[R] Specify order of groups negative binomial (glm.nb)

[Katharine Miller - NOAA Federal]

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.

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