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LightningTalk.Rmd
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---
output:
slidy_presentation:
keep_md: true
incremental: true
---
Dissertation, Thesis, or Project <br> with Knitr and Markdown
========================================================
1. Motivation
+ Reproducibility
+ Integrate data analysis and report writing
+ Plain text! Focus on content not formatting (back end)
2. Toolkit
+ Reference manager (.bib file)
+ Citation style (.csl file)
+ R Studio (Knitr and Bookdown packages)
3. Making it work for you (example)
+ https://github.com/eddiekasner/example-dissertation
Motivation
========================================================
<center>
</center>
Image source: [rosannavanhespenresearch.wordpress.com](https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/)
Toolkit
========================================================
* Reference manager that can export to BibTeX (.bib file)
+ BibTeX: Plain text tool and file format for processing lists of references (LaTeX documents)
+ Examples: [Zotero](https://libguides.mit.edu/ld.php?content_id=34248570), [Mendeley](http://guides.library.ubc.ca/bibtex/mendeley), [EndNote](https://www.rhizobia.co.nz/latex/convert), [Paperpile](http://forum.paperpile.com/t/how-to-export-a-document-and-citations-to-latex-and-bibtex/784)
* Preferred citation style (.csl file)
+ Citation Style Language (.csl): XML-based language for formatting citations and bibliographies
+ Reference managers need descriptions of each citation style in language computer can understand
+ GitHub has a [repository of ~8500+ .csl files](https://github.com/citation-style-language/styles)
+ Example: [Council of Science Editors](https://writing.wisc.edu/Handbook/DocCSE.html)
* R Studio
+ [Knitr package (Yihui Xie)](https://yihui.name/knitr/)
+ [Bookdown package (Yihui Xie)](https://bookdown.org/yihui/bookdown/)
+ YAML: An R Markdown file always has a formatting header ('front matter') written in [YAML syntax](https://en.wikipedia.org/wiki/YAML)
References
========================================================
<style>
.col2 {
columns: 2 200px; /* number of columns and width in pixels*/
-webkit-columns: 2 200px; /* chrome, safari */
-moz-columns: 2 200px; /* firefox */
}
.col3 {
columns: 3 100px;
-webkit-columns: 3 100px;
-moz-columns: 3 100px;
}
</style>
<div class="col2">
1. Stack Overflow
2. Dr. Google
3. R Markdown & R Studio Resources
+ [R Studio Intro](http://rmarkdown.rstudio.com/lesson-1.html)
+ [Authoring Bibliographies and Citations](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
+ [Knitr Package (Yihui Xie)](https://yihui.name/knitr/)
+ [Bookdown Package (Yihui Xie)](https://bookdown.org/yihui/bookdown/)
4. $\LaTeX$ ("Lay-tech" or "La-tech")
+ [LaTeX Wiki](https://en.wikipedia.org/wiki/LaTeX)
+ [LaTeX Website](https://www.latex-project.org/)
5. Managing References for LaTeX use (.bib files)
+ [Bibdesk (Apple-Mac)](http://bibdesk.sourceforge.net/)
+ [JabRef](http://www.jabref.org/)
+ [Others](https://tex.stackexchange.com/questions/9454/bibdesk-like-software-for-windows)
6. Citation Style Langauge Resources (.csl files)
+ [CSL Primer](http://docs.citationstyles.org/en/stable/primer.html)
+ [GitHub Repository](https://github.com/citation-style-language/styles)
+ [CSL Editor](http://editor.citationstyles.org/about/)
7. Example Thesis and Templates for Academic Manuscripts
+ [Rosanna's Research](https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/)
+ [An R Markdown Template for Academic Manuscripts](http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/)
</div>