With the US government shut down, many of the federal government provided data APIs are down. We write R packages to interact with many of these APIs. We have been tweeting about what APIs that are down related to R pacakges we make, but we thought we would write up a proper blog post on the issue.

NCBI services are still up! NCBI is within NIH, which is within the Department of Health and Human Services. Here is the message on the NCBI page:

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Just a quick note that the Task View we have been working on with others Web Technologies and Services is up on CRAN now. Find it here https://cran.r-project.org/web/views/WebTechnologies.html.

This is the first version - there are definitely changes to come. Changes are being suggested as I write this on Twitter…

The draft version of the task view is on Github here if you want to file an issue.

We use many packages to do stuff with the web like XML, RCurl, httr, RJSONIO, etc., and we create many packages that grab data from the web. So it made a lot of sense to work on this task view. We hope it is a good resource for everyone.

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To help you use rOpenSci packages we put tutorials up on our site at /tutorials. Up to now, we created them with combination of raw html + converting code blocks to html and inserting them, etc. – it was a slow process to update them when changes happened in our packages.

So we thought of a better plan…

Recently CRAN started accepting R package vignettes (basically, tutorials built in to packages) in R Markdown format. This is great because executable Markdown with code plus text is easy to do with the help of knitr. And since our website is created using Jekyll, we can take our package vignettes with only text and code as a .Rmd file, convert to a .md file with text + code + the output of that code, insert some yaml metadata at the top, and have Jekyll automagically generate html pages. This may sound complicated, but once we have the vignette in a package, it’s just a few lines of code away from generating the html page for this site.

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There is an increasing set of R packages for interacting with the web from R, whether it be the low level tools to interact with the web via http (see RCurl and httr), parsing data from the web (like RJSONIO and XML), or wrappers to web APIs that provide data (like twitteR).

Most of you probably know about CRAN Task Views that aggregate information about R packages and functions on a particular subject area into a simple web page. There isn’t one for interacting with the web, so we have started drafting one on Github, and it is below.

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Good discovery tools for sotware are important as they can facilitate the pace of software development, bugs are found and squashed and new features added more quickly, and users find software they need faster. We have a page on our website for our packages that provides an overview of the packages we have, with descriptions and links.

Two other ways to discover things include

• A gallery of examples, or use cases, in which the entry point is something someone would want to do. This is opposed to a list of software packages in which the entry point is a description of what the package does. Examples include the Rcpp gallery, R graph gallery, and the iPython Notebook Viewer gallery.
• Images: Scrolling through images is a fast way to select an item of interest.

We just rolled out a new page for user stories, or use cases, organized in an gallery of thumbnail images with a brief description, which goes to another page with a brief script and output. Check it out. On this page we are gathering brief examples of tasks scientists can carry out in R. So far these include:

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