Today I managed to get the alpha version of glmmADMB 0.6.2 loaded and running. I am running negative binomial model with nested random effects. <div><br></div><div>I decided to start with a reduced model of my data, so I began with the following syntax and R would just hang and I get the pinwheel of death (Mac OS 10.6.8):</div>
<div><br></div><div>> m1=glmmadmb(Y~X+(1|A/B),data=ecpad5,family="nbinom")</div><div><br></div><div>I can't find the exact mailing list message, but somewhere I believe I read that +(1|A)+(1|B) is the same as the above syntax in lme4 as long as factor B is coded with unique individual labels. </div>
<div><br></div><div>I then tried the following model syntax and it worked just fine:</div><div><br></div><div>> m2=glmmadmb(Y~X+(1|A)+(1|B),data=ecpad,family="nbinom")</div><div>> summary(m2)</div><div><br>
</div><div><div>Coefficients:</div><div> Estimate Std. Error z value Pr(>|z|) </div><div>(Intercept) -0.841 0.234 -3.59 0.00034 ***</div><div>treaty -0.702 0.311 -2.26 0.02413 * </div>
<div>---</div><div>Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 </div><div><br></div><div>Number of observations: total=160, =32, =160 </div><div>Random effect variance(s):</div><div>$tree</div><div> (Intercept)</div>
<div>(Intercept) 2.9858e-09</div><div><br></div><div>$trbr</div><div> (Intercept)</div><div>(Intercept) 1.2847</div><div><br></div><div>Negative binomial dispersion parameter: 403.43 (std. err.: 2.1584)</div>
<div><br></div><div>Log-likelihood: -162.773</div></div><div><br></div><div><br></div><div>My data structure:</div><div><br></div><div>A =(randomly selected plot) B =(randomly selected sub-plot within A) X =(disturbed=Y or N) Y =(total count of individuals present)</div>
<div><br></div><div>T01 B001 N 2</div><div>T01 B002 N 0</div>
<div>T01 B003 N 0</div><div>T01 B004 N 1</div>
<div>T01 B005 N 0</div><div>T02 B006 N 0</div>
<div>T02 B007 N 4</div><div>T02 B008 N 1</div>
<div>T02 B009 N 0</div><div>T02 B010 N 0</div>
<div>. . . .</div><div>. . . .</div>
<div>. . . .</div><div>T32 B156 Y 3</div>
<div>T32 B157 Y 0</div><div>T32 B158 Y 0</div>
<div>T32 B159 Y 1</div><div>T32 B160 Y 0</div>
<div><br></div><div>Is glmmADMB treating B as being nested in A like it does in lme4? To the best of your knowledge do the results look like they should?</div><div><br></div><div>I'll have more questions later but gotta get this sorted first.</div>
<div><br></div><div>Thanks for the help,</div><div><br></div><div>Shawn</div><div><br></div><div><br></div><div><br></div><div><br></div><div> </div>