CODEWITHSUNDEEP
rlme4glmm
Siddharth Satishchandran
Siddharth Satishchandran

Reputation: 19

I get an error when I run my model: "Error in family$family : $ operator not defined for this S4 class"

How do I resolve the error: "Error in family$family : $ operator not defined for this S4 class", when running a zipoisson model in this code? I have tried a poisson model and a quasi poisson model? I believe a 0-inflated Poisson model would better simulate the actual structure of the data, which was skewed by a large number of zeros.

# Fit the GLMM model for zero-inflated Poisson with mean duration
GLMM_freq_dur <- glmmTMB(N.x ~ duration * Sex + (1 | focalID) + (1 | videoID), 
                     data = GLMM_data, 
                     family = poisson (link='log'),zi=~1|focalID,
                     control = glmmTMBControl(optimizer = "bobyqa", optCtrl = 
list(maxfun = 1e6)))  # Increase max iterations

# Fit the GLMM model for zero-inflated Poisson with number of action units
GLMM_freq_au <- glmmTMB(N ~ Total_AU * Sex + (1 | focalID) + (1 | videoID), 
                    data = GLMM_data, 
                    family = zipoisson, 
                    control = glmmTMBControl(optimizer = "bobyqa", optCtrl = 
list(maxfun = 1e6)))  # Increase max iterations

Upvotes: 1

Views: 71

Answers (1)

Ben Bolker
Ben Bolker

Reputation: 226007

glmmTMB doesn't have a "zipoisson" family. Instead, you specify a zero-inflated model by specifying the ziformula argument, e.g.

GLMM_freq_au <- glmmTMB(N ~ Total_AU * Sex + (1 | focalID) + (1 | videoID), 
                    data = GLMM_data, 
                    family = poisson, 
                    ziformula = ~ 1)

if you want to specify a single zero-inflation probability that is constant across all observations, or ziformula ~ . if you want to include everything that's in the 'main' (conditional) model formula, or something in between, e.g. ziformula ~ Total_AU * Sex if you wanted to include the fixed effects but not the random effects in the zero-inflation term.

More specifically, I think this particular unhelpful error message occurred because you have the VGAM package (which includes VGAM::zipoisson, which returns an S4 function) loaded. The development version of glmmTMB will give a slightly more informative error message ...

Upvotes: 0

Related Questions