How to calculate NRI in survival models with R? - r

Question

My aim is to study how the inclusion of several risk factors improve a clinical model predicting the incidence of stroke in a survival analysis. I want to use the NRI to compare two models (1 baseline model vs baseline model+new risk factor). However, I would prefer to stratify the probabilities of these models in categorical variables (i.e., risk 0-3%, risk 4-6%, risk >7%...).
For that purpose I have prepared the following code with R, but I am not sure whether it is correct or not and I would prefer to clarify it =).
I will use the open survival data “lung” in order to show a reproducible example. IMPORTANT: I will not consider censored data in this analysis, but it should be analyzed as appropriate in further analyses:
library(survival)
library(pec)##To calculate probabilities of event at a point of time.
library(Hmisc)##To calculate NRI
data(lung)
lung <- na.omit(lung)
lung$status <- lung$status-1##necessary for NRI package
stats <- lung$status
tempo <- lung$time
##Create two models, 1 baseline and 1 baseline+new predictor
model1 <- coxph(Surv(tempo,stats)~age+sex, data=lung, x=T)
model2 <- coxph(Surv(tempo,stats)~age+sex+factor(ph.ecog), data=lung,
x=T)
##Estimate the survival probability at time= 500.
lung$x <- predictSurvProb(model1, newdata=lung, times=c(500))
lung$y <- predictSurvProb(model2, newdata=lung, times=c(500))
##Calculate the probability of event (1-survival) and we categorize it.
lung$x <- cut(1-lung$x, c(0, 0.25, 0.5, 0.75, 1), include.lowest=TRUE,
right=FALSE)
lung$y <- cut(1-lung$y, c(0, 0.25, 0.5, 0.75, 1), include.lowest=TRUE,
right=FALSE)
##Confusion matrix
cases <- subset(lung, stats==1)
controls <- subset(lung, stats==0)
table(lung$x, lung$y)##All patients
table(cases$x, cases$y)##cases
table(controls$x, controls$y)##controls
##Calculate NRI
x <- as.numeric(lung$x)/4##Predictions should be ranged between 0-1
y <- as.numeric(lung$y)/4
improveProb(x, y, stats)
My questions:
1) Is this mode to calculate the risk of event at t=500 correct?
2) Is it correct to calculate NRI with this function? I have tried other packages (i.e., NRIcens) and I obtained the same results…
Thanks in advance for your help!