[ADMB Users] glmmadbm error in REmat$codes. UPDATE. success.

[Sheryn Olson]

Using R ver 2.15.2, package glmmADMB_0.7.3 in Win7,  I've been attempting
to run a negative binomial model to determine the effects of season and
forest stand types on snowshoe hare pellet densities.   Year is a random
(nuisance) variable.  Each stand type (treatment) has unequal sample sizes
that vary by year.   The count data are constrained at zero, zero inflated,
and range from 0 - 990 (residuals show overdispersion).

Data Structure:

> str(ps)
'data.frame':   387 obs. of  7 variables:
 $ year     : Factor w/ 5 levels "2008","2009",..: 1 1 1 1 1 1 1 1 1 1
...                     ### random nuisance var.
 $ season : Factor w/ 2 levels "Smr","Wtr": 1 1 1 1 1 1 1 1 1 1
...                          ### fixed var. of interest
 $ stand    : Factor w/ 39 levels "AF1","AF2","AF3",..: 32 33 25 27 26 34
23 31 24 28 ...
 $ stndtyp: Factor w/ 3 levels "MT","RG","SEL": 1 1 1 1 1 1 1 1 1 1
...                   ### fixed var of interest
 $ pellets:  int  1 1 2 2 4 5 7 9 12 13 ...
 $ days   : num  114 114 127 127 127 127 122 112 115 112 ...
 $ ln.days: num  4.74 4.74 4.84 4.84 4.84
...                                                        ### offset var.

Model:
>  nb1 <- glmmadmb(pellets ~ season * stndtyp + offset(ln.days) + (1|year),
na.omit, data=ps,family="nbinom", link="logit")

    Warning in glmmadmb(pellets ~ season * stndtyp + offset(ln.days) + (1
|  :
      NAs removed in constructing fixed-effect model frame: you should
probably remove them manually, e.g. with na.omit()
    Warning in II[, ii] + REmat$codes[[i]] :
      longer object length is not a multiple of shorter object length
    Error in II[, ii] = II[, ii] + REmat$codes[[i]] :
      number of items to replace is not a multiple of replacement length

Are there syntax problems? - with the na.omit and random specification.
Model problems? - with unequal sample sizes, or wrong specification of the
link.   Do the algorithms require equal sample sizes?
I'm also confused about how to know what value of theta to specify, and
when it is appropriate to specify?

Thanks all.
############ UPDATE  ###########
Mollie informed me that the logit was inappropriate for the negbinom family
(oops).   I could not find the correct syntax for using na.omit, so ...
                         The model worked when I removed the NAs from the
dataframe!

> nb1 <- glmmadmb(pellets ~ season * stndtyp + offset(ln.days) + (1|year),
data=ps2,family="nbinom")
> summary(nb1)

Call:
glmmadmb(formula = pellets ~ season * stndtyp + offset(ln.days) +
    (1 | year), data = ps2, family = "nbinom")

Coefficients:
                                 Estimate Std. Error z value Pr(>|z|)
(Intercept)                      -3.005      0.159  -18.94  < 2e-16 ***
season[T.Wtr]                  0.552      0.184    3.00   0.0027 **
stndtyp[T.RG]                   2.342      0.161   14.53  < 2e-16 ***
stndtyp[T.SEL]                  1.096      0.179    6.13  8.6e-10 ***
season[T.Wtr]:stndtyp[T.RG]     0.218      0.215    1.02   0.3090
season[T.Wtr]:stndtyp[T.SEL]   -0.247      0.240   -1.03   0.3025
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Number of observations: total=302, year=5
Random effect variance(s):
Group=year
               Variance StdDev
(Intercept)  0.02859 0.1691
Negative binomial dispersion parameter: 2.197 (std. err.: 0.18795)

Log-likelihood: -1452.6

Sheryn
Graduate Research Assistant, The University of Maine
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