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# knitr |
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[HRUG Meetup](http://www.meetup.com/houstonr/events/227950530/) |
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# Why Knitr |
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* results need to be reproducible |
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* Documentation of code |
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* easier to read and understand later on to extend |
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* Great for making reports as well |
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* Sharing results leads to facilitating discussion |
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# History |
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## Donald Knuth |
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* On literate programming: |
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* ..."consider programs to be works of literature" |
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* comprehensible programs --> better programs |
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* Also, because he's badass, made Tex for proper typesetting. |
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Some neat trivia |
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* version number [approaches PI](http://www.tex.ac.uk/FAQ-TeXfuture.html) |
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* use to send people a [byte of money ($2.56)](https://en.wikipedia.org/wiki/Knuth_reward_check) for finding bugs |
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## DK made WEB |
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* WEB takes source file (of code and text) |
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* has 2 main functions |
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* Tangle |
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* compiles to an executable code file |
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* Weave |
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* compiles to documentation |
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## markdown rose to prevalence |
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* translates to HTML |
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* clear, concise |
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* at the cost of being somewhat restrictive |
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* almost as readable as the rendered HTML |
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## [pandoc](http://pandoc.org/) |
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* can convert between MANY different formats |
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**markdown + pandoc leads to Knitr** |
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# In Use |
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Knitr runs in a separate environment |
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If you use markdown |
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* Can include things like videos, etc. using HTML |
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Can also use [LaTex](http://kbroman.org/knitr_knutshell/pages/latex.html), and others as input |
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The rest of the talk is in reference to using Knitr with [Rmarkdown](http://rmarkdown.rstudio.com/) |
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Like [markdown](http://rmarkdown.rstudio.com/#markdown-basics) syntax except |
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* hyphens up top delineate [frontmatter/metadata in YAML](http://rmarkdown.rstudio.com/#output-options) |
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* for output options mostly |
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* [Codeblocks](http://rmarkdown.rstudio.com/authoring_rcodechunks.html) can be passed options |
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Shortcut for codeblock in RStudio |
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* <kbd>ctrl</kbd> + <kbd>alt</kbd> + <kbd>i</kbd> |
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* <kbd>cmd</kbd> + <kbd>alt</kbd> + <kbd>i</kbd> |
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# Neat Tips: |
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## As code gets longer |
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* make separate R files |
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* source them in the Knitr. |
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## Use things like [stargazer package](https://cran.r-project.org/web/packages/stargazer/index.html) |
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## can run a chunk |
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* By highlighting and right-clicking to run as with other code in RStudio |
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## can comment out |
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* using HTML commenting |
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``` |
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<!-- any markdown including mix of text and codeblocks here --> |
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``` |
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## Caching |
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* cache option, if true |
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* doesn't re-eval itself if previous chunks has updated |
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* re-evals if changed within chunk |
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## Name code blocks |
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* can see in RStudio and use as navigation |
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* can reference code blocks elsewhere in document |
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## Can write [knitr hooks](http://yihui.name/knitr/hooks/) |
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* extra customization! |
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# Examples |
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* [stackoverflow](http://health.stackexchange.com/questions/4413/how-much-of-the-difference-in-brain-size-is-attributable-to-gender-not-physical) |
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* learned about caching |
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* For taking code from an explanation to use |
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* option of ```knitr('filename', tangle=TRUE)``` |
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* slides, with `ioslides_presentation` |
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## What are some workflows that include Knitr when doing analysis in R? |
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* whole workflow in Rmd |
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* do in RStudio first, then go to Rmarkdown |
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* sourcing a lot of R code chunks |
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* source one big file that sources other things |
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## Is there a way to do interactive Rmarkdown editing online? |
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[Shiny](http://rmarkdown.rstudio.com/authoring_shiny.html) |
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## Good Practices and reports generation |
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### Why use Rmarkdown for report generation? |
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* Excel/Word with macros == sucked |
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* brittle, any small change = broken |
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* Rmarkdown is cleaner |
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* get to leverage the power of R |
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* for analysis |
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* for plots, graphs, etc |
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* easy to re-run anlysis and keep report in sync |
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* easier to publish online |
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### Downsides |
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* Difficult to have exact control over styles |
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* Lack of good `.ppt` generation for some audiences |
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## Workflow |
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* load.R, cleanup.R, figs.R, main.R |
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* source main that loads all |
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* custom ggplot theme |
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* customization can mean getting into css/html |
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# Other things! |
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Beamer for slides, and there are cool beamer themes |
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[Brew](https://learnr.wordpress.com/2009/09/09/brew-creating-repetitive-reports/) is another way to do things like we saw with Knitr |
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* Takes more up front set up though |
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you can make knitr to mark new page `\newpage` |
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* `\newpage` is a feature of Tex |
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[Reproducible Research](https://cran.r-project.org/web/views/ReproducibleResearch.html) |
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* "places knitr in context with functions and packages it plays nice with, and some alternatives" |
neerajt revised this gist
pandafulmanda created this gist