• A system for annotating a document to separate metadata from text
• E.g. TeX, LaTeX, HTML (HyperText Markup Language)
• Sometimes the markup is hidden from the author, e.g. Microsoft Word (WYSIWYG)
• Procedural markup: provides instructions for other programs to process, e.g. TeX
• Descriptive/semantic markup: the markup provides descriptive labels, e.g. HTML
• Lightweight markup language - markup language with simple syntax
  • Easy to write and easy to read
  • Markdown is a widely used example
  • Can be quickly converted to other markup languages such as HTML

• Provides a simple syntax for creating reproducible documents
• R code is executed and embedded, then report is converted to Markdown and HTML
  • Objects created in one chunk of code are available to later chunks
• In it's simplest/easiest use, any R script may be converted to HTML or PDF
• RStudio Notebooks
  • Runs R code in script, outputs results immediately after each line of code
  • Open any R script in RStudio and press Ctrl+Shift+Alt+H
• The stitch and spin functions in knitr provide additional formatting possibilties
• A quick reference document is available in RStudio and here
• Template is provided when .Rmd file started
• Mathematical notation is supported via MathJax; uses same markup to denote math as TeX
• Appearance can be customized using CSS

• Sweave and knitr use a special TeX file with extension .Rnw
• A LaTeX document that includes R code
• Code chunks are started with << >>= and ended with @
• Inline code is written \Sexpr{ }
• Helpful quick reference

<<chunkname, options>>=
  library(ggplot2)
  qplot(mpg, wt, data=mtcars)
@
Here is some inline code \Sexpr{1+1}

• cache - set to TRUE to store long calculations
  • even the slightest change to the chunk will cause it to be recalculated
  • use dependson='chunkname' to specify which chunks the current chunk depends on
• echo - FALSE to not output the code, or a numeric vector of which lines of code to hide
• eval - FALSE to not evaluate the chunk, or numeric vector on lines to not evaluate 8 include - FALSE to evaluate a chunk but not include the output
• tidy - FALSE to turn off formatting of code (useful if text isn't wrapping properly)
• highlight - FALSE to not colour code and output
• Lots of options for controlling plot output; see here
• For more customization you may need to set hooks

• Goal is to automatically generate a quiz from a test bank of questions
• Below are three questions written in syntax for .Rnw files and stored in an R vector
  • \Sexpr{...} for inline R code <<>>= ... @ for chunks

TestBank <- c("Construct a \\emph{\\Sexpr{c('box plot', 'stem-and-left plot',
  'Normal Q-Q plot')[sample(3, 1)]}} for the following sample of data
  (\\Sexpr{paste0(round(rnorm(10, mean = 60), 1), collapse = ', ')}).",
"Construct a \\Sexpr{sample(c(90, 95, 99), 1)}\\% confidence interval for
the ratio of the variances of the following two samples
(\\Sexpr{paste0(rpois(10, 10), collapse = ', ')}) and
(\\Sexpr{paste0(rpois(6, 6), collapse = ', ')}).",
"What is the probability that an expontential random variable with $\\lambda = 1$
exceeds 1.5 given that it exceeds 1.")

• We can randomly choose questions from the test bank
• Here notice the first two questions will have new data each time they are generated

Assuming we have saved the document on the previous slide as "quiz.brew"...

library(brew)
library(knitr)
brew("quiz.brew", "quiz.Rnw")
knit2pdf("quiz.Rnw", "quiz.pdf")

• Slidify and Rstudio R Presentations convert Rmd files into HTML5 slides
  • Rstudio's version is easier to use
  • Slidify allows for more customization, can use several different frameworks
• Slightly different syntax for both
  • For Slidify, slides are separated using "---"
  • For Rstudio R Presentations, new slide begins with header using "====="
• Allows users to interact with your slides
  • All the powers of JavaScript are at your fingertips
• Compilation is much faster than LaTeX/Beamer
• Easier to type and less commands to remember
• With a little CSS and HTML knowledge becomes very easy to customize and debug
  • Customizing RStudio output and customizing Slidify

Average daily temperature for several Canadian cities (click and hover on curves and names)

See rCharts, googleVis, and ggvis packages in R

Average daily temperature (℃) and total yearly rainfall (mm.)

library(googleVis)
## ... omitted formatting of cw.dat data.frame
gvisGeoChart(cw.dat, locationvar="lat.long", colorvar='ave.temp', hovervar='place',
                          sizevar='total.precip', options=list(region='CA', resolution='provinces'))

• Shiny, can be used to write applications for the web in R
• As interacts with the app (changes inputs), R code is rerun to update the outputs (reactivity)
• As with the tools presented earlier, no knowledge of HTML or Javascript is needed
• Apps can be deployed locally using the shiny package or hosted on the web
• A great tutorial and lots of examples are available on the RStudio website

• For managing changes to documents and code

• In a distributed VCS

  • There is no central repository
  • Each developer has their own copy of all code
  • No need to be connected to a server, other than to share with other developers

• The two most popular systems are Git and Subversion (SVN)

  • Git is a distributed VCS, SVN is not
  • R project uses SVN

• With Git, nearly all operations are done locally and very quickly

  • Delta compression is used: only differences between versions are stored

• Backup of all files
• Track history of all changes to every file
• Public or private depending on preference
• Easy to transfer files between workstations (e.g. home/laptop and office PC)
• Take frequent "snapshots" (commits) of code, making it easier to find where issues started
• Have a branch for working code only, one for fixing bugs, another for adding new features
  • branching and merging is so fast/easy that it can and should be done frequently
• No emailing of code to anyone, they simply checkout a copy of the repository
  • Can give permission to make (push) changes to a repo, or allow only a fork
• Users can easily report issues and suggest changes (a pull request) on GitHub

• I personally began using the GitHub GUI before knowing any Git, finding it very easy to use
  • Learn more as projects grow in size and add collaborators
• Free public repositories
  • Private starts at $7/month for five repositories
• GUI for Windows provides simple interface for many commands
• Checkout R packages hosted on GitHub using devtools's install_github function
• Can use Travis CI to automatically test your software
  • With each push to repo, Travis CI will build your project and run tests

• Makes it easy to print, search, update, import, combine references in R
• Can read in .bib files and read PDFs using Poppler to create a citation
• Citations can also be searched for on Crossref, Google Scholar, Pubmed, and Zotero
• Searching is very flexible, can search by arbitrary field plus key or entry type
• Citations can be generated for inclusion in RMarkdown and RHTML documents
• Bibliography of all cited references can be printed at end of document
  • hyperlinks automatically added, many bibliography and citation style available
• Supports BibLaTeX and Bibtex and converting BibLaTeX to BibTeX if forced
• Simple interface for setting default behaviour for the most used functions

library(RefManageR)
bib <- ReadBib(system.file("Bib", "biblatexExamples.bib", package = "RefManageR"), check = FALSE)
bib[[49:51]]

## [1] B. Malinowski. _Argonauts of the Western Pacific. An account of native enterprise and
## adventure in the Archipelagoes of Melanesian New Guinea_. 8th ed. London: Routledge and Kegan
## Paul, 1972.
##
## [2] M. Maron. _Animal Triste_. Trans. from the German by B. Goldstein. Lincoln: University of
## Nebraska Press, 2000.
##
## [3] W. Massa. _Crystal structure determination_. 2nd ed. Berlin: Spinger, 2004.

bib2 <- ReadBib(system.file("Bib", "RJC.bib", package = "RefManageR"))
print(bib2[2:3], .opts = list(style = "text", bib.style = "alphabetic", sorting = "none"))

## [Jen+13] E. M. Jennings, J. S. Morris, R. J. Carroll, et al. "Bayesian methods for
## expression-based integration of various types of genomics data". In: _EURASIP Journal on
## Bioinformatics and Systems Biology_ 2013.1 (2013), pp. 1-11.
##
## [Gar+13] T. P. Garcia, S. Müller, R. J. Carroll, et al. "Identification of important
## regressor groups, subgroups and individuals via regularization methods: application to
## gut microbiome data". In: _Bioinformatics, btt_ 608 (2013).

• Authors and other "name list" fields are stored in the person class

bib2[1]$author

## [1] "N Serban"    "A M Staicu"  "R J Carroll"

• Authors and other "name list" fields are stored in the person class
• Let's add url and urldate fields for Jennings et al and fix the journal for Garcia et al.

bib2[2:3] <- list(c(url="http://bsb.eurasipjournals.com/content/2013/1/13",
                          urldate = "2014-02-02"), c(doi="10.1093/bioinformatics/btt608",
                          journal = "Bioinformatics"))
print(bib2[2:3], .opts = list(style = "html", bib.style = "authoryear"))

Garcia, T. P, S. Müller, R. J. Carroll, et al. (2013). “Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data”. In: Bioinformatics 608. DOI: 10.1093/bioinformatics/btt608.

Jennings, E. M, J. S. Morris, R. J. Carroll, et al. (2013). “Bayesian methods for expression-based integration of various types of genomics data”. In: EURASIP Journal on Bioinformatics and Systems Biology 2013.1, pp. 1–11. URL: http://bsb.eurasipjournals.com/content/2013/1/13 (visited on Feb. 02, 2014).

• How often is someone with family name "Wang" a coauthor?

length(bib2[author = "wang"])

## [1] 37

• How often is N. Wang a coauthor?

length(SearchBib(bib2, author = "Wang, N.",
                 .opts = list(match.author = "family.with.initials")))

## [1] 19

• Use names to extract keys bib$bibtype to get entry types

• Cite functions for citations, convenience functions Citet, AutoCite, TextCite, Citep
  • Specify style as "html" or "markdown" for HTML and Markdown documents
  • Hyperlinks will be included automatically, and may be turned off if desired
  • The code in unevaluated, chunk form is as follows

BibOptions(check.entries = FALSE, style = "html")
Citep(bib, author = "Itzhaki", .opts = list(cite.style = "alphabetic"))
TextCite(bib, c("loh", "wilde"), .opts = list(cite.style = "authoryear", hyperlink = "#35"))

• Inline (wrapped in I()): Here is one citation [Itz96], two more are Loh (1992); Wilde (1899)
• Itz96 goes to the arXiv doc, the other two references go to the bibliography slide

Now we print the bibliography, using results='asis' in the knitr chunk

PrintBibliography(bib, .opts = list(bib.style = "numeric"))

[1] N. Itzhaki. Some remarks on 't Hooft's S-matrix for black holes. Mar. 11, 1996. arXiv: hep-th/9603067.

[2] N. C. Loh. “High-Resolution Micromachined Interferometric Accelerometer”. MA Thesis. Cambridge, Mass.: Massachusetts Institute of Technology, 1992.

[3] O. Wilde. The Importance of Being Earnest: A Trivial Comedy for Serious People. English and American drama of the Nineteenth Century. Leonard Smithers and Company, 1899. Google Books: googlebooks.

• On a single webpage, the hyperlinks in e.g. [1], will go to the point of first citation
  • Getting this working automatically for HTML5 slides is not implemented yet

• See the CRAN task view on reproducible research for other R packages on this topic
• These slides for more on the basics of of Sweave and knitr and also Yihui Xie's website
• CRC Press has a several titles in the works and already available on the subject
  • Dynamic Documents with R and knitr and Reproducible Research in R and RStudio
• For RStudio, see all the links for various features back on Slide 4
• Ramnath Vaidyanathan's Youtube channel for some neat demos of his packages
  • Slidify, rNotebook, rCharts, rMaps, etc. (all on Github)
• The Shiny tutorial so nice, I'm linking to it twice
• For Git see here, here, here, and Pro Git (pdf here)
• Pandoc - the "Swiss Army knife" for converting between markup languages
• The RefManager package is available on CRAN