Creating an analysis as a package and vignette

(This article was first published on Deciphering life: One bit at a time :: R, and kindly contributed to R-bloggers)

Creating an analysis as a package and vignette

Following from my last post, I am going to go step by step through the process I use to generate an analysis as a package vignette. This will be an analysis of the tweets from the 2012 and 2014 ISMB conference (thanks to Neil and Stephen for compiling the data).

I will link to individual commits so that you can see how things change as we go along.

Setup

Initialization

To start, we will initialize the package. devtools or rstudio make this rather easy:

library(devtools)
create("~/Documents/projects/personal/ismbTweetAnalysis")
Creating package ismbTweetAnalysis in ~/Documents/projects/personal
No DESCRIPTION found. Creating with values:

Package: ismbTweetAnalysis
Title: What the package does (short line)
Version: 0.1
Authors@R: "First Last <[email protected]> [aut, cre]"
Description: What the package does (paragraph)
Depends: R (>= 3.0.3)
License: What license is it under?
LazyData: true
Adding Rstudio project file to ismbTweetAnalysis

Alternatively, you can use File > New Project > New Directory > R Package in rstudio. Don't forget to Create a git repository (or git init in the directory). Note that the devtools created package will pass CRAN tests, whereas the rstudio will not.

Open the DESCRIPTION file, and you will need to change the Title, Authors or Authors@R, Description, License, and add VignetteBuilder: knitr at the end. Here is what my initial setup looks like.

RStudio Project Options

In addition, to make our life easier, we will change some options in the rstudio project.

Tools > Project Options > Build Tools, check Generate documentation with Roxygen, and select turn on all the options. We want to roxygenize when we Build & Reload especially, and have roxygen control the NAMESPACE file so we don't worry about it.

Alternatively, you can use document with reload=TRUE in devtools to update documentation and reload the functions.

Having this particular option of documenting and reloading the package every time I write a new function is what makes this easy. I write the new function, document/reload, and I can keep chugging along with my analysis document. And if I have to restart, I just run all chunks to get back to where I need to be.

Data

Now we need some data. Neil's data from 2012 uses a CSV format, however the tweets themselves have commas, so we will download the rdata file and use that, and also Stephen's data from 2014. However, there are three separate files for 2014, so we will download all three files and combine them. Both initial data sets will go in the /inst/extdata folder, and we will clean them up.

Here we have added our 4 data files.

Vignette

We are going to write this analysis as the vignette of the package, using R markdown as the language. To do that we need to create the file and add some boilerplate at the top so that the vignette gets generated properly. Here is the initial vignette, it is nothing but the engine and index definition, which are important.

Start the Analysis!

At this point we can start the analysis. The actual analysis will be done in the Rmd vignette file. The basic process is to add prose describing the analysis, with actual code to generate results and figures embedded in the Rmd, and adding functions and documentation (as roxygen tags) in the .R file, while doing iterations of document or Build/Reload along the way. Iterations of document / Build/Reload after writing new functions in the .R file will make them available to us in our workspace, with tab-completion in rstudio.

The following are bullet point summaries of points when I committed or built/reloaded, with links to the commit so you can see what has changed in the package.

And at this point I'm going to stop there. Now we have an analysis (that we will make into a nice output shortly), and we have munged 2 data sets, and wrote 6 functions, that may be useful in other contexts.

Preview Report

To preview the report, you can use the Knit HTML button in rstudio, or also use knitr directly. This will give you an html preview of the final report.

Generate Vignette

Once happy with the report, you can use devtools::build_vignettes() to generate the vignette files that will be copied to the relevant locations.

Commit and Push it ALL!

At this point, if you are happy with the package and analysis as a whole, you should commit all the package files to version control and make it available. In this case this means:

  • inst/doc: the output vignette
  • man: the function documentation
  • DESCRIPTION: our description file
  • NAMESPACE: the file documenting our namespace

You can see this commit here.

Now your package can be installed by others using devtools::install_github(). You could also submit your package to CRAN or Bioconductor if so desired.

Not Covered

Now this was a simple example. Ideally I should have included tests for my functions, you can read up 1 2 on how to do that. In addition, none of my functions use methods (see why they are useful).

I hope that you find this example useful, and will consider using packages more often even for simple analyses.

  • Reproducibility: One issue that may come up is how to make sure that you or someone else can directly reproduce the work in your package. Again, Hadley Wickham and the rstudio team have been thinking about this, and there is now the packrat package to make a project completely self-contained with all of it's dependencies.

Edit - added note on reproducibility at the end.

To leave a comment for the author, please follow the link and comment on his blog: Deciphering life: One bit at a time :: R.

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