Mary, The 10-group approach results in a low-resolution and fairly arbitrary calibration curve. Also, it is the basis of the original Hosmer-Lemeshow goodness of fit statistic which has been superceded by the Hosmer et al single degree of freedom GOF test that does not require any binning. The Design package handles both. Do ?calibrate.lrm, ?residuals.lrm, ?lrm for details.
Frank Harrell Sullivan, Mary M wrote: > 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 > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
