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:[EMAIL PROTECTED] Sent: June 15, 2005 4:24 PM To: Hanke, Alex Cc: '[email protected]' 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]] > > ______________________________________________ > [email protected] 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, [EMAIL PROTECTED] 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 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
