In stephlocke/Rtraining: Training Materials on R

Requirements

necessary package: knitr
necessary package: rmarkdown
necessary software: pandoc
recommended software: MiKTeX

Using R for documents

Producing documents / documentation directly in R means that you closely interweave (knit) your analysis and R code together. This reduces rework time when you want to change or extend your code, it reduces time to produce new versions, and because it's code it's easier to apply strong software development principles to it.

Oh, and you don't need to spend hours making text boxes in powerpoint! Win ;-)

There are two languages which you can knit your r code into:

markdown
LaTeX (pronounced lay-tech alas)

Markdown is great for very quick generation and light (or css driven) styling and is what this section focusses on. LaTeX is excellent for producing stunning, more flexible documents.

rmarkdown standard text

The following text is the default text that gets created when you produce a new rmarkdown file in rstudio

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)

You can also embed plots, for example:

plot(cars)

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

rmarkdown standard documentation

The following text is part of the standard documentation on rmarkdown. I pull it from github.com/rstudio/rmarkdown and integrate it using knitr. It is better than I could produce and the act of integrating it gives an extra example of useful ways to build documents.

#setInternet2(use = TRUE)
x <- tempfile(fileext = "Rmd")
on.exit(unlink(x))
download.file("https://raw.githubusercontent.com/rstudio/rmarkdown/gh-pages/authoring_basics.md", x, method="curl", extra = "-k")