When working with counts, having many zeros does not necessarily indicate zero inflation. I demonstrate this by simulating data from the negative binomial and generalized Poisson distributions. I then show one way to check if the data has excess zeros compared to the number of zeros expected based on the model.
Analyzing positive data with 0 values can be challenging, since a direct log transformation isn't possible. I discuss some of the things to consider when deciding on an analysis strategy for such data and then explore the effect of the value of the constant, c, when using log(y + c) as the response variable.
Checking for model fit from generalized linear mixed models (GLMM) can be challenging. The DHARMa package helps with this by giving simulated residuals but doesn't work with all model types. I show how to use tools in DHARMa to extend it for use with unsupported models fit with glmmTMB() and zeroinfl().
I currently work as a consulting statistician, advising natural and social science researchers on statistics, statistical programming, and study design. I create and teach R workshops for applied science graduate students who are just getting started in R, where my goal is to make their transition to a programming language as smooth as possible. See my workshop materials at my website.