## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5,
  fig.align = 'center',
  warning = FALSE,
  message = FALSE
)

## ----libraries----------------------------------------------------------------
library(ggmosaic2)
library(ggplot2)
library(dplyr)

## ----titanic-data-------------------------------------------------------------
data(titanic)
head(titanic)

## ----basic-mosaic-------------------------------------------------------------
print(ggplot(data = titanic,
             aes(x = product(Class, Survived), fill = Survived)) +
  geom_mosaic() +
  labs(title = "Titanic: Class by Survival",
       subtitle = "Basic mosaic plot") +
  theme_mosaic())

## ----independence-model-------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Survived))) +
  geom_mosaic(expected = "independence") +
  scale_fill_residual() +
  labs(title = "Titanic: Class by Survival",
       subtitle = "Independence model with residual shading") +
  theme_mosaic())

## ----shortcuts----------------------------------------------------------------
# Independence model
p1 <- ggplot(data = titanic, aes(x = product(Class, Sex))) +
  geom_mosaic(expected = "independence") +
  scale_fill_residual() +
  labs(title = "Independence Model",
       subtitle = "~ Class + Sex") +
  theme_mosaic()

# Saturated model (no residuals - perfect fit)
p2 <- ggplot(data = titanic, aes(x = product(Class, Sex))) +
  geom_mosaic(expected = "saturated") +
  scale_fill_residual() +
  labs(title = "Saturated Model",
       subtitle = "~ Class * Sex") +
  theme_mosaic()

print(p1)
print(p2)

## ----custom-formula-----------------------------------------------------------
# Model with Class + Sex main effects only (no interaction)
print(ggplot(data = titanic, aes(x = product(Class, Sex, Survived))) +
  geom_mosaic(expected = ~ Class + Sex) +
  scale_fill_residual() +
  labs(title = "Custom Model: Class + Sex",
       subtitle = "Testing for Survival associations given Class and Sex") +
  theme_mosaic())

## ----conditional, eval=FALSE--------------------------------------------------
# # Conditional independence: Health and Marital Status given Sex
# ggplot(data = happy,
#        aes(x = product(health, marital), conds = sex)) +
#   geom_mosaic(expected = "conditional") +
#   scale_fill_residual() +
#   labs(title = "Health × Marital | Sex") +
#   theme_mosaic()

## ----three-way----------------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Sex, Survived))) +
  geom_mosaic(expected = "independence") +
  scale_fill_residual() +
  labs(title = "Titanic: Complete Independence Model",
       subtitle = "Class, Sex, and Survival all independent") +
  theme_mosaic())

## ----observed-counts----------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Sex))) +
  geom_mosaic(aes(fill = Survived)) +
  geom_mosaic_text(display_values = "observed",
                   format_digits = 0,
                   size = 3) +
  labs(title = "Observed Frequencies") +
  theme_mosaic())

## ----residual-labels----------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Sex))) +
  mosaic_settings(expected = "independence") +
  geom_mosaic() +
  scale_fill_residual() +
  geom_mosaic_text(display_values = "residual",
                   format_digits = 2,
                   colour = "black",
                   size = 3) +
  labs(title = "Residuals from Independence",
       subtitle = "Values show Pearson residuals") +
  theme_mosaic())

## ----expected-values----------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Survived))) +
  mosaic_settings(expected = "independence") +
  geom_mosaic() +
  scale_fill_residual() +
  geom_mosaic_text(display_values = "expected",
                   format_digits = 1,
                   colour = "black",
                   size = 3.5) +
  labs(title = "Expected Frequencies Under Independence") +
  theme_mosaic())

## ----custom-scale-------------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Sex))) +
  mosaic_settings(expected = "independence") +
  geom_mosaic() +
  scale_fill_residual(
    low = "firebrick",
    mid = "white",
    high = "steelblue",
    limits = c(-6, 6),  # Set symmetric limits
    name = "Pearson\nResidual"
  ) +
  geom_mosaic_text(display_values = "residual",
                   format_digits = 1,
                   size = 3) +
  labs(title = "Custom Color Scale") +
  theme_mosaic())

## ----ggplot2-scale------------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Survived))) +
  geom_mosaic(expected = "independence") +
  scale_fill_gradient2(
    low = "purple",
    mid = "gray95",
    high = "orange",
    midpoint = 0,
    name = "Residual"
  ) +
  labs(title = "Custom ggplot2 Scale") +
  theme_mosaic())

## ----text-aesthetics----------------------------------------------------------
print(ggplot(data = titanic, aes(x = product(Class, Survived))) +
  mosaic_settings(expected = "independence") +
  geom_mosaic() +
  scale_fill_residual() +
  geom_mosaic_text(display_values = "residual",
                   format_digits = 2,
                   size = 4,           # Text size
                   colour = "white",   # Text color
                   fontface = "bold",  # Font weight
                   family = "serif") + # Font family
  labs(title = "Custom Text Aesthetics") +
  theme_mosaic())

## ----model-comparison, fig.height=8-------------------------------------------
# 1. Independence of all three variables
p1 <- ggplot(data = titanic, aes(x = product(Class, Sex, Survived))) +
  mosaic_settings(expected = "independence") +
  geom_mosaic() +
  scale_fill_residual(limits = c(-10, 10)) +
  geom_mosaic_text(display_values = "residual",
                   format_digits = 1,
                   size = 2.5) +
  labs(title = "Complete Independence",
       subtitle = "~ Class + Sex + Survived") +
  theme_mosaic()

# 2. Survival independent of Class and Sex jointly
p2 <- ggplot(data = titanic, aes(x = product(Class, Sex, Survived))) +
  mosaic_settings(expected = ~ Class + Sex) +
  geom_mosaic() +
  scale_fill_residual(limits = c(-10, 10)) +
  geom_mosaic_text(display_values = "residual",
                   format_digits = 1,
                   size = 2.5) +
  labs(title = "Survival Independent of Class × Sex",
       subtitle = "~ Class + Sex (no Survived interaction)") +
  theme_mosaic()

# 3. Class and Sex independent, both related to Survival
p3 <- ggplot(data = titanic, aes(x = product(Class, Sex, Survived))) +
  mosaic_settings(
    expected = ~ Class + Sex + Survived + Class:Survived + Sex:Survived
  ) +
  geom_mosaic() +
  scale_fill_residual(limits = c(-10, 10)) +
  geom_mosaic_text(display_values = "residual",
                   format_digits = 1,
                   size = 2.5) +
  labs(title = "Class ⊥ Sex | Survival",
       subtitle = "~ Class + Sex + Survived + Class:Survived + Sex:Survived") +
  theme_mosaic()

print(p1)
print(p2)
print(p3)

## ----session-info-------------------------------------------------------------
sessionInfo()