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rmarkdown.Rmd
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rmarkdown.Rmd
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---
title: "R Markdown"
author: "Anton Antonov"
date: 'Saturday, April 25, 2015 <br><img src="tcts_logo.png" alt="Logo here" width=128 height=128>'
output:
revealjs::revealjs_presentation:
theme: solarized
center: false
---
## Reprodicuble research
>- [The "Duke saga"](http://www.economist.com/node/21528593)
>- Linear regression -- so simple!
>- Now:
+ Complex models, (pre-)processing tools
+ Huge amounts of data (TB)
+ Research impact, show how you do it
+ Internet services
>- [Ropensci reproducibility guide](http://ropensci.github.io/reproducibility-guide/)
## R Markdown, links
>- [Rmarkdown official documentation](http://rmarkdown.rstudio.com/)
>- [Supercool cheatsheet](http://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf)
>- [Complete reference](http://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)
>- [github repository](https://github.com/rstudio/rmarkdown)
>- [Stack Overflow tag](http://stackoverflow.com/questions/tagged/rmarkdown)
## R + <u>markdown</u> + ...
Markdown: plain text -> formatted HTML
. . .
Output types:
>- HTML
>- PDF (LaTeX)
>- doc (MS Word/OpenOffice/LibreOffice)
>- presentations (Beamer, ioslides, Slidy, reveal.js)
. . .
(demo)
## <u>R</u> + markdown + ...
R code can be embedded directly to the document:
"Hi, today's value of $\pi$ is `r pi`!"
. . .
>- **Inline code** or **code chunks** with _options:_
+ eval/echo
+ warning/error/message
+ tidy/results
+ cache
+ fig.width/fig.height
>- `knitr` is awesome (therefore "Knit" button in RStudio)
. . .
(demo)
## R + markdown + <u>...</u>
Additional features:
>- math equations $i \hbar \frac{\partial}{\partial t}\Psi = \hat H \Psi$
>- multiple output formats with minimal changes
>- YAML header and templates
>- full power of HTML/CSS
>- bonus: htmlwidgets
. . .
(demo)
## Your turn!
Prepare a report with these elements:
* plain markdown formatting
* R code chunk with custom options
* some image (static or generated)
. . .
Use the [cheatsheet](http://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf), [documentation](http://rmarkdown.rstudio.com/), [my github repository](https://github.com/tonytonov/tcts-rmarkdown) and your imagination.
Good luck!
[https://github.com/tonytonov/tstc-rmarkdown](https://github.com/tonytonov/tstc-rmarkdown)