[R] logistic regression

[Sullivan, Mary M]

Greetings,
 

I am working on a logistic regression model in R and I am struggling with the code, as it is a relatively new program for me.  In searching Google for 'logistic regression diagnostics' I came Elizabeth Brown's Lecture 14 from her Winter 2004 Biostatistics 515 course  (http://courses.washington.edu/b515/l14.pdf) .  I found most of the code to be very helpful, but I am struggling with the lines on to calculate the observed and expected values in the 10 groups created by the cut function.  I get error messages in trying to create the E and O matrices:  R won't accept assignment of "fi1c==j" and it won't calculate the sum.  

 

I am wondering whether someone might be able to offer me some assistance...my search of the archives was not fruitful.

 

Here is the code that I adapted from the lecture notes:

 

fit <- fitted(glm.lyme)

fitc <- cut(fit, br = c(0, quantile(fit, p = seq(.1, .9, .1)),1))  

t<-table(fitc)

fitc <- cut(fit, br = c(0, quantile(fit, p = seq(.1, .9, .1)), 1), labels = F)

t<-table(fitc)

 

#Calculate observed and expected values in ea group

E <- matrix(0, nrow=10, ncol = 2)

O <- matrix(0, nrow=10, ncol=2)

for (j in 1:10) {

      E[j, 2] = sum(fit[fitc==j])

      E[j, 1] = sum((1- fit)[fitc==j])

      O[j, 2] = sum(pcdata$lymdis[fitc==j])

      O[j, 1] = sum((1-pcdata$lymdis)[fitc==j])

            

}

 

Here is the error message:  Error in Summary.factor(..., na.rm = na.rm) : 
        sum not meaningful for factors

 

 

I understand what it means; I just can't figure out how to get around it or how to get the output printed in table form.  Thank you in advance for any assistance.

 

Mary Sullivan