What is the best resource to learn an R package? Many R users know the almighty question mark
? in R. For example, type
?lm and you will see the documentation of the function
lm. If you know nothing about a package, you can take a look at the HTML help by
where you can find the complete list of documentation by clicking the link
Packages. The individual help pages are often boring and difficult to read, because you cannot see the whole picture of the elephant. That is where package vignettes can help a lot. A package vignette is like a short paper (in fact some are real journal papers), which gives you an overview of this package, and sometimes with examples. Package vignettes are not a required component of an R package, so you may not find them in all packages. For those packages which contain vignettes, you can find them by
browseVignettes(), e.g. for the knitr package
browseVignettes<span class="p">(</span>package <span class="o">=</span> <span class="s">'knitr'</span><span class="p">)</span> <span class="c1"># or go to</span> system.file<span class="p">(</span><span class="s">'doc'</span><span class="p">,</span> package <span class="o">=</span> <span class="s">'knitr'</span><span class="p">)</span>
You can also see links to vignettes from
Packages and go to the package documentation, or
help.start<span class="p">()</span> browseURL<span class="p">(</span>paste0<span class="p">(</span><span class="s">'http://127.0.0.1:'</span><span class="p">,</span> tools<span class="p">:::</span>httpdPort<span class="p">,</span> <span class="s">'/library/knitr/doc/index.html'</span><span class="p">))</span>
Most vignettes are written in LaTeX/Sweave since that is the official approach (see Writing R Extensions). In the past Google Summer of Code, Taiyun Wei explored a few interesting directions of the knitr package, and one of them was to build HTML vignettes for R packages from Markdown, which is much easier to write than LaTeX.
For package authors who are interested, Taiyun’s corrplot package (on Github) can serve as an example. The markdown vignette is inst/doc/index.Rmd, and it is built to HTML by knitr with the Makefile. When you run
R CMD build corrplot,
index.Rmd will be converted to
index.html, which you can view it in
R CMD INSTALL corrplot_*.tar.gz (DO NOT use
devtools::install_github() here because it does not run
R CMD build).
The Makefile should be pretty clear: it is merely a call to
knitr::knit2html(). The vignette
index.Rmd is a simple R Markdown document; if you are not familiar with this format, see this video for a brief introduction:
Note you need
Suggests: knitrin your package DESCRIPTION file to pass
R CMD check, and
- a fake
inst/doc/to trigger the Makefile
Once you have this HTML vignette, you can also publish it elsewhere. For example, either RPubs.com or GitHub pages to gain more publicity (see an example of the phyloseq package). It is important to let users be aware of package vignettes, and a web link is apparently easier to tell other people than
browseVignettes() (I felt very uncomfortable when I was writing the first half of this post because the vignettes are hidden so deep, hence so hard to describe).
So why not start building an HTML vignette for your package with R Markdown now? Think about animations, interactive content (e.g. googleVis), MathJax equations and other exciting web stuff.