index.Rmd

--- 
title: '`r ifelse(knitr::is_latex_output(), "Statistical Inference via Data Science:  A ModernDive into R and the tidyverse", "Statistical Inference via Data Science")`'
subtitle: "A ModernDive into R and the tidyverse"
author: '`r ifelse(knitr::is_latex_output(), "Chester Ismay and Albert Y. Kim", "Chester Ismay and Albert Y. Kim <br> Foreword by Kelly S. McConville")`'
date: "`r format(Sys.time(), '%B %d, %Y')`"
site: bookdown::bookdown_site
documentclass: krantz
bibliography: [bib/books.bib, bib/packages.bib, bib/articles.bib]
biblio-style: apalike
fontsize: '12pt, krantz2'
monofont: "Inconsolata" #"Source Code Pro"
monofontoptions: "Scale=0.85"
link-citations: yes
colorlinks: yes
lot: false
lof: false
always_allow_html: yes
github-repo: moderndive/moderndive_book
twitter-handle: ModernDive
graphics: yes
description: "An open-source and fully-reproducible electronic textbook for teaching statistical inference using tidyverse data science tools."
cover-image: "images/logos/book_cover.png"
url: 'https\://moderndive.com/'
apple-touch-icon: "images/logos/favicons/apple-touch-icon.png"
favicon: "images/logos/favicons/favicon.ico"
---


```{r set-options, include=FALSE}
# Current version information: Date here should match the date in the YAML above.
# Remove .9000 tag and set date to release date when releasing

version <- "0.7.0.9000"
date <- format(Sys.time(), '%B %d, %Y')


# Latest release information:
latest_release_version <- "0.6.1"
latest_release_date <- "August 28, 2019"
# Set output options
if(knitr:::is_html_output())
  options(width = 80)
if(knitr:::is_latex_output())
  options(width = 75)
options(digits = 7, bookdown.clean_book = TRUE, knitr.kable.NA = 'NA')
knitr::opts_chunk$set(
  tidy = FALSE, 
  out.width = '\\textwidth', 
  fig.align = "center", 
  comment = NA
) 

# CRAN packages needed
needed_CRAN_pkgs <- c(
  # Data packages:
  "nycflights13", "ggplot2movies", "fivethirtyeight", "gapminder", "ISLR",
  
  # Explicitly used packages:
  "tidyverse", "rmarkdown", "knitr", "janitor", "skimr",
  "infer",
  "moderndive",
  
  # Internally used packages:
  "webshot", "mvtnorm", "remotes", "devtools", "dygraphs", "gridExtra",
  "kableExtra", "scales", "viridis", "ggrepel"
  ) 

new_pkgs <- needed_CRAN_pkgs[!(needed_CRAN_pkgs %in% installed.packages())]
if(length(new_pkgs)) {
  install.packages(new_pkgs, repos = "http://cran.rstudio.com")
}

# GitHub packages needed
if(!"patchwork" %in% installed.packages()){
  remotes::install_github("thomasp85/patchwork")
}

#remotes::install_github("tidymodels/infer")
#remotes::install_github("moderndive/moderndive)

needed_pkgs <- unique(c(needed_CRAN_pkgs, "patchwork", "moderndive", "infer"))

# Check that phantomjs is installed to create screenshots of apps
if(is.null(webshot:::find_phantom()))
  webshot::install_phantomjs()

# Automatically create a bib database for R packages
knitr::write_bib(
  c(.packages(), "bookdown", "knitr", "rmarkdown", "nycflights13",
    "ggplot2", "webshot", "dygraphs", "dplyr",
    "ggplot2movies", "fivethirtyeight", "tibble", "readr", "tidyr",
    "janitor", "infer", "skimr", "kableExtra", "moderndive", "tidyverse",
    "broom"
  ),
  "bib/packages.bib"
)

# Add all simulation results here
if(!dir.exists("rds"))
  dir.create("rds")

# Create empty docs folder
if(!dir.exists("docs")) dir.create("docs")

# Make sure all images copy to docs folder
if(!dir.exists("docs/images")) dir.create("docs/images")
system("cp -r images/* docs/images/")

# These steps are only needed for generating the moderndive.com page
# with relevant links. Not needed for PDF generation.
if(knitr::is_html_output()){
  # Add all knitr::purl()'ed chapter R scripts here
  system("rm -rf docs/scripts/")
  if(!dir.exists("docs/scripts"))
    dir.create("docs/scripts")
  system("R CMD batch purl.R")
  system("rm purl.Rout")
  
  # Copy all needed csv and txt files to docs/
  # Should switch to use purrr here at some point
  if(!dir.exists("docs/data"))
    dir.create("docs/data")
  file.copy("data/dem_score.csv", "docs/data/dem_score.csv", overwrite = TRUE)
  file.copy("data/dem_score.xlsx", "docs/data/dem_score.xlsx", overwrite = TRUE)
  file.copy("data/le_mess.csv", "docs/data/le_mess.csv", overwrite = TRUE)
  file.copy("data/ideology.csv", "docs/data/ideology.csv", overwrite = TRUE)
  # For Appendix B
  file.copy("data/ageAtMar.csv", "docs/data/ageAtMar.csv", overwrite = TRUE)
  file.copy("data/offshore.csv", "docs/data/offshore.csv", overwrite = TRUE)
  file.copy("data/cleSac.txt", "docs/data/cleSac.txt", overwrite = TRUE)
  file.copy("data/zinc_tidy.csv", "docs/data/zinc_tidy.csv", overwrite = TRUE)
  
  # To be updated to include the actual link to labs (likely in blogdown format?)
  # when Albert has those ready
  file.copy("labs.html", "docs/labs.html", overwrite = TRUE)

  # Copy previous_versions/ to docs/previous_versions/
  # Should switch to use purrr here at some point
  if(!dir.exists("docs/previous_versions"))
    dir.create("docs/previous_versions/")
  system("cp -r previous_versions/* docs/previous_versions/")
  
  # For some reason logo needs to be done separately.
  # Loaded in _includes/logo.html
  file.copy("images/logos/wide_format.png", "docs/wide_format.png", 
            overwrite = TRUE)
}

# Set ggplot2 theme to be light if outputing to PDF.
library(ggplot2)
if(knitr::is_latex_output()){
  theme_set(theme_light())
} else {
  theme_set(theme_grey())
}

# For generating the R script files at the end of relevant chapters
generate_r_file_link <- function(file){
  if(knitr::is_latex_output()){
    cat(glue::glue("An R script file of all R code used in this chapter is available at <https://www.moderndive.com/scripts/{file}>."))
  } else {
    cat(glue::glue("An R script file of all R code used in this chapter is available [here](scripts/{file})."))
  }
}

# To get kable tables to print nicely in .tex file
if(knitr::is_latex_output())
  options(kableExtra.auto_format = FALSE, knitr.table.format = "latex")

```

```{r images, include=FALSE}
include_image <- function(path,                           
                          html_opts = "width=45%", 
                          latex_opts = html_opts,
                          alt_text = ""){
  if(knitr:::is_html_output()){
    glue::glue("![{alt_text}]({path}){{ {html_opts} }}")
  } else if(knitr:::is_latex_output()){
    glue::glue("![{alt_text}]({path}){{ {latex_opts} }}")    
  }
}

image_link <- function(path,
                       link,
                       html_opts = "height: 200px;",
                       latex_opts = "width=0.2\\textwidth",
                       alt_text = "",
                       centering = TRUE){
  if(knitr:::is_html_output()){
    if(centering){
      glue::glue('
      <center><a target="_blank" class="page-link" href="{link}"><img src="{path}" style="{html_opts}"/></a></center>')
    } else {
      glue::glue('
      <a target="_blank" class="page-link" href="{link}"><img src="{path}" style="{html_opts}"/></a>')
    }
  }
  else if(knitr:::is_latex_output()){
    if(centering){
      glue::glue('\\begin{{center}}
        \\href{{{link}}}{{\\includegraphics[{latex_opts}]{{{path}}}}}
        \\end{{center}}')
    } else
      glue::glue('\\href{{{link}}}{{\\includegraphics[{latex_opts}]{{{path}}}}}')
  }
}
```


```{r echo=FALSE, results="asis"}
if(knitr::is_html_output())
  cat("# Special Announcement {-}")
```

<!-- include=FALSE for PDF sending to CRC -->

```{block, type='announcement', purl=FALSE, include=knitr::is_html_output()}
**We're excited to announce that we've signed a book deal with CRC Press! We will be publishing our first fully complete online version of ModernDive in Summer 2019, with a corresponding print edition to follow in Fall 2019. Don't worry though, our content will remain freely available on [ModernDive.com](https://moderndive.com/).**
```

<center> 
```{r echo=FALSE, purl=FALSE, results="asis"}
if(knitr::is_html_output()){
  include_image(path = "images/logos/crc_press.jpg", 
                html_opts="height=150px")
}
```
</center>

<!--
```{block, type='announcement', purl=FALSE}
**This is a previous version (v`r version`) of ModernDive and may be out of date. For the current version of ModernDive, please go to [ModernDive.com](https://moderndive.com/).**
```
-->

```{block, type='learncheck', include=!knitr::is_latex_output(), purl=FALSE}
**Please note that you are currently looking at the "development version" of ModernDive, which is a work in progress currently being edited and thus subject to frequent change. For the latest "released version" of ModernDive, which is updated around twice a year, please visit [ModernDive.com](https://moderndive.com/).**
```
```{r, echo=FALSE, include=!knitr::is_latex_output(), purl=FALSE}
dev_version <- TRUE
```


<!-- index.Rmd has to have some content in it or it won't create an index.html file. When we remove the Special Announcement, make sure to keep this in so that index.html is included. -->

# Foreword {-}