Blog Archives

Making sense of random effects

November 16, 2012
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Making sense of random effects

The other night in my office I got into a discussion with my office mate, the brilliant scientist / amazing skier Dr. Thor Veen about how to understand the random effect variance term in a mixed-effects model. Thor teaches the R statistics course here at UBC, and last night a student came to the office...

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rfigshare tutorial

November 6, 2012
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Recently we at rOpenSci released our rfigshare package up on cran (or you can check out the most up to date version on github. So what’s so great about being able to create figshare articles through R? For some time now I’ve been advocating the use of a workflow that involves documents written in R...

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rGtrends 0.01

October 4, 2012
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rGtrends 0.01

I’m happy to announce that I’ve finally finished my rGtrends package, an interface for the unofficial python Google trends API. It’s a simple function that will allow you to search Google Trends from within R. I haven’t really come up with how this is really relevant to ecology, but it is pretty interesting from a social perspective. For instance you...

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Discrete colors in ggplot

September 1, 2012
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Discrete colors in ggplot

Have you ever wanted an easy way to generate continuous color pallettes for a discrete factor? I came across a question over on Stackoverflow about how add color to a ggplot figure. I often find myself with lot’s of categories that are discrete when I want a continuous color plot. This can be achieved by writing a quick...

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impacTwit : How big is your work on twitter?

June 29, 2012
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impacTwit : How big is your work on twitter?

There’s a great Tom Waits song from the album “Mule Variations” called “Big in Japan”. The beauty of saying you’re big in Japan is that no one can ever really verify the statement (or at least that was more true in 1999). You might assert “my work is big on twitter”, and hey, how would I know?...

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How many ecologists were on ECOLOG in 1992?

June 25, 2012
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How many ecologists were on ECOLOG in 1992?

Remember 1992? I had just turned 13 and was still a year away from highschool when my true descent into nerdom and the internet would begin. Back then it was with a local BBS (Bulletin Board System) run by a guy in a trailer park named Charlie and a 1200 baud modem on...

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Randomization thoughts

April 27, 2012
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Randomization thoughts

Le Grand Casino of Monte CarloOn Monday I’m going to be leading a little stats workshop on randomization tests and null models. In preparation for this I wrote up code for null model examples I wanted to write a post that introduced the basics of these models (Null models, bootstrapping,...

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Fast paced food-web plotting action

December 20, 2011
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Fast paced food-web plotting action

A simple foodwebOne of my interests is in food web topology and food web dynamics. My research in experimental ponds has left me with 2430 food webs to make sense of, and one way to facilitate understanding that many networks, and really any food web, is through visualization. There are...

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Plotting implicit functions in R

November 11, 2011
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Plotting implicit functions in R

So in prepping for my latest manuscript on population dynamics I have been creating all the necessary figures.  One of them I considered was a 2-d surface plot of a modified Ricker equation showing the transitions from extinction stability, and stability to limit cycles.  Inconveniently though the only way to do this is with an implicit function.  Since becoming...

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March insanity

March 22, 2010
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So I took a brief break from ecology yesterday to pursue another project, modeling the NCAA bracket. I decided to run a stochastic simulation of the tournament. I know this has nothing to do with ecology, but I believe its a good exercise in modeling. Modeling has very little to do with the specifics of a...

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