Dear all, I am facing some problem with how to fit a "Baseline category Logit model" with R. Basically I am considering famous "Alligator" data as discussed by Agresti. This data can also be found here:
https://onlinecourses.science.psu.edu/stat504/node/174 (there is also an accompanying R file, however the underlying R code could not load the data properly!!!) Below are the stuffs what I have done so far: My_Data <- structure(list(Number = c(7L, 4L, 1L, 0L, 0L, 0L, 0L, 1L, 5L, 2L, 16L, 3L, 3L, 0L, 2L, 1L, 2L, 2L, 3L, 3L, 2L, 13L, 2L, 7L, 0L, 6L, 0L, 0L, 1L, 0L, 3L, 0L, 9L, 1L, 1L, 0L, 0L, 1L, 2L, 0L, 3L, 8L, 7L, 6L, 1L, 6L, 0L, 3L, 1L, 5L, 2L, 0L, 4L, 1L, 1L, 0L, 1L, 0L, 4L, 0L, 13L, 9L, 10L, 0L, 0L, 0L, 2L, 1L, 2L, 2L, 3L, 8L, 9L, 1L, 1L, 0L, 0L, 0L, 1L, 1L), Food = structure(c(2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L, 2L, 3L, 5L, 1L, 4L), .Label = c("Bird", "Fish", "Invertebrate", "Other", "Reptile"), class = "factor"), Size = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L), .Label = c("Large", "Small"), class = "factor"), Sex = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Female", "Male"), class = "factor"), Lake = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("George", "Hancock", "Oklawaha", "Trafford"), class = "factor")), .Names = c("Number", "Food", "Size", "Sex", "Lake"), row.names = c(NA, 80L), class = "data.frame") library(VGAM) vglm(Food~Size+Sex+Lake, data = My_Data, fam=multinomial, weights = Number) However I am getting following error: Error in if (max(abs(ycounts - round(ycounts))) > smallno) warning("converting 'ycounts' to integer in @loglikelihood") : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon) : 96 elements replaced by 1.819e-12 2: In checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon) : 96 elements replaced by 1.819e-12 3: In checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon) : 96 elements replaced by 1.819e-12 4: In checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon) : 96 elements replaced by 1.819e-12 5: In checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon) : 96 elements replaced by 1.819e-12 6: In checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon) : 96 elements replaced by 1.819e-12 Can somebody points me why I am getting this error? Thanks for you help ______________________________________________ [email protected] 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.
