From: Hanke, Alex <HankeA_at_mar.dfo-mpo.gc.ca>

Date: Fri 17 Jun 2005 - 00:49:58 EST

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jun 17 02:10:05 2005

Date: Fri 17 Jun 2005 - 00:49:58 EST

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@u.washington.edu]
Sent: June 16, 2005 11:00 AM

To: Hanke, Alex

Cc: 'r-help@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@stats.ox.ac.uk]
**> Sent: June 15, 2005 4:24 PM
**> To: Hanke, Alex
**> Cc: 'r-help@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]]
**>>
**>> ______________________________________________
**>> R-help@stat.math.ethz.ch mailing list
**>> https://stat.ethz.ch/mailman/listinfo/r-help
**>> PLEASE do read the posting guide!
**> http://www.R-project.org/posting-guide.html
**>>
**>
**> --
**> Brian D. Ripley, ripley@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
**>
**> ______________________________________________
**> R-help@stat.math.ethz.ch mailing list
**> https://stat.ethz.ch/mailman/listinfo/r-help
**> PLEASE do read the posting guide!
*

http://www.R-project.org/posting-guide.html

*>
*

Thomas Lumley Assoc. Professor, Biostatistics tlumley@u.washington.edu University of Washington, Seattle ______________________________________________R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jun 17 02:10:05 2005

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