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.
