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`. To make sure only
  files from this directory are used, get the devel versio of bookdown  and 
  add a corresponding confirugartion 
  (for details, see https://github.com/rstudio/bookdown/issues/242).
  
* 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, e.g. Word and html.
* 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 such as plots, tables, figures
  directly in your writing has never been easier than with bookdown. You can turn
  a data frame into a latex table using the power of R packages such as
  `kableExtra`. 
* 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.]
* Because it's native R, you can place R variables in the floating text. Check
  out the Rmd source of this document to see that we used R to compute the square
  root of three (`r sqrt(3)`), print todays date with `Sys.Date()` right into the
  text: `r Sys.Date()`

**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