---
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**

bookdown in general 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.


**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.

**How this template works**

There ar different directories in this template.

```{bash}
tree -d -L 2
```

* _book: Contains the compilied 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 tis folder.
* pdf: Put PDFs you want to include in your thesis in tis 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.
* 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 delcare 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 safisfy all R package dependencies.
* index.R: 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.
  
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 stackoverflow / 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 behaviour. 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. We want to 
make sure that students working this template have a great experience writing 
their master thesis.

Best,

Nicola Gnecco and Lorenz Walthert