[R-sig-ME] glmmADMB definition of levels for random component

[Juan Santos]

First at all I would like to Thank Ben Bolker for his suggestion on how 
to install package glmmADMB in Linux, definitely it worked. Now I would 
ask for some
issued regarding the mixed model specification on my data.

As a reminder, say that I'm working with 2003-2010  fishing data 
(clustered data, Primary sampling unit [PSU]=trip, secondary sampling 
unit [SSU]=haul);
Specifically,  I am trying to model the numbers of fishes of a given 
species thrown back to sea (discarded individuals as the Ultimate 
sampling Unit [USU]) with a set of available
covariates. The main aim of  the model is to assess if  yearly increase 
in discards found in previous EDA,  is also found significant using a 
formal and well fitted model.  I fitted an starting model using (1| 
trip/ haul) as random component  (fishing hauls nested on trips, 
following the hierarchicalsamplingdesign):

mod.admb.1<-glmmadmb(ndiscarded~year + quarter+deep+duration+ 
(1|trip/haul), zeroInflation=TRUE,family="nbinom",data=dmod.1)

(I used zero inflation link  because previous study indicates that a 
model with zeroInflation=FALSE  does not account for the excess of zeros 
in the data).

"Trip" coding is

dat<-ddply(dat,.(year),function(x){
         levels(x$trip) <-1:length(levels(x$trip))
         return(data.frame(x))})

Meaning that trip levels restarts in every sampled year. Similar 
approach is used for hauls within trips (hauls coding restarts for every 
sampled trip).

But I am not sure of this codification, because using this coding means 
that I have same trips ID in every year, but obviously  they are not the 
same trips from one year to another (Perhaps the only similarity is that 
they are sampled in  same temporal interval each year).  As expected, 
random coefficients [ranef ()] from mod.admb.1does not  take into 
consideration that trip number "n" differs between years. I have some 
ideas to solve this problem:

a) To recode trip level with not regard of the sampled  year  (using 
factor(1: N) as levels, being N=total number of trips sampled across the 
years)
b) Fit models for each year separately and compare intercepts
c) use (1|year/trip/haul) as random component,

Can someone indicate a right practice to deal with this model 
specification problem ?


Juan Santos
Research Technician
Instituto Español de Oceanografía
C.O.Vigo

juan. santos at vi.ieo.es