Articles by Recology - R

Working with climate data from the web in R

August 17, 2013 | 0 Comments

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, ... [Read more...]

R ecology workshop

July 31, 2013 | 0 Comments

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... [Read more...]

R to GeoJSON

June 30, 2013 | 0 Comments

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 (... [Read more...]

Put some cushions on the sofa

June 21, 2013 | 0 Comments

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 ... [Read more...]

Stashing and playing with raw data locally from the web

June 17, 2013 | 0 Comments

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 ... [Read more...]

Fylopic, an R wrapper to Phylopic

June 1, 2013 | 0 Comments

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 ... [Read more...]

Couch, apis and all that

May 30, 2013 | 0 Comments

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 ... [Read more...]

BISON USGS species occurrence data

May 27, 2013 | 0 Comments

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 ... [Read more...]

Scholarly metadata in R

March 16, 2013 | 0 Comments

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 ... [Read more...]

Visualizing rOpenSci collaboration

March 8, 2013 | 0 Comments

We (rOpenSci) have been writing code for R packages for a couple years, so it is time to take a look back at the data. What data you ask? The commits data from GitHub ~ data that records who did what and when. Using the Github commits API we can gather ... [Read more...]

Getting a simple tree via NCBI

February 14, 2013 | 0 Comments

I was just at the Phylotastic hackathon in Tucson, AZ at the iPlant facilities at the UofA. A problem that needs to be solved is getting the incrasingly vast phylogenetic information to folks not comfortable building their own phylogenies. Phylomatic has made this super easy for people that want plant ...
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Waiting for an API request to complete

January 26, 2013 | 0 Comments

Dealing with API tokens in R In my previous post I showed an example of calling the Phylotastic taxonomic name resolution API Taxosaurus here. When you query their API they give you a token which you use later to retrieve the result (see examples on their page above). However, you ... [Read more...]

Resolving species names when you have a lot of them

January 25, 2013 | 0 Comments

taxize use case: Resolving species names when you have a lot of them Species names can be a pain in the ass, especially if you are an ecologist. We ecologists aren't trained in taxonomy, yet we often end up with huge species lists. Of course we want to correct any ... [Read more...]

Open Science Challenge

January 8, 2013 | 0 Comments

Open Science Science is becoming more open in many areas: publishing, data sharing, lab notebooks, and software. There are many benefits to open science. For example, sharing research data alongside your publications leads to increased citation ra...
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Is invasive?

December 13, 2012 | 0 Comments

The Global Invasive Species Database (GISD) (see their website for more info here) has data on the invasiveness status of many species. From taxize you can now query the GISD database. Introducing the function gisd_isinvasive. This function was contributed to taxize by Ignasi Bartomeus, a postdoc at the Swedish ... [Read more...]

Shiny apps are awesome

December 10, 2012 | 0 Comments

RStudio has a new product called Shiny that, quoting from their website, "makes it super simple for R users like you to turn analyses into interactive web applications that anyone can use". See here for more information. A Shiny basically consists of two files: a ui.r file and a ... [Read more...]

One R package for all your taxonomic needs

December 6, 2012 | 0 Comments

UPDATE: there were some errors in the tests for taxize, so the binaries aren't avaiable yet. You can install from source though, see below. Getting taxonomic information for the set of species you are studying can be a pain in the ass. You have to manually type, or paste in, ... [Read more...]

Displaying Your Data in Google Earth Using R2G2

October 24, 2012 | 0 Comments

Have you ever wanted to easily visualize your ecology data in Google Earth? R2G2 is a new package for R, available via R CRAN and formally described in this Molecular Ecology Resources article, which provides a user-friendly bridge between R and the Google Earth interface. Here, we will provide ... [Read more...]

Getting taxonomic names downstream

October 16, 2012 | 0 Comments

It can be a pain in the ass to get taxonomic names. For example, I sometimes need to get all the Class names for a set of species. This is a relatively easy problem using the ITIS API (example below). The much harder problem is getting all the taxono... [Read more...]
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