Jabberwocky Ecology

Experimental ecology is dead, long live experimental ecology!

I read a handful of experimental ecology papers the other day. I liked some of them and didn’t like some of them. It wasn’t that there was anything inherently wrong with the ones I didn’t like, they just didn’t fit in with my world view.

Yeah, this doesn’t make any sense to me either, but apparently that’s how we’re using this phrase these days.

P.S. I was going to let this one go until Ecotone used the original post to question “the reality (or not) of macroecology as its own discipline.” There’s nothing wrong with creative titles (we enjoy them here at Jabberwocky), but when contrasted with EEB & Flow’s other posts from ESA it’s not surprising that Ecotone took this as being a passive agressive critique of the state of the field. My main concern is that EEB & Flow seems to conflate an important methodological approach with particular interpretations of ecological process resulting from an application of that approach. Just because I disagree with a particular paper using an experiment doesn’t lead me to have “an unsure feeling about this field.” I mean really.

Frequency distributions for ecologists IIa: Data Visualization: Histograms

Well, I guess that grant season was a bit of an optimistic time to try to do a 4 part series on frequency distributions, but I’ve got a few minutes before heading off to an all day child birth class so I thought I’d see if I could squeeze in part 2.

OK, so you have some data and you’d like to get a rough visual idea of its frequency distribution. What do you do know? There are 3 basic approaches that I’ve seen used:

  1. Histograms. This is certainly the simplest and easiest to understand approach and most of the time for visualizing frequency distributions it is perfectly acceptable. A histogram simply divides the range of possible values for your data into bins, counts the number of values in each bin and plots this count on the y-axis against the center value of the bin on the x-axis. Any statistics program will be able to do this or  you can easily do it yourself. If all of the bins are of equal width (as is the default in stats packages) then your basically done. If you want to convert the y-axis into the probability that a value falls in a bin, just divide the counts by the total number of data points. If you want to convert it to a proper probability density estimate then you’ll also want to divide this number by the width of the bin (i.e., the upper edge of the bin minus the lower edge of the bin). If the bins are not equal width (which includes if you have transformed the data in some way) you should divide by the the linear width of the bin regardless of whether you are concerned about turning your y-axis into a probability density estimate or not. This is to make sure that you are visualizing the distribution in the way you are thinking about it (most people are thinking about the distribution of x). Of course there are good reasons for wanting to visualize the distributions of transformed data. Just make sure you have one if you’re not going to divide by the linear width of the bin.

Well, I’m out of time so I’ll go ahead and post this and come back with the other two options for visualization later.

Amen brothers: why stimulus funding for science was a good idea

We just read this great piece from the Huffington Post by Todd Palmer and Rob Pringle on why including funds for NSF and NIH in the stimulus bill was a good idea (thanks to Ecotone for pointing us to the article). The great thing about the piece is that it doesn’t just make a cogent argument for the stimulus funds, but for why funding basic science is economically beneficial in general. Probably the high point of the article was this little gem:

Truthfully, the return on our relatively modest investment in basic research over the last half-century is so astronomical that it’s impossible to calculate. Science hasn’t just stimulated the economy; it has revolutionized the economy, and our lives along with it.

which seems like it must be hyperbole, but at least from our perspective it certainly is not. However, if we had to pick our favorite moment in the article it would definitely be the paraphrase of Paul Baskin’s concern about the utility of this funding:

Aren’t we just subsidizing a bunch of nerds who already have cushy academic jobs and buy fancy Japanese-made instruments? No.

This is definitely one of the clearest, best, and funniest explanations of why funding basic science is critical to the economy and to society in general. Go check it out.

Frequency distributions for ecologists I: Introduction

Dealing with frequency distribution data is something that we as ecologists haven’t typically done in a very sophisticated way. This isn’t really our fault. Proper methods aren’t typically taught in undergraduate statistics courses or in the graduate level classes targeted at biologists. That said, as ecology becomes a more quantitative science it becomes increasingly important to analyze data carefully so that we can understand its precise quantitative structure and its relationship to theoretical predictions.

Frequency distribution data is basically any data that you would think about making a histogram out of. Any time you have a single value that you (or someone else) has measured, for example the size or abundance of a species, and you are interested in how the number of occurrences changes as a function of that value, for example – are there more small species than large species or more small patches than large patches, then you are talking about a frequency distribution. Technically what we’re often interested in is the probability distribution underlying the data and you will often have more luck using this term when looking for information. Many major ecological patterns are probability/frequency distributions including the species-abundance distribution, species size distribution (also known as the body size distribution), individual size distribution (also known as the size spectrum), Levy flights, and many others.

Last year I wrote a paper with Jessica Green and Brian Enquist on one of the problems that can result from the approaches to this kind of data typically employed by ecologists and the more sophisticated methods available for addressing the question. As a result I’ve been receiving a fair bit of email recently about related problems; enough that I thought it might be worth a couple of posts to lay out some of the basic ideas regarding the analysis of frequency distribution data. Over the next week or so I’ll try to cover what I’ve learned about basic data visualization, parameter estimation, and comparing the fits of different models to the data. Along the way I may have a couple of things to say about some recently published papers that have the potential to cause confusion with respect to these subject.

Please keep in mind that I am not a professionally trained statistician and that this is not intended to be an authoritative treatment of the subject. I’m just hoping to provide folks with an entryway into thinking about what to do with this kind of data and I’ll try to point to useful references to help take you further if you’re interested.

Data scientists

Nathan over at Flowing Data just posted an interesting piece on the emergence of a new class of scientists whose work focuses on the manipulation, analysis and presentation of data. The take home message is that in order to fully master the ability to understand and communicate patterns in large quantities of data that one needs to have some ability in:

  • Computer science – for acquiring, managing and manipulating data
  • Mathematics and Statistics – for mining and analyzing data
  • Graphic design and Interactive interface design – to present the results of analyses in an easy to understand manner and encourage interaction and additional analysis by less technical users

His point is that while one could get together a group of people (one with each of these skills) to undertake this kind of task, that the challenges of cross-disciplinary collaboration can slow down progress (or even prevent it entirely). As such, there is a need for individuals that have at least some experience in several of these fields to help facilitate the process. I think this is a good model for this kind of work in ecology, though given the already extensive multidisciplinarity required in the field I view this role as one occupied only be fairly small fraction of folks.

The other thing that I really liked about this post (and about Flowing Data’s broader message) is the focus on the end user. The goal is to make ideas and tools available to the broadest possible audience and sometimes often the more technical folks in the biological scientists seem to forget that their goal should be to make things easy to understand and simple for non-technical users to use. This is undoubtedly a challenging task, but one that we should work to accomplish whenever possible.

Hurlbert’s unicorn

Over at EEB and Flow, Marc aesthetically pleasing details” to our figures. I’m a big fan of visually pleasing figures and the examples that Marc gives show how a little extra effort can really improve communication. The post made me think of one of the earliest examples of adding… a little something extra… to one’s figures – Stuart Hurlbert’s unicorn (Hurlbert 1990).
Part of Figure 1 from Hurlbert 1990

Part of Figure 1 from Hurlbert 1990

April fools for the statistically inclined

You can always count on Andrew Gelman for quality April Fools Day posts.