function works (boot.stepAIC ) but throws an error inside another function - environment issue?
r, statistics-bootstrap
Solution
Using `do.call` as in anova test fails on lme fits created with pasted formula provides the answer.
`boot.stepAIC` doesn't have access to `form` when run within a function; that can be recreated in the global environment like this; we see that `lm` is using `form.1` as the formula, and removing it makes `boot.stepAIC` fail.
> form.1<-as.formula(res~x+y+z)
> mm <- lm(form.1, dat.test)
> mm$call
lm(formula = form.1, data = dat.test)
> rm(form.1)
> boot.stepAIC(mm,dat.test)
# same error as OP
Using `do.call` does work. Here I use `as.name` as well; otherwise the `mm` object carries around the entire dataset instead of just the name of it.
> form.1<-as.formula(res~x+y+z)
> mm <- do.call("lm", list(form.1, data=as.name("dat.test")))
> mm$call
lm(formula = res ~ x + y + z, data = dat.test)
> rm(form.1)
> boot.stepAIC(mm,dat.test)
To apply this to the original problem, I'd do this:
fun.boot.lm.stepAIC<-function(dat,form) {
if(!inherits(form, "formula")) stop("No formula given")
mm <- do.call("lm", list(form, data=as.name(dat)))
do.call("boot.stepAIC", list(mm,data=as.name(dat)))
}
form.1<-as.formula(res~x+y+z)
fun.boot.lm.stepAIC(dat="dat.test",form=form1)
This works too but the entire data set gets included in the final output object, and the final output to console, as well.
fun.boot.lm.stepAIC<-function(dat,form) {
if(!inherits(form, "formula")) stop("No formula given")
mm <- do.call("lm", list(form, data=dat))
boot.stepAIC(mm,data=dat)
}
form.1<-as.formula(res~x+y+z)
fun.boot.lm.stepAIC(dat=dat.test,form=form.1)
Problem
I realized a strange behavior today with in my R code. I tried a package {boot.StepAIC} which includes a bootstrap function for the results of the stepwise regression with the AIC. However I do not think the statistical background is here the problem (I hope so). I can use the function at the top level of R. This is my example code. ``` require(MASS) require(boot.StepAIC) n<-100 x<-rnorm(n); y<-rnorm(n,sd=2); z<-rnorm(n,sd=3); res<-x+y+z+rnorm(n,sd=0.1) dat.test<-as.data.frame(cbind(x,y,z,res)) form.1<-as.formula(res~x+y+z) boot.stepAIC(lm(form.1, dat.test),dat.test) # should be OK - works at me ``` However, I wanted to wrap that in an own function. I pass the data and the formula to that function. But I get an error within boot.stepAIC() saying: the model fit failed in 100 bootstrap samples Error in strsplit(nam.vars, ":") : non-character argument ``` # custom function fun.boot.lm.stepAIC<-function(dat,form) { if(!inherits(form, "formula")) stop("No formula given") fit.lm<-lm(formula=form,data=dat) return(boot.stepAIC(object=fit.lm,data=dat)) } fun.boot.lm.stepAIC(dat=dat.test,form=form.1) # results in an error ``` So where is the mistake? I suppose it must have something to do with the local and global environment, doesn't it?