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, purl=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 <- "1.1.0"
date <- "July 2, 2020"

# Latest release information:
latest_release_version <- "1.1.0"
latest_release_date <- "July 2, 2020"

# knitr pkg is needed throughout book
if (!"knitr" %in% installed.packages()) {
  install.packages("knitr", repos = "http://cran.rstudio.com")
}
library(knitr)

# Set output options
if (is_html_output()) {
  options(width = 80)
}
if (is_latex_output()) {
  options(width = 75)
}
options(digits = 7, bookdown.clean_book = TRUE, knitr.kable.NA = "NA")
opts_chunk$set(
  tidy = FALSE,
  out.width = "\\textwidth",
  fig.align = "center",
  comment = NA
)

# New dplyr warning message when running group_by() %>% summarize() that is not
# addressed in v1 (print edition). 
# See https://github.com/moderndive/ModernDive_book/issues/353
# v2 TODO: Remove this option and fix group_by() section in Ch3
options(dplyr.summarise.inform = FALSE)

# Install CRAN packages needed
needed_CRAN_pkgs <- c(
  # Packages used by book reader (except skimr, see below):
  "dygraphs", "fivethirtyeight", "gapminder", "ggplot2movies", "infer", "ISLR", 
  "janitor", "knitr", "moderndive", "nycflights13", "scales", "tidyverse", 
  "broom",

  # Packages only used internally for bookdown book building
  "devtools", "ggrepel", "here", "kableExtra", "mvtnorm", "patchwork", 
  "remotes", "rmarkdown", "sessioninfo", "viridis", "webshot"
)
new_pkgs <- needed_CRAN_pkgs[!(needed_CRAN_pkgs %in% installed.packages())]
if (length(new_pkgs)) {
  install.packages(new_pkgs, repos = "http://cran.rstudio.com")
}

# Install non-2.0 version of skimr so that histograms can be removed easily
# v2 TODO: Fix https://github.com/moderndive/ModernDive_book/issues/271
if (!"skimr" %in% installed.packages()) {
  remotes::install_version("skimr", version = "1.0.6", 
                           repos = "http://cran.rstudio.com")
}
```

```{r}
# Used in 95-appendixE.Rmd
needed_pkgs <- unique(c(
  needed_CRAN_pkgs, "skimr", "bookdown"
))

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

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

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

# Create empty docs folder which will ultimately contain output
if (!dir.exists("docs")) {
  dir.create("docs")
}

# Make sure all images copy to docs folder
if (!dir.exists(here::here("docs", "images"))) {
  dir.create(here::here("docs", "images"))
}
file.copy(from = "images", to = "docs", recursive = TRUE)

# These steps are only needed for generating the moderndive.com page
# with relevant links. Not needed for PDF generation.
if (is_html_output()) {
  # Add all purl()'ed chapter R scripts here
  if (dir.exists(here::here("docs", "scripts"))) {
    unlink(here::here("docs", "scripts"), recursive = TRUE)
  }
  if (!dir.exists(here::here("docs", "scripts"))) {
    dir.create(here::here("docs", "scripts"))
  }
}
```


```{r results="asis", echo=FALSE, purl=FALSE}
if (is_html_output()) {
  cat("# Welcome to ModernDive {-}")
}
```


<!-- purl() all the chapter Rmd's in a new session -->
```{bash, include=FALSE, purl=FALSE}
Rscript -e "source('purl.R', local = TRUE)"
```


```{r set-options2, include=FALSE, purl=FALSE}
if (is_html_output()) {
  file.remove("purl.Rout")

  # Copy all needed csv and txt files to docs/
  if (!dir.exists(here::here("docs", "data"))) {
    dir.create(here::here("docs", "data"))
  }
  data_files <- c(
    "dem_score.csv", "dem_score.xlsx", "le_mess.csv", "ideology.csv",
    # For Appendix B
    "ageAtMar.csv", "offshore.csv", "cleSac.txt", "zinc_tidy.csv",
    # For Appendix C
    "movies.csv",
    # For moderndive package paper
    # https://www.kaggle.com/c/house-prices-advanced-regression-techniques
    "train.csv", "test.csv"
  )
  from_vec <- here::here("data", data_files)
  to_vec <- here::here("docs", "data", data_files)
  purrr::walk2(from_vec, to_vec, file.copy, overwrite = TRUE)
  
  # To be updated to include the actual link to labs website
  # when Albert has those ready
  file.copy("labs.html", here::here("docs", "labs.html"), overwrite = TRUE)
  file.copy("regression-plane.html",
    here::here("docs", "regression-plane.html"),
    overwrite = TRUE
  )

  # Copy previous_versions/ to docs/previous_versions/
  if (!dir.exists(here::here("docs", "previous_versions"))) {
    dir.create(here::here("docs", "previous_versions"))
  }
  file.copy(from = "previous_versions", to = "docs", recursive = TRUE)

  # For some reason widelogo in header needs to be done separately.
  # Loaded in _includes/logo.html
  file.copy(here::here("images", "logos", "wide_format.png"),
    here::here("docs", "wide_format.png"),
    overwrite = TRUE
  )
}


# Set ggplot2 theme to be light if outputting to PDF
library(ggplot2)
if (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 (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 (is_latex_output()) {
  options(kableExtra.auto_format = FALSE, knitr.table.format = "latex")
}
```

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


<!--
```{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=!is_latex_output(), purl=FALSE}
**Please note that you are currently looking at a preview of a future version of *ModernDive*, which is currently being edited. For the current version of *ModernDive*, please visit [ModernDive.com](https://moderndive.com/).**
```
-->


```{r, echo=FALSE, include=!is_latex_output(), purl=FALSE}
dev_version <- FALSE
```

<!-- include=FALSE for PDF sending to CRC -->
```{block, include=is_html_output(), purl=FALSE}
This is the [website](https://moderndive.com/) for *Statistical Inference via Data Science:  A ModernDive into R and the Tidyverse*! Visit the [GitHub repository for this site](https://github.com/moderndive/ModernDive_book) and find the book on [Amazon](https://www.amazon.com/Statistical-Inference-via-Data-Science/dp/0367409828/). You can also purchase it at [CRC Press](https://www.routledge.com/Statistical-Inference-via-Data-Science-A-ModernDive-into-R-and-the-Tidyverse/Ismay-Kim/p/book/9780367409821) using promo code **ADC22** for a discounted price.
```

</br>
```{r results="asis", echo=FALSE, purl=FALSE}
if (is_html_output()) {
  include_image(
    path = "images/logos/book_cover.png",
    html_opts = "width=350px"
  )
}
```
</br>

<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a><br />This work by [Chester Ismay](https://chester.rbind.io/) and [Albert Y. Kim](https://rudeboybert.rbind.io/) is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.


<!-- index.Rmd has to have some content in it or it won't create an index.html 
file. Make sure to keep this in so that index.html is included. -->

# Foreword {-}