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

Date: Thu 16 Jun 2005 - 22:23:34 EST

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 Which is a nice change but still short of knowing what is going on. Regards

Alex

Date: Thu 16 Jun 2005 - 22:23:34 EST

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 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]]
**>
**> ______________________________________________
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**> 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.htmlReceived on Thu Jun 16 22:33:22 2005

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