Dear list: I'm (still) working on a model of snag (dead tree) abundance
before, after, & 5 yr after forest treatments using negative binomial
distribution with glmmADMB. The data suggest that variance may differ
sharply before and after treatment (factor variable 'time', values 1/2/3),
so I have tried specifying the random term to model variance within time.
e.g., glmmadmb(snag ~ time + Ecozone + (time|plot)), where Ecozone is a
factor variable which takes values East or West, and 'plot' is a subject
variable. The issue is that log-likelihood does not change whether I use
(1|plot) or (time|plot). Am I missing something obvious, or is there a bug
in the way likelihood is being calculated/reported?

 

Appreciatively, Seth W. Bigelow

 

glmmadmb(formula = snag ~ time + Ecozone + (1 | SettingID), data = l2, 

    family = "nbinom1", zeroInflation = F)

 

 

Coefficients:

            Estimate Std. Error z value Pr(>|z|)   

(Intercept)   -0.764      0.359   -2.13   0.0334 * 

time2         -0.588      0.186   -3.16   0.0016 **

time3         -0.604      0.189   -3.20   0.0014 **

EcozoneW       1.249      0.487    2.57   0.0103 * 

---

Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

 

Number of observations: total=192, SettingID=64 

Random effect variance(s):

Group=SettingID

            Variance StdDev

(Intercept)     2.37   1.54

Negative binomial dispersion parameter: 1.812 (std. err.: 0.33774)

 

Log-likelihood: -255.758

 

 

glmmadmb(formula = snag ~ time + Ecozone + (time | SettingID), 

    data = l2, family = "nbinom1", zeroInflation = F)

 

 

Coefficients:

            Estimate Std. Error z value Pr(>|z|)   

(Intercept)   -0.764      0.359   -2.13   0.0334 * 

time2         -0.588      0.186   -3.16   0.0016 **

time3         -0.604      0.189   -3.20   0.0014 **

EcozoneW       1.249      0.487    2.57   0.0103 * 

---

Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

 

Number of observations: total=192, SettingID=64 

Random effect variance(s):

Group=SettingID

             Variance    StdDev

(Intercept) 2.370e+00 1.5396428

time2       1.765e-07 0.0004201

time3       8.542e-08 0.0002923

Negative binomial dispersion parameter: 1.812 (std. err.: 0.33774)

 

Log-likelihood: -255.758

 

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