How much is enough? A new technique for quantifying precision of community surveys

Being an ecologist is all about the trade-off between effort, and time and money. Given infinite amounts of both, we would undoubtedly sample the heck out of nature. But it would be an exercise in diminishing returns: after a certain amount of sampling, we would fail to unturn any stone that has not already been unturned. Thus, ecology is a balancing act of effort: too little, and we have no real insight. Too much, and we’ve wasted a lot of time and money.

I’m always looking for ways to improve my balance, which is why I was interested to see a new paper in Ecology Letters called “Measures of precision for dissimilarity-based multivariate analysis of ecological communities” by Marti Anderson and Julia Santana-Garcon.

In a nutshell, the paper introduces a method for, “assessing sample-size adequacy in studies of ecological communities.” Put in a slightly different way, the authors have devised a technique for determining when additional sampling does not really improve one’s ability to describe whole communities — both the number of species, and their relative abundances. Perfect for evaluating when enough is enough, and adjusting the output of time and money!

In this post, I dig into this technique, show its applications using an example, and introduce a new R function to assess multivariate precision quickly and easily.

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Marine biodiversity and ecosystem functioning: what’s new and what’s next

(This is a cross-post with the Oikos blog promoting our new synthesis on marine biodiversity and ecosystem function research. Check out the open-access PDF here!)

In our new paper just published online early in Oikos, we synthesise our current understanding of the functional consequences of changes in species richness in the marine realm. For those familiar with the field of biodiversity and ecosystem functioning, the first question might well be: do we really need yet another meta-analysis on this topic? I mean, really. There have been several meta-analyses published in recent years. Do we really need this work?

Well, our answer to the question is yes.  Here’s why.

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What is functional diversity, and why do we care?

(This post is written to highlight a recent experiment which is now hosted as a preprint in PeerJ Preprints. You can find that paper here. Check it out and provide some open peer review!)

We live in an era of widespread human-driven extinction: the Anthropocene. Its a fact that many more species are being lost now than at any point in recorded history, and the future is grim. We are forecasted to lose 6,300% more species by 2100 than we have lost in the last 66 million years (based on evidence from the fossil record). So naturally there has been intense interest in cataloging the world’s biodiversity, and conducting experiments to understand the consequences of losing all these species. But are we looking at the right metric of diversity?

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In the pipeline…

I’ve been suspiciously quiet as of late — working on finishing up my dissertation — but in doing so have come up with a slew of new blog posts that should begin to trickle out shortly. For those who follow the blog, I wanted to put out a short post letting you know what to expect:

-an update to my post on R2 for linear mixed effects models (already live)

-an introduction to piecewise structural equation modeling (SEM), including a new function for automating Shipley’s tests of d-separation. The function is already hosted on GitHub

-how to download, align, and concatenate gene sequence data, and how to construct phylogenetic trees using maximum likelihood and Bayesian inference, all through R

Looking forward to getting these posts out there!

Taking the biodiversity challenge

mesocosm_exptI wanted to share a post by my friend Sharon Baruch-Mordo at my other blog, BioDV, on communicating biodiversity science. Sharon is a thoughtful, insightful scientist and I think she makes some really awesome points.

In her article, she challenges readers to, “write a 500 word essay about your science for a popular media outlet.” Never one to back down from a challenge, I thought I would give it a shot. My effort is below (499 words!)…what do you think Sharon?

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Collaboration: a problem shared


I wanted to quickly highlight an article by Cameron Walker titled “Collaboration: A problem shared” that appeared in Nature Jobs this week. It highlights some of my research done as part of the Dimensions of Biodiversity Distributed Graduate Seminar. I’ve wrote about collaboration before, specifically this program, so I was happy to see it get the press it deserves! Moving forward, I think educational models such as this one will be critical in preparing young ecologists to answer relevant questions in ecology–so check it out!

R^2 for linear mixed effects models

Linear mixed effects models are a powerful technique for the analysis of ecological data, especially in the presence of nested or hierarchical variables. But unlike their purely fixed-effects cousins, they lack an obvious criterion to assess model fit.

[Updated October 13, 2015: Development of the R function has moved to my piecewiseSEM package, which can be found here under the function sem.model.fits]

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Black theme for ggplot2

[EDIT 06/05/16: See updated version of this code here for ggplot2 version 2.X.X:]

I’ve long extolled the virtues of using ggplot2 as a graphing tool for R for its versatility and huge feature set. One of my favorite aspects of ggplot2 is the ability to tweak every aspect of the plot using intuitive commands. With the recent release of version 0.9.2 though, creator Hadley Wickham overhauled the theme options, which broke my preferred black theme, theme_black(), found here. I’ve updated theme_black() to work with the current version of ggplot Enjoy!

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Why students should start reading blogs (and commenting!)

Yesterday, Jeremy Fox posted a rather lengthy blog on why academics should read blogs. I’m going to convince the neophyte academic, the graduate student, why you especially should be reading blogs, and commenting too.

I will skip topics like “What is a blog?” and “What do blogs cover?” because Jeremy and his team at Dynamic Ecology have done an excellent job compiling the answers to these questions.

So, why should students read blogs? I’ll keep it simple: connection.

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An ode to the hagfish

As a marine ecologist, I would be remiss if I let my blog go so long without a shoutout to my favorite of marine critters, the noble and misunderstood hagfish. Slimy, ancestral, largely unknown: what’s not to love?

As an undergrad, I put together some materials on the biology and physiology of the Atlantic hagfish for a fisheries class at the Mount Desert Island Biological Labs. I’ve held onto the document in the (misguided?) sense that it may be useful to someone one day, but was never sure of the appropriate venue to disseminate it. Hello, blog. Below, find the 36-page document in all its pictorial glory, including close up images of its five–count ’em, FIVE–hearts.

Anatomical Review and Standard Operating Procedure for the Atlantic Hagfish (Myxine glutinosa)

Happy dissecting!

(Image credit: Wikimedia commons)