• first language: Chinese
• second language: R (10 years)
• third language: English
• graduated from Iowa State Univ (Stats, 2013)
• joined RStudio
• (co-)author and maintainer of some R packages (e.g. animation, knitr, cranvas, formatR, testit, highr, Rd2roxygen, fun, servr, tikzDevice, shiny, evaluate, markdown)

• read the P-values into R
• adjust the P-values
• compare to the alpha level
• the source document and data hwk5_q1.txt

• report = text (prose, narrative) + code
• code chunk = chunk header (chunk options) + code
• 001-minimal.Rmd
• 002-minimal.Rnw
• https://github.com/yihui/knitr-examples/

• computing language + documentation language
• (R | Python | C++ | …) + (LaTeX | Markdown | HTML | …)
• file extensions: .Rmd, .Rnw/.Rtex, .Rhtml, …

• keyword: automation
• the Duke Saga: http://www.economist.com/node/21528593
• not easy for large projects

# install.packages('knitr')
library(knitr)
knit("your-document.Rmd")  # compiles a document

• text output
• graphics
• cache
• cross references
• output hooks and chunk hooks
• language engines

• give me an R script, and I give you a report
• internally converted to R Markdown/LaTeX/…

#' today I built a model
fit = lm(dist ~ speed, data = cars)

#' and I got the slope `r coef(fit)[2]`

#+ dist-speed, fig.width=5, fig.height=4
plot(cars)
abline(fit)

• Sweave (R + LaTeX)

• LaTeX produces high-quality PDF output, but when you introduce it to other people…

  

• knitr supports LaTeX, though

• if you cannot master the basic syntax of Markdown in 10 minutes, I give you 10 dollars
• RPubs: http://rpubs.com
  • forget about reproducible research, because you are doing it unconsiously

• primarily for HTML
• the R package markdown

• a Word document? No!
• but my boss wants it…
• okay…
• Pandoc
• the R package rmarkdown http://rmarkdown.rstudio.com
• RStudio preview version http://www.rstudio.com/ide/download/preview

• Jekyll
  • blog like a hacker
  • based on Markdown, supported by Github
  • Rcpp gallery: http://gallery.rcpp.org
  • Vistat: http://vis.supstat.com
• WordPress (not recommended for ninja)
  • https://yihui.org/knitr/demo/wordpress/

• Gentleman and Temple Lang (2004)
• one R package to rule them all!
• data, R, man, tests, demo, src, vignettes
• VignetteBuilder: knitr in DESCRIPTION
• \VignetteEngine{knitr::knitr} in vignettes
• see details

# see list of vignettes
help(package = "knitr", help_type = "html")
# Docco Classic Style

• LyX + knitr
• https://github.com/yihui/knitr-book
• Why LyX: https://yihui.org/en/2012/10/lyx-vs-latex/
• writing a book: https://yihui.org/en/2013/06/tips-for-writing-an-r-book/
• reproducibility: https://yihui.org/en/2013/09/cannot-reproduce-my-own-book/

• courses, blog posts, workshops, papers, R packages, …
• https://yihui.org/knitr/demo/showcase/

• documentation: https://yihui.org/knitr (video)
• development: https://github.com/yihui/knitr
• examples: https://github.com/yihui/knitr-examples
• questions first go to StackOverflow please
• email? at the bottom of https://github.com/yihui/knitr-book

echo oybuwycxy.trpb | tr bopcrbtucwxyc+ exmiaen@iyuih