Blog Archives

Exploring phylogenetic tree balance metrics

October 10, 2012
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Exploring phylogenetic tree balance metrics

I need to simulate balanced and unbalanced phylogenetic trees for some research I am doing. In order to do this, I do rejection sampling: simulate a tree -> measure tree shape -> reject if not balanced or unbalanced enough. But what is enough? We ne...

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GBIF biodiversity data from R – more functions

October 8, 2012
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GBIF biodiversity data from R – more functions

We have been working on an R package to get GBIF data from R, with the stable version available through CRAN here, and the development version available on GitHub here. We had a Google Summer of code stuent work on the package this summer - you can se...

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Vertnet – getting vertebrate museum record data and a quick map

September 19, 2012
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Vertnet – getting vertebrate museum record data and a quick map

We (rOpenSci) started a repo to wrap the API for VertNet, an open access online database of vertebrate specimen records across many collection holders. Find the open source code here - please contribute if you are so inclined. We had a great Google Su...

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Getting data from figures in published papers

September 18, 2012
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Getting data from figures in published papers

The problem: There are a lot of figures in published papers in the scholarly literature, like the below, from (Attwood et. al. 2012)): At some point, a scientist wants to ask a question for which they can synthesize the knowledge on that question b...

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Scholarly metadata from R

September 17, 2012
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Metadata! Metadata is very cool. It's super hot right now - everybody is talking about it. Okay, maybe not everyone, but it's an important part of archiving scholarly work. We are working on a repo on GitHub rmetadata to be a one stop shop for quer...

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Getting data on your government

September 1, 2012
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Getting data on your government

I created an R package a while back to interact with some APIs that serve up data on what our elected represenatives are up to, including the New York Times Congress API, and the Sunlight Labs API. What kinds of things can you do with govdat? Here ...

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Getting ecology and evolution journal titles from R

August 31, 2012
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So I want to mine some #altmetrics data for some research I'm thinking about doing. The steps would be: Get journal titles for ecology and evolution journals. Get DOI's for all papers in all the above journal titles. Get altmetrics data on each DO...

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Making matrices with zeros and ones

August 30, 2012
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So I was trying to figure out a fast way to make matrices with randomly allocated 0 or 1 in each cell of the matrix. I reached out on Twitter, and got many responses (thanks tweeps!). Here is the solution I came up with. See if you can tell why it...

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ggplot2 maps with insets

August 22, 2012
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ggplot2 maps with insets

Here's a quick demo of creating a map with an inset within it using ggplot. The inset is achieved using the gridExtra package. Install libraries, set directory, read file setwd("/Users/ScottMac/Dropbox/CANPOLIN_networks_ms/data") # change ...

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Recent R packages for ecology and evolution

June 14, 2012
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Many R packages/tools have come out recently for doing ecology and evolution. All of the below were described in Methods in Ecology and Evolution, except for spider, which came out in Molecular Ecology Resources. Here are some highlights. mvabund pap...

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