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... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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 ... [Read more...]

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... [Read more...]

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... [Read more...]

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 ... [Read more...]

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... [Read more...]

There is a new R package in town, mvabund, which does, as they say "statistical methods for analysing multivariate abundance data". The authors introduced the paper in an online early paper in Methods in Ecology and Evolution here, R package here. Th... [Read more...]

Many ecologists are R users, but we vary in our understanding of the math and statistical theory behind models we use. There is no clear consensus on what should be the basic mathematical training of ecologists. To learn what the community thinks, we ... [Read more...]

So Flora of North America is an awesome collection of taxonomic information for plants across the continent. However, the information within is not easily machine readable. So, a little web scraping is called for. rfna is an R package to collect inf... [Read more...]

Described in a new Methods in Ecology and Evolution paper here, a new R package RNetLogo allows you to use NetLogo from R. NetLogo is software is a "multi-agent programmable modeling environment". NetLogo can be used in individual- and agent-based mod... [Read more...]