[ADMB Users] help with a negative binomial, zero inflated model formula

Danson, Bryan Bryan.Danson at MyFWC.com
Mon Feb 6 14:40:58 PST 2012


I am attempting to run a glmm on data which I have already determined display a negative binomial distribution and are zero inflated.  My question is in the syntax of the formula for the proper analysis.  I have a count of the number of legal lobsters within a trap.  There are five trap designs and were pulled on 12 different occasions.  The trap pulls are independent, and therefore a random effect.  The trap design is my fixed effect.  Of those five trap designs, four are alternatives to a standard trap (control).

I am trying to determine if the legal lobster catch rate differs between the alternative trap designs and the standard wood trap.  I have run the model as follows:

mod <- glmmadmb(legal~trap_type+(1|pull/trap_type), data=l.lob, family="nbinom", zeroInflation=T); summary(mod)

Is this correct? This is the output:


glmmadmb(formula = legal ~ trap_type + (1 | pull/trap_type),
    data = l.lob, family = "nbinom", zeroInflation = T)

                                                                Estimate   Std. Error   z value   Pr(>|z|)
(Intercept)                                          0.2450        0.2612        0.94          0.348
trap_typewire basket                    -0.0949       0.1923       -0.49         0.622
trap_typewire w/ wood frame   0.3045       0.1761        1.73          0.084       .
trap_typewire w/ wood slats     0.1134        0.1804        0.63          0.530
trap_typewood                                 0.1037       0.1797        0.58          0.564
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Number of observations: total=1004, date=12, pull:trap_type=60
Random effect variance(s):
                                                Variance   StdDev
(Intercept)                          0.5152        0.7178
                                                Variance   StdDev
(Intercept)                          0.04389      0.2095
Negative binomial dispersion parameter: 2.8077 (std. err.: 0.84525)
Zero-inflation: 0.40333  (std. err.:  0.036329 )

Log-likelihood: -1316.88

In the output, it appears that there is no difference between the alternative trap types and the standard wood trap (control).  But which p-value do I refer to?  Also, the last alternative trap design (vertical wood) is not on the coefficients list, is this because all of the other trap types are being compared to it?  If so, how do I change the syntax in the formula to test the alternatives against the standard wood trap?

Any help would greatly appreciated,

Thank you,

Bryan Danson
Biological Scientist I
Fish and Wildlife Research Institute
Florida Fish and Wildlife Conservation Commission
Marathon, FL

"The significant problems we have cannot be solved at the same level of thinking with which we created them."
~Albert Einstein

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