index.Rmd

--- 
title: Bayesian Basics
author:  |
  <span class="noem">Michael Clark</span> <br>
  [m-clark.github.io](https://m-clark.github.io/)
# date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output:
  bookdown::gitbook:
    anchor_sections: FALSE
documentclass: book
bibliography: ['packages.bib', 'BayesBasics.bib']
biblio-style: apalike
always_allow_html: true
link-citations: yes
github-repo: 'm-clark/bayesian-basics/'
description: "This document provides an introduction to Bayesian data analysis.  It is conceptual in nature, but uses the probabilistic programming language Stan for demonstration (and its implementation in R via rstan). From elementary examples, guidance is provided for data preparation, efficient modeling, diagnostics, and more."
cover-image: 'img/nineteeneightyR.png'
favicon: 'img/R.ico'
url: 'https\://m-clark.github.io/bayesian-basics/'  # the \: is required or you'll get text in the title/toc area

nocite: |
  @kruschke2014doing, @gelman_arm, @mcgrayne_theory_2012, @gelmanPardoe2006, @carpenter2017stan,
  @gelmanHwangVehtari, @gelmanVehtariWAIC, @mcelreath2020, @vehtari2017practical, @vehtari2015pareto
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(
  echo    = TRUE,
  message = FALSE,
  warning = FALSE,
  error   = FALSE,
  comment = NA,
  R.options = list(width = 220),
  # code
  dev.args = list(bg = 'transparent'),
  dev = 'svg',
  fig.align = 'center',
  # viz
  cache.rebuild = FALSE,
  cache = TRUE
)   

library(tidyverse)

# create a theme
theme_clean <- function (
  font_size = 12,
  font_family = "",
  center_axis_labels = FALSE
) {
  
  if (center_axis_labels) {
    haxis_just_x <- 0.5
    vaxis_just_y <- 0.5
    v_rotation_x <- 0
    v_rotation_y <- 0
  }
  else {
    haxis_just_x <- 0
    vaxis_just_y <- 1
    v_rotation_x <- 0
    v_rotation_y <- 0
  }
  
  ggplot2::theme(
    text = ggplot2::element_text(
      family = font_family,
      face   = "plain",
      color  = "gray30",
      size   = font_size,
      hjust  = 0.5,
      vjust  = 0.5,
      angle  = 0,
      lineheight = 0.9,
      margin = ggplot2::margin(),
      debug  = FALSE
    ),
    axis.title.x = ggplot2::element_text(
      hjust = haxis_just_x,
      angle = v_rotation_x,
      size  = 0.8 * font_size
    ),
    axis.title.y = ggplot2::element_text(
      vjust = vaxis_just_y,
      hjust = 0,
      angle = v_rotation_y,
      size  = 0.8 * font_size
    ),
    axis.ticks        = ggplot2::element_line(color = "gray30"),
    title             = ggplot2::element_text(color = "gray30", size = font_size * 1.25),
    plot.subtitle     = ggplot2::element_text(color = "gray30", size = font_size * .75, hjust = 0),
    plot.caption      = ggplot2::element_text(color = "gray30", size = font_size * .5, hjust = 0),
    legend.position   = 'bottom', 
    legend.key        = ggplot2::element_rect(fill = "transparent", color = NA),
    legend.background = ggplot2::element_rect(fill = "transparent", color = NA),
    legend.title      = ggplot2::element_blank(), 
    panel.background  = ggplot2::element_blank(),
    panel.grid        = ggplot2::element_blank(),
    strip.background  = ggplot2::element_blank(),
    plot.background   = ggplot2::element_rect(fill = "transparent", color = NA),
  )
}

# set the theme as default
theme_set(theme_clean())

# set other point/line default colors; in most cases, we can use the color from
# default discrete scale for more consistency across plots.
# paletteer::palettes_d$colorblindr$OkabeIto
update_geom_defaults('vline',   list(color = 'gray25',  alpha = .25))  # vlines and hlines are typically not attention grabbers so set alpha
update_geom_defaults('hline',   list(color = 'gray25',  alpha = .25))  # usually a zero marker
update_geom_defaults('point',   list(color = '#E69F00', alpha = .5))   # alpha as usually there are many points
update_geom_defaults('smooth',  list(color = '#56B4E9', alpha = .15))
update_geom_defaults('line',    list(color = '#56B4E9', alpha = .5))
update_geom_defaults('bar',     list(color = '#E69F00', fill = '#E69F00'))  
update_geom_defaults('col',     list(color = '#E69F00', fill = '#E69F00'))
update_geom_defaults('dotplot', list(color = '#E69F00', fill = '#E69F00'))

# use colorblind safe colors for categories; if you supply a continuous value to
# color you'll get an error, but you just have to use `myplot +
# scale_color_continous()` or whatever to override this; likewise you can always
# override this scale for categorical schemes if desired also. Note that this
# will apply for both color and fill, which is usually what we want.

ggplot <- function(...) ggplot2::ggplot(...) + 
  # okabe ito colorblind safe scheme
  scale_color_manual(
    values = c(
      '#E69F00',
      '#56B4E9',
      '#009E73',
      '#F0E442',
      '#0072B2',
      '#D55E00',
      '#CC79A7',
      '#999999'
    ),
    drop = FALSE,
    aesthetics = c('color', 'fill')
  )


# automatically create a bib database for R packages
knitr::write_bib(c(.packages(), 'bookdown', 'knitr', 'rmarkdown'), 'packages.bib')
```

```{r load_packages, echo=FALSE, cache=FALSE}
library(tidyverse)
library(lazerhawk)
library(pander)
library(visibly)
library(kableExtra)
```


##### {-}

```{r rimg, fig.align='center',  out.width=200, echo=FALSE, cache=FALSE}
knitr::include_graphics('img/198R.png', dpi = NA)
```

```{r ccimg, fig.align='center', out.width=0, fig.show='hide', echo=FALSE}
knitr::include_graphics('img/mc_logo.png', dpi = NA)
knitr::include_graphics('img/mc_sunset_2.png', dpi = NA)
```