Li, Jia
2005-Oct-25 20:41 UTC
[R] One more about Error in step() (or stepAIC) for Cox model
Thank you for Prof.Ripley's suggestion. I fixed the program by adding a lower scope, and the program ran, but I still got warning messages, and don't know what is going on, would this affect my results? ... Step: AIC= 12337.74 Surv(tlfup, cen) ~ MI[[j]]$trt + MI[[j]]$agem40 + MI[[j]]$agem40sq + mhtypeed1 + mhtypeed2 Df AIC <none> 12338 - MI[[j]]$agem40sq 1 12338 - MI[[j]]$agem40 1 12339 - mhtypeed2 1 12353 - mhtypeed1 1 12365 There were 50 or more warnings (use warnings() to see the first 50) Warning messages: 1: X matrix deemed to be singular; variable 8 9 in: coxph(Surv(tlfup, cen) ~ MI[[j]]$trt + MI[[j]]$nodes + MI[[j]]$ngraded2 + ... 2: X matrix deemed to be singular; variable 7 8 in: coxph(formula Surv(tlfup, cen) ~ MI[[j]]$nodes + MI[[j]]$ngraded2 + ... ... 7: X matrix deemed to be singular; variable 7 8 in: coxph(formula Surv(tlfup, cen) ~ MI[[j]]$trt + MI[[j]]$nodes + ... 8: X matrix deemed to be singular; variable 8 in: coxph(formula Surv(tlfup, cen) ~ MI[[j]]$trt + MI[[j]]$nodes + ... 11: X matrix deemed to be singular; variable 7 in: coxph(formula Surv(tlfup, cen) ~ MI[[j]]$nodes + MI[[j]]$ngraded2 + ... ... Thanks, Jia -----Original Message----- From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] Sent: Monday, October 24, 2005 4:05 PM To: Li, Jia Cc: r-help at stat.math.ethz.ch Subject: Re: [R] Error in step() (or stepAIC) for Cox model On Mon, 24 Oct 2005, Li, Jia wrote:> Hello all, > > I am trying to use stepwise procedure to select covariates in Cox > model and use bootstrap to repeat stepwise selection, then record how> many times variables are chosen by step() in bootstrap replications.> When I use step() (or stepAIC) to do model selection, I got errors. > Here is the part of my code > > for (j in 1:mm){ #<--mm=10 > > for (b in 1:nrow(reg.bs)){ #<--bootstrap 10 times > > mi<-data.frame(tlfup,cen,complete(imp,j)) #<--completed data sets > after MI > > in.star<-sample(1:n,n,replace=T) #<--to sample id number 1-1851. > > data.star<-mi[in.star,] > > M<-coxph(Surv(tlfup,cen)~mi$trt+mi$nodes+mi$htypeed1+mi$htypeed2+mi$ng > ra > ded2+mi$agem40 > > +mi$agem40sq+mi$er+mi$pr,data=data.star) > > reg.model<-step(M) #<--do stepwise selection > > reg.step[[b]]<-c((reg.model$coef)) #<-store selected variables > > chosen.vb[[b]]<-names(reg.step[[b]]) #<--store names of selected > variables > > } > > tot.vb[[j]]<-c(unlist(chosen.vb)) > > } > > Error in reg.step[[b]] : subscript out of bounds > > > varibles<-unlist(tot.vb) #<--change to a vector > > table(varibles) #<--how many times the names have been > selected > > Error in sort(unique.default(x), na.last = TRUE) : > 'x' must be atomic > > > I figure the reason may be that when stepwise procedure selects the > chosen model with no varibles, that is > > Start: AIC= 12436.85 > Surv(tlfup, cen) ~ mi$trt + mi$nodes + mi$htypeed1 + mi$htypeed2 + > mi$ngraded2 + mi$agem40 + mi$agem40sq + mi$er + mi$pr > > Df AIC > - mi$pr 1 12435 > - mi$trt 1 12435 > - mi$agem40sq 1 12435 > - mi$agem40 1 12435 > - mi$htypeed2 1 12435 > - mi$nodes 1 12435 > - mi$er 1 12436 > - mi$ngraded2 1 12436 > - mi$htypeed1 1 12436 > <none> 12437 > > Step: AIC= 12425.91 > Surv(tlfup, cen) ~ mi$htypeed1 + mi$ngraded2 + mi$er > > Df AIC > - mi$er 1 12425 > - mi$ngraded2 1 12425 > - mi$htypeed1 1 12426 > <none> 12426 > > Step: AIC= 12424.77 > Surv(tlfup, cen) ~ 1 > > then reg.model$coef dosen't exist anymore (am I right?), but I need to> count the variables that are selected by step() in bootstrap > replications, what should I do?Specify the lower scope suitably. -- 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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