About

This page shows you all the instructions on how to contribute to Vistat. Before you get started, you need to fork the supstat/vistat repository to your own Github account (click the Fork button). You are assumed to have basic knowledge of GIT and R.

New Article

To start a new article, run

rake post title="A Title"

and you will get an R Markdown (Rmd) file under _source/ named yyyy-mm-dd-a-title.Rmd, which is a plain text file and you can edit it with your favorite text editor. At the moment, RStudio has the best support for Rmd files. Here is an Rmd sample file and its output.

If you do not have or understand rake, just copy an existing Rmd file, rename and open it with a text editor.

Edit an Article

There are a few fields in the header such as author and tags; if you have multiple entries, use the comma to separate them, e.g. author: [taiyun, yihui]. Note all authors need to put their information in _config.yml, and input the author id’s to the author field (the same applies to reviewers).

You can write math in the LaTeX syntax, e.g. $$\alpha+\beta$$ in a paragraph renders inline like $\alpha+\beta$, and $$f(x)=\frac{1}{\sqrt{2\pi}}e^{-x^2/2}$$ in a separate paragraph renders the display style

If you want to generate animations, set animation: true in the preamble of the article and use the chunk option fig.show='animate' in the chunk header (example).

Compilation

The executable script _bin/knit is essentially an R script. For Linux/Mac users, you can compile an Rmd file to md by

./_bin/knit _source/yyyy-mm-dd-your-post.Rmd

For Windows users, use Rscript instead:

Rscript ./_bin/knit _source/yyyy-mm-dd-your-post.Rmd

You can certainly preview the article inside your editor like RStudio, and the above approach is necessary only when you are ready to submit the article. Do not worry about images – we will compile your article again after it is accepted, and images will be re-generated and stored in the right place.

Preview

If you want to preview your articles locally (http://localhost:4000), you can run

rake preview

which is basically a wrapper to jekyll --server --auto. Of course you need to install Jekyll first.

Submission

After you are done with an article, commit it to your forked repository and submit a pull request to us. We will get it reviewed and you will see comments online. Further revisions may be required, in which case you just make the revision and continue to commit in the changes, and they will appear in the previous pull request.

Please commit the source file only (*.Rmd) and do not commit the output files (*.md and figures). We will re-compile the source files and upload images after we accept the article. Therefore if your article involves special packages or data, you should add clear instructions on them in the article.

Reviewers

Everyone is welcome to become a reviewer for Vistat. Reviews are public in the pull requests on Github. There are no anonymous reviewers here.

Contributors

We have had 7 contributors so far:

• Carl Boettiger A post-doctoral researcher with Marc Mangel and Steve Munch in the Center for Stock Assessment Research, at UC Santa Cruz, working on regime shifts in ecology and evolution.

• R Core Team The R Project for Statistical Computing.

• Taiyun Wei School of Statistics, Renmin University of China; author of the corrplot package.

• Yihui Xie Department of Statistics, Iowa State University; interested in statistical computing and graphics; author of knitr, animation and a few other R packages.

• Lijia Yu A master candidate majoring in Bioinformatics at Beijing Institute of Genomics.

• Karl Broman Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison; research in statistical genetics; developer of R/qtl (for R)

• Kevin Ushey MSc., University of British Columbia; interested in statistical genetics and data visualization