R

Eduard Szöcs and I started developing a taxonomic toolbelt for the R language a while back , which lets you interact with a multitude of taxonomic databases on the web. We have a paper in F1000Research if you want to find out more (see here). I thought it would be fun to rewrite some of taxize in other languages to learn more languages. Ruby and Python made the most sense to try. I did try others (Julia, Node), but gave up on those for now. The goal here isn’t to port taxize to Python and Ruby right now - it’s for me to learn myself some coding. ...

I started an R package a while back, and a few people have shown interest, so I thought it was time to revist the code. govdat is an interface to various APIs for government data: currently the Sunlight Labs APIs, and the New York Times congress API. Returned objects from functions are simple lists. In future versions of govdat, I may change how data is returned. The following are examples (which is also the package vignette) of using the Sunlight Labs API. I will add examples of using the New York Times Congress API once their site is up again; I’m doing this on 2013-08-28, just after the takedown of their site. ...

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. The following is an abbreviated demo of what I did in the workshop showing some of what you can do with climate data in R using our packages. ...

After my presentation yesterday to a group of grad students on R resources, I did a presentation today on intro to R data manipulation, visualizations, and analyses/visualizations of biparite networks and community level analyses (diversity, rarefaction, ordination, etc.). As I said yesterday I’ve been playing with two ways to make reproducible presentations in R: RStudio’s presentations built in to RStudio IDE, and Slidify. Yesterday I went with RStudio’s product - today I used Slidify. See the Markdown file for the presentation here. ...

I’m doing a presentation today to grad students on R resources. I have been writing HTML presentations recently, but some great tools are now available to convert text that is easy to read and write to presentations. RStudio has something called R presentations, that is basically Markdown. This tool is built in to RStudio. See some docs here. A cool feature of RStudio’s presentations is that the preview of the presentation live updates on each save - nice Another option is the slidify package, made by Ramnath Vaidyanathan. The canonical url for slidify is here. Slidify gives you more options and flexibity than RStudio presentations. For this presentation I went with RStudio’s product. See the Markdown file for the presentation here. ...

UPDATE As you can see in Patrick’s comment below you can convert to GeoJSON format files with rgdal as an alternative to calling the Ogre web API described below. See here for example code for converting to GeoJSON with rgdal. GitHub recently introduced the ability to render GeoJSON files on their site as maps here, and recently introduced here support for TopoJSON, an extension of GeoJSON can be up to 80% smaller than GeoJSON, support for other file extensions (.topojson and .json), and you can embed the maps on other sites (so awesome). The underlying maps used on GitHub are Openstreet Maps. ...

It is getting easier to get data directly into R from the web. Often R packages that retrieve data from the web return useful R data structures to users like a data.frame. This is a good thing of course to make things user friendly. However, what if you want to drill down into the data that’s returned from a query to a database in R? What if you want to get that nice data.frame in R, but you think you may want to look at the raw data later? The raw data from web queries are often JSON or XML data. This type of data, especially JSON, can be easily stored in schemaless so-called NoSQL databases, and queried later. ...

What is PhyloPic? PhyloPic is an awesome new service - I’ll let the creator, Mike Keesey, explain what it is (paraphrasing here): PhyloPic stores silhouette images of organisms, and each image is associated with taxonomic names, and stores the taxonomy of all taxa, allowing searching by taxonomic names. Anyone can submit silhouettes to PhyloPic. What is a silhouette? It’s like this: by Gareth Monger What makes PhyloPic not just awesome, but super awesome? All or most images are licensed under Creative Commons licenses. This means you can use the silhouettes without having to ask or pay - just attribute. ...

The USGS recently released a way to search for and get species occurrence records for the USA. The service is called BISON (Biodiversity Information Serving Our Nation). The service has a web interface for human interaction in a browser, and two APIs (application programming interface) to allow machines to interact with their database. One of the APIs allows you to search and retrieve data, and the other gives back maps as either a heatmap or a species occurrence map. The latter is more appropriate for working in a browser, so I’ll leave that to the web app folks. ...

Scholarly metadata - the meta-information surrounding articles - can be super useful. Although metadata does not contain the full content of articles, it contains a lot of useful information, including title, authors, abstract, URL to the article, etc. One of the largest sources of metadata is provided via the Open Archives Initiative Protocol for Metadata Harvesting or OAI-PMH. Many publishers, provide their metadata through their own endpoint, and implement the standard OAI-PMH methods: GetRecord, Identify, ListIdentifiers, ListMetadataFormats, ListRecords, and ListSets. Many providers use OAI-PMH, including DataCite, Dryad, and PubMed. ...