## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE,
  fig.height = 6,
  fig.width = 7,
#  fig.path = "fig/tut05-",
  fig.align = "center",
  dev = "png",
  comment = "##"
)

# save some typing
knitr::set_alias(w = "fig.width",
                 h = "fig.height",
                 cap = "fig.cap")

# preload datasets ???
set.seed(1071)
library(vcd)
library(vcdExtra)
library(ggplot2)
data(Arthritis, package="vcd")
art <- xtabs(~Treatment + Improved, data = Arthritis)
#if(!file.exists("fig")) dir.create("fig")


## ----spine1-------------------------------------------------------------------
(spine(Improved ~ Age, data = Arthritis, breaks = 3))
(spine(Improved ~ Age, data = Arthritis, breaks = "Scott"))

## -----------------------------------------------------------------------------
cdplot(Improved ~ Age, data = Arthritis)

## -----------------------------------------------------------------------------
cdplot(Improved ~ Age, data = Arthritis)
with(Arthritis, rug(jitter(Age), col="white", quiet=TRUE))

## ----donner1------------------------------------------------------------------
data(Donner, package="vcdExtra")
str(Donner)

## ----donner2a, fig=FALSE, eval=FALSE------------------------------------------
# # separate linear fits on age for M/F
# ggplot(Donner, aes(age, survived, color = sex)) +
#   geom_point(position = position_jitter(height = 0.02, width = 0)) +
#   stat_smooth(method = "glm",
#               method.args = list(family = binomial),
#               formula = y ~ x,
#               alpha = 0.2, size=2, aes(fill = sex))

## ----donner2b, fig=FALSE, eval=FALSE------------------------------------------
# # separate quadratics
# ggplot(Donner, aes(age, survived, color = sex)) +
#   geom_point(position = position_jitter(height = 0.02, width = 0)) +
#   stat_smooth(method = "glm",
#               method.args = list(family = binomial),
#               formula = y ~ poly(x,2),
#               alpha = 0.2, size=2, aes(fill = sex))

## -----------------------------------------------------------------------------
# separate linear fits on age for M/F
ggplot(Donner, aes(age, survived, color = sex)) +
  geom_point(position = position_jitter(height = 0.02, width = 0)) +
  stat_smooth(method = "glm", 
              method.args = list(family = binomial), 
              formula = y ~ x,
              alpha = 0.2, size=2, aes(fill = sex))

# separate quadratics
ggplot(Donner, aes(age, survived, color = sex)) +
  geom_point(position = position_jitter(height = 0.02, width = 0)) +
  stat_smooth(method = "glm", 
              method.args = list(family = binomial), 
              formula = y ~ poly(x,2),
              alpha = 0.2, size=2, aes(fill = sex))