Reproducible thesis writing with R Markdown

# Reproducible thesis writing with R Markdown
### Dr. Priyanga D. Talagala 
### Research Lounge Meet, University of Moratuwa
### 18/10/2022 <img src="fig/thesisdownlogo.png" width="223" />

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- A open-source R package to facilitate writing books and long-form articles/reports with R Markdown.

- Generate printer-ready books and ebooks from R Markdown documents
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<img src="fig/prithesis.png" width="85%" style="display: block; margin: auto;" />
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<img src="fig/thesiscode.png" width="100%" style="display: block; margin: auto;" />
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<img src="fig/bookdowncover.jpeg" width="75%" style="display: block; margin: auto;" />
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## Learn more about bookdown:

https://pkgs.rstudio.com/bookdown/

You can install the package from CRAN as follows:

install.packages("bookdown")
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# thesisdown

Inspired by the bookdown package

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## Prerequisites

- To compile PDF documents using R, you are going to need to have LaTeX installed.

- By far the easiest way to install LaTeX on any platform is with the `tinytex` R package:

```r
install.packages(c('tinytex', 'rmarkdown'))
tinytex::install_tinytex()
# after restarting RStudio, confirm that you have LaTeX with
tinytex:::is_tinytex()
```
--

- Install the `bookdown` and `thesisdown` packages.

```r
if (!require("remotes")) 
  install.packages("remotes", repos = "https://cran.rstudio.org")
remotes::install_github("rstudio/bookdown")
remotes::install_github("ismayc/thesisdown")
```

- Note that {thesisdown} is not available on CRAN at the moment and that’s why `install.packages("thesisdown")` won’t work.

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# Tip

### You may need to restart RStudio at this point for the following dialog to show up.
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File > New Project > New Directory

Then select **Thesis Project using thesisdown**
from the dropdown

<img src="fig/thesis_proj1.png" width="70%" style="display: block; margin: auto;" />
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Give your project a name and specify where you’d like the files to appear

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## Directory structure

<img src="fig/thesisfolder1.png" width="60%" style="display: block; margin: auto;" />
].pull-right[
`index.Rmd`: Contains your YAML (metadata) that will tell bookdown how to render your book

`.Rmd files` that comprise the body of your book

`thesis.bib` is a bib file containing your references. Most popular reference management tools have the option to export your references to a .bib file.
]

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].pull-right[

[Generated thesis](https://github.com/RETINALAB/rmd_workshop_with_blogdown/blob/master/static/slides/3Thesisdown/fig/thesis.pdf)

[To learn more about different thesis templates visit https://github.com/ismayc/thesisdown](https://github.com/ismayc/thesisdown)
]

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# Coming Soon !!

## morathesisdown

An R Markdown thesis template for the University of Moratuwa

Development version  at : "https://github.com/RETINALAB/morathesisdown"

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# morathesisdown

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pridiltal and thiyangt

# Acknowledgements:

This work was supported in part by RETINA research lab funded by the OWSD, a program unit of United Nations Educational, Scientific and Cultural Organization (UNESCO).