## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## -----------------------------------------------------------------------------
library(drmTMB)

set.seed(13)
n_site <- 18
n_per_site <- 6
site <- factor(rep(seq_len(n_site), each = n_per_site))
site_effect <- rnorm(n_site, sd = 0.45)

fish_site <- data.frame(
  site = site,
  temperature = runif(n_site * n_per_site, -1.5, 1.5),
  habitat = factor(
    sample(c("reef", "kelp"), n_site * n_per_site, replace = TRUE)
  )
)

site_mu <- site_effect[as.integer(fish_site$site)]
fish_site$growth <- rnorm(
  nrow(fish_site),
  mean = 1 + 0.7 * fish_site$temperature +
    0.35 * (fish_site$habitat == "kelp") + site_mu,
  sd = 0.35
)

fit_site <- drmTMB(
  bf(growth ~ temperature + habitat + (1 | site), sigma ~ 1),
  family = gaussian(),
  data = fish_site
)

## -----------------------------------------------------------------------------
profile_targets(fit_site)

## -----------------------------------------------------------------------------
confint(fit_site, parm = "fixed_effects")

## -----------------------------------------------------------------------------
ci_site <- confint(
  fit_site,
  parm = "sd:mu:(1 | site)",
  method = "profile"
)
ci_site

## -----------------------------------------------------------------------------
ci_site[, c("parm", "lower", "upper", "conf.status", "profile.boundary")]