## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center",
  message = FALSE,
  fig.height = 4,
  fig.width = 6
)

## -----------------------------------------------------------------------------
library(dplyr)
library(ggplot2)
library(ggResidpanel)

## -----------------------------------------------------------------------------
str(penguins)

## -----------------------------------------------------------------------------
table(penguins$bird)

## ----echo = FALSE-------------------------------------------------------------
penguins |>
  mutate(bird = forcats::fct_recode(
    bird, 
    "Penguin 1" = "1", "Penguin 2" = "2",
    "Penguin 3" = "3", "Penguin 4" = "4", 
    "Penguin 5" = "5", "Penguin 6" = "6", 
    "Penguin 7" = "7", "Penguin 8" = "8", 
    "Penguin 9" = "9")
  ) |>
ggplot(aes(x = depth, y = heartrate, color = bird)) + 
  geom_point() + 
  facet_wrap( ~ bird) + 
  theme_bw() + 
  scale_color_manual(
    values = wesanderson::wes_palette("Zissou1", 9, type = "continuous")[1:9]
  ) +
  labs(
    x = "Depth (m)", 
    y = "Heart Rate (beats per minute)", 
    color = "Penguin"
  ) + 
  theme(legend.position = "none")

## ----echo = FALSE-------------------------------------------------------------
penguins |>
    mutate(bird = forcats::fct_recode(
    bird, 
    "Penguin 1" = "1", "Penguin 2" = "2",
    "Penguin 3" = "3", "Penguin 4" = "4", 
    "Penguin 5" = "5", "Penguin 6" = "6", 
    "Penguin 7" = "7", "Penguin 8" = "8", 
    "Penguin 9" = "9")
  ) |>
  ggplot(aes(x = duration, y = heartrate, color = bird)) + 
  geom_point() + 
  facet_wrap( ~ bird) + 
  theme_bw() + 
  scale_color_manual(
    values = wesanderson::wes_palette("Zissou1", 9, type = "continuous")[1:9]
  ) +
  labs(
    x = "Duration (min)",
    y = "Heart Rate (beats per minute)", 
    color = "Penguin"
  ) + 
  theme(legend.position = "none")

## -----------------------------------------------------------------------------
library(lme4)
penguin_model <- lmer(heartrate ~ depth + duration + (1|bird), data = penguins)

## -----------------------------------------------------------------------------
summary(penguin_model)

## ----fig.height = 3, fig.width = 5--------------------------------------------
resid_panel(penguin_model)

## ----fig.height = 3, fig.width = 6--------------------------------------------
resid_panel(penguin_model, plots = "all")

## ----fig.height = 2-----------------------------------------------------------
resid_interact(penguin_model, plots = c("resid", "qq"))

## ----fig.height = 3, fig.width = 5--------------------------------------------
resid_xpanel(penguin_model, jitter.width = 0.1)

## ----fig.height = 3, fig.width = 5--------------------------------------------
resid_xpanel(penguin_model, yvar = "response", jitter.width = 0.1)

## -----------------------------------------------------------------------------
penguin_model_log <- 
  lmer(
    log(heartrate) ~ depth + duration + (1|bird), 
    data = penguins
  )
penguin_model_log2 <- 
  lmer(
    log(heartrate) ~ depth + duration + I(duration^2) + (1|bird), 
    data = penguins
  )

## ----fig.width = 5, fig.height = 3--------------------------------------------
resid_compare(
  models = list(penguin_model, penguin_model_log, penguin_model_log2),
  plots = c("resid", "qq"),
  smoother = TRUE,
  qqbands = TRUE,
  title.opt = FALSE
)

## -----------------------------------------------------------------------------
penguin_tree <- rpart::rpart(heartrate ~ depth + duration, data = penguins)

## -----------------------------------------------------------------------------
penguin_tree_pred <- predict(penguin_tree)
penguin_tree_resid <- penguins$heartrate - penguin_tree_pred

## ----fig.height = 2, fig.width = 4.5------------------------------------------
resid_auxpanel(
  residuals = penguin_tree_resid, 
  predicted = penguin_tree_pred, 
  plots = c("resid", "index")
)

## -----------------------------------------------------------------------------
# Fit an example model with one of the penguins
penguin1_model <- 
  lm(
    heartrate ~ depth + duration,
    data = penguins |> dplyr::filter(bird == 1)
  )

# Create panel of simulated and real plots
resid_calibrate(
  model = penguin1_model, 
  plots = c("resid", "qq"), 
  nsim = 3, 
  shuffle = TRUE, 
  identify = TRUE
)

## -----------------------------------------------------------------------------
resid_panel(penguin_model, plots = c("resid", "index")) +
  ggplot2::theme_dark(header_family = "Times")

## -----------------------------------------------------------------------------
list_of_plots <-
  resid_panel(
    penguin_model, 
    plots = c("resid", "index"), 
    return_plot_list = TRUE
  )

## -----------------------------------------------------------------------------
typeof(list_of_plots)
names(list_of_plots)

## -----------------------------------------------------------------------------
list_of_plots$resid + ggplot2::theme_dark(header_family = "Times")
list_of_plots$index + ggplot2::theme_dark(header_family = "Times")

## -----------------------------------------------------------------------------
list_of_custom_plots <-
  purrr::map(
    .x = list_of_plots, 
    .f = function(x) x + ggplot2::theme_dark(header_family = "Times")
  )
list_of_custom_plots

## -----------------------------------------------------------------------------
cowplot::plot_grid(plotlist = list_of_custom_plots)