Blog Archives

Guide to using rOpenSci packages during the US Gov’t shutdown

October 8, 2013
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Note: This is cross-posted from the rOpenSci blog, which will update with this post when our technical snafu is fixed. With the US government shut down, many of the federal government provided data APIs are down. We write R packages to interact with m...

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Working with climate data from the web in R

August 17, 2013
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Working with climate data from the web in R

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...

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R ecology workshop

July 31, 2013
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R ecology workshop

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, rarefactio...

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R to GeoJSON

June 30, 2013
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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...

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Put some cushions on the sofa

June 21, 2013
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I posted earlier this week about sofa (here), introducing a package I started recently that interacts with CouchDB from R. There's been a fair amount of response at least in terms of page views, so I'll take that as a sign to keep going. One thing that would be nice while you are CouchDB-ing is to interact with local...

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Stashing and playing with raw data locally from the web

June 17, 2013
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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...

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Fylopic, an R wrapper to Phylopic

June 1, 2013
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Fylopic, an R wrapper to Phylopic

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...

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Couch, apis and all that

May 30, 2013
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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 like a data.frame or plot. 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...

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BISON USGS species occurrence data

May 27, 2013
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BISON USGS species occurrence data

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...

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Scholarly metadata in R

March 16, 2013
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Scholarly metadata in R

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....

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