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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hello,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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). <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>mod <- glmmadmb(legal~trap_type+(1|pull/trap_type), data=l.lob, family="nbinom", zeroInflation=T); summary(mod)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Is this correct? This is the output:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>summary(mod)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Call:<o:p></o:p></p><p class=MsoNormal>glmmadmb(formula = legal ~ trap_type + (1 | pull/trap_type), <o:p></o:p></p><p class=MsoNormal> data = l.lob, family = "nbinom", zeroInflation = T)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Coefficients:<o:p></o:p></p><p class=MsoNormal> Estimate Std. Error z value Pr(>|z|) <o:p></o:p></p><p class=MsoNormal>(Intercept) 0.2450 0.2612 0.94 0.348 <o:p></o:p></p><p class=MsoNormal>trap_typewire basket -0.0949 0.1923 -0.49 0.622 <o:p></o:p></p><p class=MsoNormal>trap_typewire w/ wood frame 0.3045 0.1761 1.73 0.084 .<o:p></o:p></p><p class=MsoNormal>trap_typewire w/ wood slats 0.1134 0.1804 0.63 0.530 <o:p></o:p></p><p class=MsoNormal>trap_typewood 0.1037 0.1797 0.58 0.564 <o:p></o:p></p><p class=MsoNormal>---<o:p></o:p></p><p class=MsoNormal>Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Number of observations: total=1004, date=12, pull:trap_type=60 <o:p></o:p></p><p class=MsoNormal>Random effect variance(s):<o:p></o:p></p><p class=MsoNormal>Group=date<o:p></o:p></p><p class=MsoNormal> Variance StdDev<o:p></o:p></p><p class=MsoNormal>(Intercept) 0.5152 0.7178<o:p></o:p></p><p class=MsoNormal>Group=pull:trap_type<o:p></o:p></p><p class=MsoNormal> Variance StdDev<o:p></o:p></p><p class=MsoNormal>(Intercept) 0.04389 0.2095<o:p></o:p></p><p class=MsoNormal>Negative binomial dispersion parameter: 2.8077 (std. err.: 0.84525)<o:p></o:p></p><p class=MsoNormal>Zero-inflation: 0.40333 (std. err.: 0.036329 )<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Log-likelihood: -1316.88<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Any help would greatly appreciated, <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Bryan<o:p></o:p></p><p class=MsoNormal>______________________<o:p></o:p></p><p class=MsoNormal>Bryan Danson<o:p></o:p></p><p class=MsoNormal>Biological Scientist I<o:p></o:p></p><p class=MsoNormal>Fish and Wildlife Research Institute<o:p></o:p></p><p class=MsoNormal>Florida Fish and Wildlife Conservation Commission<o:p></o:p></p><p class=MsoNormal>Marathon, FL <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>"The significant problems we have cannot be solved at the same level of thinking with which we created them."<br>~Albert Einstein</span><o:p></o:p></p><p class=MsoNormal><br><br><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>