Bootstrapping in R. By Using Nagelkerke R-Squared - r

Question

I am new in R. I try to use the boot() function in R, by using the Nagelkerke R-squared as the statistics parameter. I know that I need a function that measure Nagelkerke R-squared of original over the resample. However, I have no idea what should I put as the statistical function.
I know that Nagelkerke R-squared can be compute by using deviance and Null.deviance given Logit regression. I write the function to compute Nagelkerke R-squared.
NagR2 <- function(Objects){
n <- nrow(Objects)
reg <- glm(form,
family = binomial("logit"), data = datainput)
mo <- stepAIC(regression,direction = c("backward"), trace = FALSE)
R2cox <- 1- exp((mo$deviance - mo$null.deviance)/n)
R2nag <- R2cox/(1-exp((-mo$null.deviance)/n))
R2nag
}
How should I change my NagR2 function so that I can use it as statistic in the boot() function?

Answer 1

You need to alter the function, to take in a input data.frame as first argument, and indices of the data.frame as the second, and other arguments, so changing your existing function a bit:
NagR2 <- function(datainput,ind,form){
n <- nrow(datainput[ind,])
reg <- glm(form,family = binomial("logit"), data = datainput[ind,])
mo <- stepAIC(reg,direction = c("backward"), trace = FALSE)
R2cox <- 1- exp((mo$deviance - mo$null.deviance)/n)
R2nag <- R2cox/(1-exp((-mo$null.deviance)/n))
R2nag
}
And applying onto a test dataset:
library(MASS)
library(boot)
dat = iris
dat$Species=factor(ifelse(dat$Species=="versicolor","v","o"))
bo = boot(dat,statistic=NagR2,R=100,form = as.formula(Species ~ .))
ORDINARY NONPARAMETRIC BOOTSTRAP
Call:
boot(data = dat, statistic = NagR2, R = 100, form = as.formula(Species ~
.))
Bootstrap Statistics :
original bias std. error
t1* 0.3650395 0.01470299 0.0720022