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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# amsterdown <img src="man/figures/logo.png" align="right" width="120" />
<!-- badges: start -->
[](https://github.com/lcreteig/amsterdown/actions/workflows/R-CMD-check.yaml)
[](https://github.com/lcreteig/amsterdown/actions/workflows/pkgdown.yaml)
[](https://www.tidyverse.org/lifecycle/#maturing)
[](https://mybinder.org/v2/gh/lcreteig/amsterdown/master?urlpath=rstudio)
[](https://doi.org/10.5281/zenodo.3733132)
<!-- badges: end -->
`amsterdown` is an RMarkdown PhD thesis template for the University of Amsterdam. It's based on [my PhD thesis](https://github.com/lcreteig/thesis) that I wrote with the [bookdown package](https://bookdown.org/yihui/bookdown/).
(R)Markdown enables you to write a reproducible PhD thesis using the lightweight and plain-text [Markdown](https://daringfireball.net/projects/markdown/) formatting. It forms a great [notebook style](https://en.wikipedia.org/wiki/Notebook_interface) workflow to integrate all your text, code, figures, and other output that together make up your PhD thesis work. Finally, `bookdown` allows you to easily create an html-version of your thesis that you can host online, and to harness the power of LaTeX to make a beautifully formatted PDF for printing your thesis.
This template is an easy way to get started, by:
* Providing a common and complete structure for the thesis, including appendices, acknowledgments, etc.
* Removing the need to write any LaTeX commands yourself (or at least, prolonging it as long as possible).
* Making sure you adhere to the University of Amsterdam thesis requirements.
## Installation
`amsterdown` is not (yet) available on CRAN, so install it from [GitHub](https://github.com/) with:
```{r, eval = FALSE}
if(!require(devtools)) install.packages("devtools") # devtools package allows installation of packages from github
devtools::install_github("lcreteig/amsterdown") # install amsterdown from github
```
If you just want a peek at the template without installing it as an R package, check out the folder with all the files [here on Github](https://github.com/lcreteig/amsterdown/tree/master/inst/rmarkdown/templates/thesis/skeleton).
Alternatively, to try out using the template without having to install anything locally, click this button to launch an RStudio session with everything you need pre-installed: [](https://mybinder.org/v2/gh/lcreteig/amsterdown/master?urlpath=rstudio) Then simply follow the [Usage] instructions below.
## Usage
If you've installed the package and are using [RStudio](https://rstudio.com/), simply navigate to "File" > "New File" > "R Markdown..." > "From Template" > "UvA thesis {amsterdown}". Use `index` for the new directory name (feel free to change this after), so that the main file will be called `index.Rmd`, then hit OK.
Then, create a new RStudio project by going to "File" > "New Project..." > "Existing Directory", then "Browse..." to the directory you just created (`index`, or whatever you named it to), and finally hit "Create Project".
Click "Build Book" from the Build pane to render the thesis to an output format of your choosing.
Or, (e.g., if you're not using the RStudio IDE), run the following lines of R code to render the template:
``` r
rmarkdown::draft('index.Rmd', # create new draft based off template
template = 'thesis', package = 'amsterdown',
create_dir = TRUE, edit = FALSE)
setwd("index") # navigate to new directory
# render the thesis template to all output formats
bookdown::render_book("index.Rmd", output_format = "all")
# or
#bookdown::render_book("index.Rmd", output_format = 'bookdown::gitbook') # to render to html
#bookdown::render_book("index.Rmd", output_format = 'bookdown::pdf_book') # to render to PDF
```
See the [package documentation](https://lcreteig.github.io/amsterdown/articles/amsterdown.html) for more detailed instructions and further information.
## Example output
The template supports `html` and `pdf` outputs. To inspect the outputs as produced by the latest version of the template, see here: [html](https://lcreteig.github.io/amsterdown/sample_output/index.html), [pdf (A4)](https://lcreteig.github.io/amsterdown/sample_output/thesis_A4.pdf), [pdf (book)](https://lcreteig.github.io/amsterdown/sample_output/thesis_B5.pdf)
## Requirements
If you're using [RStudio](https://rstudio.com/), all you should have to do is install the `amsterdown` package (the `bookdown` package will be installed along with it). You'll also need a [LaTeX](https://www.latex-project.org/) distribution to be able to create the `pdf` outputs. If you don't have one yet, I'd recommend [TinyTeX](https://yihui.name/tinytex/).
If you don't have RStudio installed, you'll also need to install [pandoc](https://pandoc.org/) if you don't have it already (in addition to a LaTex distribution).
## Attribution
This project was inspired by other RMarkdown PhD thesis templates that use [`bookdown`](https://bookdown.org/yihui/bookdown/), notably:
* Chester Ismay's [thesisdown](https://github.com/ismayc/thesisdown) for Reed College
* Ben Marwick's [huskydown](https://github.com/benmarwick/huskydown) for the University of Washington
* Ulrik Lyng's [oxforddown](https://github.com/ulyngs/oxforddown) for Oxford University
## PhD theses that have used this template
| **User** :nerd_face: | **University** :school: | **Link** :link: |
|---------------------------------------------------|-----------------------------------|----------------------------------------------------------------------------------------|
| [noorseijdel](https://github.com/noorseijdel) | University of Amsterdam | [noorseijdel.github.io/thesis](https://noorseijdel.github.io/thesis) |
| [LDSamson](https://github.com/LDSamson) | University of Groningen | [ldsamson.github.io/Thesis/](https://ldsamson.github.io/Thesis/) |
| [lukassnoek](https://github.com/lukassnoek) | University of Amsterdam | [lukassnoek/thesis](https://github.com/lukassnoek/thesis) |
| [BenGoudsmit](https://github.com/BenGoudsmit) | University of Leiden | [BenGoudsmit/Thesis](https://github.com/BenGoudsmit/Thesis) |
| [Leo4Luffy](https://github.com/Leo4Luffy) | Universitat Autònoma de Barcelona | [Leo4Luffy/Repo_TFM](https://leo4luffy.github.io/Repo_TFM/Escrito/TFM.pdf) |
| [lynnsoerensen](https://github.com/lynnsoerensen) | University of Amsterdam | [UvA-DARE](https://dare.uva.nl/search?identifier=4f39681f-920d-4334-9bcf-f5d2b6ec1322) |