README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "figures/README-",
  out.width = "100%"
)
```

# A few words from the authors {-}

This repository is a bookdown template, derived from the LaTeX template 
from the semiar for statistics, ETH Zurich. 

**How bookdown works**

In a nutshell, bookdown works as follows:

* use knitr to convert Rmd to markdown.
* use pandoc to convert markdown to latex, pdf, word, html books (with featuers
  like font size, background selection, full text search etc), epub.


The basic workflow is as follows: 

* Change a source file: In our template, the source of the body of the thesis
  is under `./rmd/`. For example, change `02-features.Rmd`
* Re-compile the book using Cmd + Shift + B (for build) on a Mac and Ctrl + 
  Shift + B on Windows / Linux.
* You can customize the build in the RStudio Build Tab, where you can specify
  which output (html, pdf, etc.) you want to generate. This is remembered for 
  the next build you are doing.s

**Getting started**

Fork the upstream repository and clone the fork. Then, you will have one remote
repository: origin, which refers to the fork. Add the upstream repo as an 
upstream remote so you can later rebase on it in case you need. We recommend
using ssh over https.


**Why using bookdown**

The advantages of using bookdown instead of plain LaTeX are, in the eyes of the 
creator of this template:

* Generalization. Not just latex or PDF output, but any output supported by 
  Pandoc.
* The best of two worlds. Use intuitive markdown syntax where possible, use 
  the full power of LaTeX syntax where needed. This includes a real-time latex
  equation previewer in RStudio, bibtex reference, LaTeX cross-, text- and 
  figure reference.
* It's native R. Integrate R code and R output in your writing has never been
  easier than with bookdown. You can also use other languages supported by 
  knitr such as python, stan etc.^[Below, we even used the bash command `tree`
  to show the directory structure of this repo. Since unicode is not suppored
  with pdflatex, we used R code to tell knitr to use the tree command 
  with the option `charset unicode` for pdf output and without it for html 
  output.] 

**How this template works**

There are different directories in this template:

```{bash, include = knitr::is_html_output()}
tree -d -L 2
```

```{bash, include = !knitr::is_html_output()}
tree -d -L 2 --charset unicode
```

* _book: Contains the compiled book, e.g. a PDF or html version.
* _bib: Contains BibTeX reference data bases.
* figure: Contains figures you created from your (R) code in the rmd source.
* images: Put images you want to include in your thesis in this folder.
* pdf: Put PDFs you want to include in your thesis in this folder.
* rmd: The source folder of thesis. When you build a book, the following 
  happens: By default, all rmd files in this folder get merged into one big 
  rmd file, according to their name. We suggest to use one file per chapter.
  Then, the file containing all the rmd sources will get processed by knitr and 
  later by Pandoc.
* scratch: A random directory which is not tracked by git by default. The idea
  is that you can put things that are not ready to commit or that have a 
  temporary character here.
* style: Latex .sty files. Taken from the sfs LaTeX template.
* tex: All tex data, most importantly, the sfs LaTeX template itself. Note that 
  the abstract, preface, epilogue, summary, notation are still in tex, i.e. 
  you need to change these files if you want the PDF output to change. This 
  will **not** affect the html output. You can create chapters that show 
  up in a particular output and not in the other forms as shown in 
  `rmd/99-references.Rmd`.
  
Furthermore, we want to highlight a few files in the root directory of the
project:

* `DESCRIPTION`: You can use it to declare dependent packages of your thesis in 
  the `Imports:` field. If someone want's to rebuild you thesis from scratch,
  the can use `remotes::install_deps()` to satisfy all R package dependencies.
* `index.Rmd`: Contains a YAML header where a few important variables are defined.
  You can also put markdown below the header.
* `README.(R)md`: This document.
* `thesis-template-bookdown.Rproj`: An RStudio project. We recommend using 
  RStudio for authoring your master thesis with bookdown.

**A few recommendations**

* We strongly suggest to use a different folder for the data / code of your 
  thesis and reserve this directory for the thesis document only. You can 
  reaname this directory `analysis-communication` (since this will be the
  means used for communicating the results and process of your thesis) and
  use `analysis-raw` for the code and `data` for all data. Ideally, you 
  place them in the same directory so you can still work with relative paths,
  e.g. `../data`.
* We suggest to use git version control for the thesis and the raw analsyis.
* If your thesis is open source, you can use netlify.com to deploy it, i.e. 
  for every commit you push to a remote repo like GitHub, you can use netlify's
  CLI to build your book on a CI machine like travis. See file `travis.yml` for
  the bookdown book 
  [Advanced R](https://github.com/hadley/adv-r/tree/88dcb07e2b2ae634af6cdeafff2f3ea976077064)
  for an example. That makes tracking the `_book` folder in git redundant.

**Further material**

This is obviously a very short introduction to the template and it is in no way
comprehensive. To learn more about bookdown, we encourage the reader to have 
a look at the [bookdown guide](https://bookdown.org/yihui/bookdown/) as well 
as searching through stack overflow / Google for particular questions. In 
addition, inspect the different files in this repo, in particular the ones 
in the rmd directory to develop a deeper understanding of the template. 

As of early 2018, this template is still in alpha testing phase, so you may 
experience unexpected behavior. Please file an issue on the git repository
where you have obtained the source of this template in case 
you are stuck for some time with a problem or if you found a solution to a 
problem you believe others are likely to encounter in the future. Pull requests
on typos are also welcome. We want to 
make sure that students working this template have a great experience writing 
their master thesis.

Best,

Nicola Gnecco and Lorenz Walthert