Previously on this blog we have discussed making geojson maps and uploading to Github for interactive visualization with USGS BISON data, and with GBIF data, and on my own personal blog. This is done using a file format called geojson , a file format based on JSON (JavaScript Object Notation) in which you can specify geographic data along with any other metadata.

Open access week is here! We love open access, and think it’s extremely important to publish in open access journals. One of the many benefits of open access literature is that we likely can use the text of articles in OA journals for many things, including text-mining. What’s even more awesome is some OA publishers provide API (application programming interface) access to their full text articles.

I attended the recent ALM Workshop 2013 and data challenge hosted by Public Library of Science (PLOS) in San Francisco. The workshop covered various issues having to do with altmetrics, or article-level metrics (ALM). The same workshop last year definitely had a feeling of we don’t know x, y, and z , while the workshop this year felt like we know a lot more. There were many great talks - you can see the list of speakers here.

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.

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.

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.

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.

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.

I recently attended ScienceOnline Climate, a conference in Washington, D.C. at AAAS. You may have heard of the ScienceOnline annual meeting in North Carolina - this was one of their topical meetings focused on Climate Change. I moderated a session on working with data from the web in R, focusing on climate data. Search Twitter for #scioClimate for tweets from the conference, and #sciordata for tweets from the session I ran.

We have started a new R package interacting with NOAA climate data called rnoaa . You can find our package in development here and documentation for NOAA web services here. It is still early days for this package, but we wanted to demo what you can do with the package.