Hello all
I am a very new R user I am used to using STATA My problem: I want to build a Cox model and validate this. I have a large number of clinical relevant factors and feel the need to reduce these. Meanwhile I have some clinical variables I deem sufficiently important to force into the model regardless of AIC or p value. This is my present log over commands ************ library(rms) library(survival) library(Hmisc) data1 <- read.table("optimism.csv", header=T, sep=",") attach(data1) coxmodel4 <- coxph(formula=Surv(OS,mors) ~ iAJCC2+iAJCC3+iPS2+iPS3++alder_diag+gender+vol_GTV+iforb2+iforb3+hem_LNL+ser o_thromb+LDH_UNL+ALAT_UNL+BASP_UNL+sero_bili+resection_perf+sero_WBC, data=data1, x=TRUE, y=TRUE,method=c("efron")) coxmodel.streg<-step(coxmodel4) I would like to "lock" iAJCC2 iAJCC3 and iPS2 + iPS3 regardless, but I cannot seem to get the step function to accept this. Further Once I have the model I would like to validate it with the validate command I am presently using this**************** fit <- cph(formula=Surv(OS,mors) ~ iAJCC2+iAJCC3+iPS2+iPS3+alder_diag+gender+vol_GTV+iforb2+iforb3+hem_LNL+sero _thromb+LDH_UNL+ALAT_UNL+BASP_UNL+sero_bili+resection_perf+sero_WBC, data=data1, x=TRUE, y=TRUE) fit validate(fit, method="boot", B=40,bw=TRUE, rule="p", type="residual", sls=0.15, aics=0, pr=TRUE) Due to my small data set 153 patients with 130 events I have chosen to lift the p limit from 5% to 15% as suggested by Steyerberg. ************************************************************************ I would appreciate any help with the lock term (also if it cannot be done) As I mentioned I am a bit of a rookie, and not too experienced as a programmer (I am a MD after all) However I am quite impressed with R so far since I have been trying to get this far in STATA for a few weeks. Sincerely Jon Kroll Bjerregaard, MD. Dep of Oncology Odense University Hospital [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.