Hi, I am using the glm.nb function to evaluate differences in the catch of individual species of fish across three river tributaries. The dependent variable is catch per unit effort (CPUE), and the independent variable is the the tributary (Trib_cat). CPUE is derived from the fish counts divided by the effort, so the response is not a count per se, but I think the negative binomial is appropriate because of the large numbers of zeros in the dependent variable. Trib_cat is a column with 1, 2, or 3 depending on which tributary it is representing.
I have the following code: dataS<-read.table("OtherSpecies.txt", sep="", header=T) dataS <- within(dataS, { Trib_cat <- factor(Trib_cat, levels = 1:3, labels = c("MM", "NM", "SM")) Year<-factor(Year) }) ## separate out the species of interest coregonid<-subset(dataS, Spec_age=="Coregonid") fit.CT<-glm.nb(CPUE ~ Trib_cat, data=coregonid, link = log) summary(fit.CT) The result comes out like this: Call: glm.nb(formula = CPUE ~ Trib_cat, data = coregonid4, init.theta = 0.1723775759, link = log) Deviance Residuals: Min 1Q Median 3Q Max -0.9239 -0.8055 -0.6687 -0.6286 2.9020 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -0.7805 0.2497 -3.125 0.00178 ** Trib_catNM -0.2140 0.3485 -0.614 0.53921 Trib_catSM 0.7393 0.3296 2.243 0.02488 * --- This gives me the difference in CPUE between the NM and SM tributaries compared to the MM tributary (acting here as the reference group). What I need is to compare all of the tributaries with all the others - so I need to run the model twice with a different reference group on the second run. I can do this by changing the numbering of the Trib_cat field in the underlying database (e.g. changing MM from 1 to 3, SM from 2 to 1, etc) and re-running the model, but I, as I have a number of species to do this for, I was wondering if there was an easier way to specify which group to use as the reference group when calling the model. Thanks for any help. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.