082 2.21 0.5484 0.4460 1.773 7.6e-02
>> Prior.f4 2.04189 7.71 0.6008 0.4685 4.358 1.3e-05
>> Prior.f5 1.20450 3.34 0.6423 0.5481 2.198 2.8e-02
>>
>> exp(coef) exp(-coef) lower .95 upper .95
>> Week 1.01 0.994 0.960 1.05
>> LagAOO 2.05 0.487 1.618 2.61
>> Prior.f2 1.14 0.879 0.517 2.50
>> Prior.f3 2.21 0.453 0.920 5.29
>> Prior.f4 7.71 0.130 3.076 19.30
>> Prior.f5 3.34 0.300 1.139 9.76
>>
>> Rsquare= 0.047 (max possible= 0.25 )
>> Likelihood ratio test= 91 on 6 df, p=0
>> Wald test = 209 on 6 df, p=0
>> Score (logrank) test = 142 on 6 df, p=0, Robust = 17.4 p=0.00803
>>
>> (Note: the likelihood ratio and score tests assume independence of
>> observations within a cluster, the Wald and robust score tests do
> not).
>>>
>> newdat
>> Week LagAOO Prior.f2 Prior.f3 Prior.f4 Prior.f5
>> 1 17.55218 1.191693 1 0 0 0
>> 2 17.55218 1.191693 0 0 0 0
>>
>>> survfit(fit,newdata=newdat)
>> Error in model.frame(formula, rownames, variables, varnames, extras,
>> extranames, :
>> variable lengths differ
>> In addition: Warning message:
>> 'newdata' had 2 rows but variable(s) found have 1878 rows
>>
>> Regards,
>> Alex
>>
>>
>> Alex Hanke
>> Department of Fisheries and Oceans
>> St. Andrews Biological Station
>> 531 Brandy Cove Road
>> St. Andrews, NB
>> Canada
>> E5B 2L9
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
>
> ______________________________________________
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Thomas Lumley Assoc. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle
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