Category Archives: Ecology

IBS 2017: Weak case for experimental macroecology, dynamic macroecology on the rise, and the problem of process vs mechanism

By | January 17, 2017

I’ve returned from IBS meeting in Tucson. Here are my thoughts on experimental and dynamic macroecology, the two big issues discussed this year: Experimental macroecology needs better justification One entire morning was dedicated to experimental macroecology. Presented were results from small-grain manipulative experiments, sometimes replicated over large extents, sometimes not. However, it all felt like a… Read More »

Kéry & Royle have a new book on hierarchical modeling in ecology. It's good

By | January 7, 2016

Marc Kéry's books are as important for learning (and teaching) hierarchical modeling as Crawley's The R Book is for learning R. I hold Kéry's Introduction to WinBUGS high for the uncompromising didactic clarity. J. Andrew Royle is one of the founding minds (with James Nichols and Darryl MacKenzie) of the so called occupancy modeling, and… Read More »

On soil larvae, Beverly Hills, passion, macroecology, and the problem of describing what I do

By | December 3, 2015

I have always found it difficult to explain my profession to people. For my bachelor degree I studied larvae of inconspicuous flies (Insecta: Diptera: Therevidae) in soils of remote forests of central Europe. About five people around the world have ever heard of these flies, but I did not care as I was passionately in… Read More »

Survival analysis: basic terms, the exponential model, censoring, examples in R and JAGS

By | May 13, 2015

I have put together some basic material on survival analysis. It is available as: .html document with highlighted syntax here. Printer-ready .pdf document here. GitHub repository with all the source files here. Main motivation was that I wanted to learn the basics myself; also, it's tricky to find simple examples of survival models fitted in… Read More »

Simple template for scientific manuscripts in R markdown

By | March 12, 2015

I've made a really simple template for the classical manuscript format for R markdown and knitr. Here are the resulting .pdf and .html. The template contains the four usual components of any scientific manuscript: equations (using LaTeX syntax) table with caption (done by kable package, but you can also use xtable) figure with caption citations… Read More »

Species Distribution Models on the right track. Finally.

By | September 2, 2014

Species Distribution Models (SDM) a.k.a. Niche Models have always been a busy pile of confusion, ideology and misguided practices, with the real mess being the “presence only” SDMs. Interestingly, when you go to conservation or biogeography symposiums, you can hear the established SDM gurus starting their talks with: “During the last ten years SDMs have… Read More »

Is my brilliant idea any good? I am not sure, so I've pre-printed it on PeerJ

By | July 24, 2014

As a scientist, what should I do when I encounter a seemingly fundamental problem that also seems strangely unfamiliar? Is it unfamiliar because I am up to something really new, or am I re-discovering something that has been around for centuries, and I have just missed it? This is a short story about an exploration… Read More »

Do 'macrosystems ecologists' know about macroecology?

By | February 18, 2014

Paper by Levy et al. in Frontiers in Ecology and the Environment announces emergence of a new ecological discipline called macrosystems ecology (MSE). The authors define MSE like this: MSE studies explore how broad-scale variation in fine-scale characteristics – such as organismal behavior and fitness, nutrient transformations, and water-use efficiency – relate to broad-scale spatial… Read More »

Do simple models lead to generality in ecology? Opinion of a simpleton

By | September 25, 2013

Evans et al. have a paper in Trends in Ecology and Evolution with this abstract: Modellers of biological, ecological, and environmental systems cannot take for granted the maxim ‘simple means general means good’. We argue here that viewing simple models as the main way to achieve generality may be an obstacle to the progress of… Read More »

The effect of ski-pistes on butterflies

By | July 19, 2013

I have a weak spot for butterflies, and I love skiing. Every time I go up a ski lift I wonder how such a major landscape modification (ski pistes or ski slopes) affects nature. I have always had the impression that clear-cutting long and wide strips in mountain forests is not necessarily a bad thing.… Read More »

Seeing Pierre Legendre

By | June 10, 2013

As suggested by his name, the guy is a legend. One of the most cited authors in ecology, I have him in (almost) the same league with James H. Brown, sir Robert M. May or Stephen P. Hubbell. Legendre is not famous for creating a revolutionary ecological theory and he does not stand out as… Read More »

Where do birders go?

By | April 30, 2013

Yesterday during our spatial ecology class we explored geographic patterns of localities which bird observers like to go to in the US. Here is the map which I produced - it is based on eBird 3.0 reference dataset and it shows density of all birding checklist submitted between 2000 and 2012, at 10 x 10… Read More »

On ensemble forecasting

By | April 27, 2013

Yesterday, professor Ronald Smith gave a talk at Yale about how to predict future climate. One of his central subjects was ensemble forecasting. Here I give it a bit of a dissection. Climatologists and ecologists do "predictive models". Once they have the model, they use it to predict the future, e.g.: How will global temperature… Read More »