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A Minimal Book Example: sources.
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‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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_publish.R
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_book
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_bookdown_files
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rsconnect

‎.travis.yml

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language: r
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cache: packages
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pandoc_version: 1.19.2.1
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before_script:
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- chmod +x ./_build.sh
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- chmod +x ./_deploy.sh
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script:
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- ./_build.sh
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- ./_deploy.sh

‎01-intro.Rmd

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# Introduction {#intro}
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You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \@ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \@ref(methods).
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Figures and tables with captions will be placed in `figure` and `table` environments, respectively.
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```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'}
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par(mar = c(4, 4, .1, .1))
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plot(pressure, type = 'b', pch = 19)
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```
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Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table \@ref(tab:nice-tab).
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```{r nice-tab, tidy=FALSE}
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knitr::kable(
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head(iris, 20), caption = 'Here is a nice table!',
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booktabs = TRUE
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)
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```
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You can write citations, too. For example, we are using the **bookdown** package [@R-bookdown] in this sample book, which was built on top of R Markdown and **knitr** [@xie2015].

‎02-literature.Rmd

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# Literature
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Here is a review of existing methods.

‎03-method.Rmd

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# Methods
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We describe our methods in this chapter.

‎04-application.Rmd

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# Applications
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Some _significant_ applications are demonstrated in this chapter.
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## Example one
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## Example two

‎05-summary.Rmd

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# Final Words
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We have finished a nice book.

‎06-references.Rmd

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`r if (knitr:::is_html_output()) '
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# References {-}
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'`

‎DESCRIPTION

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Package: placeholder
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Type: Book
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Title: Does not matter.
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Version: 0.0.1
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Imports: bookdown
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Remotes: rstudio/bookdown

‎Dockerfile

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FROM conoria/alpine-r-bookdown
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WORKDIR /usr/src
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COPY . .
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RUN R -q -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")' && mv _book /public

‎LICENSE

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CC0 1.0 Universal
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Statement of Purpose
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The laws of most jurisdictions throughout the world automatically confer
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Certain owners wish to permanently relinquish those rights to a Work for the
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For more information, please see
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<http://creativecommons.org/publicdomain/zero/1.0/>
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‎README.md

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This is a minimal example of a book based on R Markdown and **bookdown** (https://github.com/rstudio/bookdown). Please see the page "[Get Started](https://bookdown.org/yihui/bookdown/get-started.html)" at https://bookdown.org/yihui/bookdown/ for how to compile this example into HTML. You may generate a copy of the book in `bookdown::pdf_book` format by calling `bookdown::render_book('index.Rmd', 'bookdown::pdf_book')`. More detailed instructions are available here https://bookdown.org/yihui/bookdown/build-the-book.html.
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You can find the preview of this example at https://bookdown.org/yihui/bookdown-demo/.

‎_bookdown.yml

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book_filename: "bookdown-demo"
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language:
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ui:
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chapter_name: "Chapter "
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delete_merged_file: true

‎_build.sh

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#!/bin/sh
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set -ev
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Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"
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Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::pdf_book')"
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Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::epub_book')"
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‎_deploy.sh

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#!/bin/sh
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set -e
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[ -z "${GITHUB_PAT}" ] && exit 0
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[ "${TRAVIS_BRANCH}" != "master" ] && exit 0
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git config --global user.email "[email protected]"
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git config --global user.name "Yihui Xie"
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git clone -b gh-pages https://${GITHUB_PAT}@github.com/${TRAVIS_REPO_SLUG}.git book-output
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cd book-output
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cp -r ../_book/* ./
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git add --all *
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git commit -m"Update the book" || true
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git push -q origin gh-pages

‎_output.yml

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bookdown::gitbook:
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css: style.css
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config:
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toc:
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before: |
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<li><a href="./">A Minimal Book Example</a></li>
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after: |
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<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
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edit: https://github.com/rstudio/bookdown-demo/edit/master/%s
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download: ["pdf", "epub"]
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bookdown::pdf_book:
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includes:
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in_header: preamble.tex
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latex_engine: xelatex
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citation_package: natbib
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keep_tex: yes
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bookdown::epub_book: default

‎book.bib

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@Book{xie2015,
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title = {Dynamic Documents with {R} and knitr},
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author = {Yihui Xie},
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publisher = {Chapman and Hall/CRC},
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address = {Boca Raton, Florida},
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year = {2015},
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edition = {2nd},
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note = {ISBN 978-1498716963},
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url = {http://yihui.name/knitr/},
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}

‎bookdown-demo.Rproj

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: knitr
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Website

‎index.Rmd

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---
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title: "A Minimal Book Example"
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author: "Yihui Xie"
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date: "`r Sys.Date()`"
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site: bookdown::bookdown_site
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output: bookdown::gitbook
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documentclass: book
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bibliography: [book.bib, packages.bib]
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biblio-style: apalike
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link-citations: yes
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github-repo: rstudio/bookdown-demo
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description: "This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook."
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---
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# Prerequisites
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This is a _sample_ book written in **Markdown**. You can use anything that Pandoc's Markdown supports, e.g., a math equation $a^2 + b^2 = c^2$.
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The **bookdown** package can be installed from CRAN or Github:
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```{r eval=FALSE}
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install.packages("bookdown")
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# or the development version
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# devtools::install_github("rstudio/bookdown")
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```
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Remember each Rmd file contains one and only one chapter, and a chapter is defined by the first-level heading `#`.
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To compile this example to PDF, you need XeLaTeX. You are recommended to install TinyTeX (which includes XeLaTeX): <https://yihui.name/tinytex/>.
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```{r include=FALSE}
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# automatically create a bib database for R packages
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knitr::write_bib(c(
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.packages(), 'bookdown', 'knitr', 'rmarkdown'
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), 'packages.bib')
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```

‎now.json

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{
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"type": "static",
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"public": true
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}

‎packages.bib

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@Manual{R-base,
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title = {R: A Language and Environment for Statistical Computing},
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author = {{R Core Team}},
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organization = {R Foundation for Statistical Computing},
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address = {Vienna, Austria},
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year = {2017},
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url = {https://www.R-project.org/},
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}
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@Manual{R-basr,
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title = {basr: Basic, but hopefully useful, functions},
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author = {Mathieu Basille and contributions from Samuel Brown and Marc in the box and Clement Calenge and Michael Hallquist and Jean Lobry and Emiel {van Loon} and Kevin Wright},
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year = {2018},
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note = {R package version 0.12},
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url = {http://ase-research.org/basille/basr},
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}
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@Manual{R-bookdown,
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title = {bookdown: Authoring Books and Technical Documents with R Markdown},
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author = {Yihui Xie},
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year = {2019},
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note = {R package version 0.14},
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url = {https://CRAN.R-project.org/package=bookdown},
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}
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@Manual{R-conflicted,
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title = {conflicted: An Alternative Conflict Resolution Strategy},
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author = {Hadley Wickham},
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year = {2019},
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note = {R package version 1.0.4.9000},
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url = {https://github.com/r-lib/conflicted},
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}
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@Manual{R-cowsay,
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title = {cowsay: Messages, Warnings, Strings with Ascii Animals},
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author = {Scott Chamberlain and Amanda Dobbyn},
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year = {2018},
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note = {R package version 0.7.0},
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url = {https://CRAN.R-project.org/package=cowsay},
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}
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@Manual{R-knitr,
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title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
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author = {Yihui Xie},
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year = {2019},
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note = {R package version 1.25},
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url = {https://CRAN.R-project.org/package=knitr},
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}
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@Manual{R-rmarkdown,
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title = {rmarkdown: Dynamic Documents for R},
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author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
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year = {2019},
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note = {R package version 1.16},
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url = {https://CRAN.R-project.org/package=rmarkdown},
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}

‎preamble.tex

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\usepackage{booktabs}
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\usepackage{amsthm}
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\makeatletter
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\def\thm@space@setup{%
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\thm@preskip=8pt plus 2pt minus 4pt
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\thm@postskip=\thm@preskip
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}
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\makeatother

‎style.css

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p.caption {
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color: #777;
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margin-top: 10px;
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}
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p code {
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white-space: inherit;
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}
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pre {
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word-break: normal;
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word-wrap: normal;
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}
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pre code {
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white-space: inherit;
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}

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