## ----set-options, echo = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  dev = "png",
  fig.width = 7,
  fig.height = 3.5,
  message = FALSE, warning = FALSE
)
options(width = 800)
arrow_color <- "#FF00cc"

pkgs <- c("ggplot2", "see", "marginaleffects", "glmmTMB")

if (!all(vapply(pkgs, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1L)))) {
  knitr::opts_chunk$set(eval = FALSE)
}

## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
library(modelbased)
library(glmmTMB)

data(Salamanders)
m <- glmmTMB(count ~ mined + (1 | site),
  ziformula = ~mined,
  family = poisson(),
  data = Salamanders
)

## ----message=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# predicting the conditional mean
estimate_means(m, "mined", predict = "conditional")

estimate_contrasts(m, "mined", predict = "conditional")

## ----message=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# predicting the expected value of the response
estimate_means(m, "mined")

estimate_contrasts(m, "mined")

## ----message=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# predicting the zero-inflation probabilities
estimate_means(m, "mined", predict = "zprob")

estimate_contrasts(m, "mined", predict = "zprob")