[R-sig-ME] Fitting a zero inflated mixed-effects mode to proportion data using glmmTMB

Sonia Bejarano @on|@@bej@r@no @end|ng |rom |e|bn|z-zmt@de
Fri May 3 17:13:46 CEST 2019

Dear R-sig-mixed-models Listers

I am trying to fit a zero inflated mixed-effects model to determine 
whether my response variable (i.e. proportion of organisms with 
parasite) differs between 2 conditions (protected zones vs. open zones), 
and between 2 zones (inner, outer). Aside from these two fixed factors, 
I have 2 random factors (i.e. transect and site). As my response 
variable is zero-inflated (i.e. I have 41% observations are 0)  I tried 

MZINF<- glmmTMB(organisms.with.parasites/total.num.organisms.checked ~ 
condition + zone + +(1 | site)+ (1 | transect), + zi=~., + disp=~zone, + 
family = binomial, + weights=total.num.organisms.checked, + data=zanvic)

Here my questions:

1) if I fitzi = ~.  or evenzi = ~ condition + zone  I get convergence problems and NAs
but I get no NAs or convergence problems when I fitzi = ~ 1, zi = ~ condition, orzi = ~ zone
does this mean that due to insufficient observations per condition or per zone, I cannot test
simultaneously whether the probability of observing a structural 0 is influenced by zone and by condition?

2) If when I fitzi = ~ 1
Zero-inflation model:
             Estimate Std. Error z value Pr(>|z|)
(Intercept)   -21.37   12320.75  -0.002    0.999

Does the p value > 0.05 values in here mean that the probability of observing structural zeroes
is independent of by zone or condition? or is*not *independent of zone or condition?

2) Different from the outputs explained in Brooks et al 2019 (The R 
Journal Vol. 9/2, December 2017) when fitting the above I do not get a 
Dispersion model section in my output, why is this? have I coded 
something wrong in my model?

Many thanks,


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