Question

I’m probably doing something very silly but I can’t extract the parameter values from a series of models my function is looping through.

Data:

library(difR)
data(verbal)
TotScore=rowSums(verbal[,c(1:24)])
mydata=verbal[,c(1:24)]

I can then get the model BIC in a loop

library(BMA)
a<-rep(NA,length(1:24))
for (i in (1:24)){
  a[i]<-bic.glm(mydata[,i]~ TotScore, glm.family=binomial,data=mydata)$bic
}
a

But if I try to put this in a function I can’t extract “a”

myB<-function(mydata){
  a<-rep(NA,length(ncol(mydata)))
  for (i in (1:ncol(mydata))){
    a[i]<-bic.glm(mydata[,i]~ TotScore, glm.family=binomial,data=mydata)$bic
  }
  return(a)
}

myB(mydata)

Or rather the bic is only for the very last model

I can build the same function for the mean and manage to extract the results so maybe it’s something to do with the structure of the bic output?

Many thanks

M

Answer 1

It seems as though bic.glm only reads objects from the global environment – the problem with your function was that it did recognize the i created locally within the function. Try the following:

library(difR)
data(verbal)
TotScore=rowSums(verbal[,c(1:24)])
mydata=verbal[,c(1:24)]

myB<-function(mydata){
    a<-rep(NA,length(ncol(mydata)))
    for (i in (1:ncol(mydata))){
        # force this.col to be in the global environment
        this.col <<- mydata[,i]
        # Alternatively:
        # assign("this.col", mydata[,i], envir=.GlobalEnv)
        a[i]<-bic.glm(this.col ~ TotScore, glm.family=binomial,data=mydata)$bic
    }
    return(a)
}

myB(mydata)

Your function was still reading the global i created by the first loop, which was at 24.

It seems very strange that it should do this; after a quick google search I found references to the problem here and here (it wasn’t a very thorough search and I’m sure there are better examples). I couldn’t find anything in the documentation for bic.glm, which is a bit surprising.

From the first answer to the second link I provided, it seems like this would happen if you use a formula but do not specify a data parameter.