Yesterday during an iDiv seminar we stumbled across dark diversity. For those unfamiliar with the concept, it has been defined by Pärtel et al. (2011) : It is possible to specify species that belong to a particular species pool but that are not locally present. We call this unaccounted set … Continue reading

## What did Novak Djokovic really smell?

As reported by BBC, men’s tennis World number one Novak Djokovic complained to the umpire that he could smell cannabis on court during his Rogers Cup win over Jeremy Chardy. After winning the first set, the Serb approached the chair, saying: “Someone is smoking weed, I can smell it, I’m … Continue reading

## 2015 Pulitzer prize awarded to book on conservation biogeography: The Sixth Extinction by Elisabeth Kolbert reviewed

Elisabeth Kolbert: The Sixth Extinction. Published on Feb 2014 by Henry Holt & Co., New York. The 2015 Pulitzer prize in the General Nonfiction category (awarded on May 28) went to Elisabeth Kolbert for her book on science of extinction, which also happens to be an intro to conservation biogeography. … Continue reading

## Typesetting beautiful conference posters with Tickzposter

To make a conference poster you probably use some vector editor: Inkscape, Adobe Illustrator, CorelDraw, or maybe LibreOffice Draw, Impress or MS PowerPoint. But you can also code it, and by that I mean using some markup language to actually write how the poster should look like, and then compile … Continue reading

## Math vs. language, extinctions vs. climate change

Two unrelated insights that I’ve recently had: Math isn’t more abstract than language, it’s just exact The reason is that mathematical notation is part of the same language that we speak, and any mathematical formula is, in fact, a written (or spoken) sentence. Example: Which is equivalent to: The value … Continue reading

## Do ecological journals accept LaTeX and open document formats?

Last week I started to draft a manuscript that is heavy on the computation side and it uses large data. This requires everything to be well documented and organized, otherwise I get lost in my own code. The real challenge is then to confront my analyses with the co-authors and, … Continue reading

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

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 … Continue reading

## The age of Postdoc: towards liberation of academic middle class

Nature has an article about the daunting prospects for current postdocs in some countries (Nature 520, 144-147). The article is stimulating but reports only a few relatively ad-hoc ways to fix the situation. In the discussion below the article Peter Jurica mentions postdocs as middle class (of academia). I think … Continue reading

## Simple template for scientific manuscripts in R markdown

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 … Continue reading

## GAM splines now easy in JAGS and OpenBUGS. An example on 2D spatial data

Last week I met Simon Wood, creator of mgcv package, which is THE tool for fitting Generalized Additive Models (GAM) in R. Simon brought my attention to function jagam which he has just added to mgcv. The function allows to transform the ‘spline’ or ‘smooth’ component of GAM model formula … Continue reading

## 12 nifty tips for scientists who use computers

Simple things are good. Here is a list of 12 things that I find simple and useful, yet not many of my colleagues use them. The list is R-biased. Knitr. Intuitive tool to integrate R and text to make reports with fancy fonts, figures, syntax-highlighted R code and equations. If … Continue reading

## Bayesian Biostatistics 2015

Authors: Petr Keil, Jan Smyčka This post contains materials for Bayesian stats course (2-4 Feb 2015 at Faculty of Science, Charles University, Prague, Czech Republic). The complete materials and their source codes (Markdown and R) are on my GitHub repository. The lectures can also be accessed directly as follows: DAY … Continue reading

## Bayesian PCA

Authors: Jan Smycka, Petr Keil This post introduces experimental R package bPCA which we developed with Jan Smycka, who actually came with the idea. We do not guarantee the very idea to be correct and there certainly are bugs – we invite anyone to show us wrong, or to contribute. … Continue reading

## The cathedral, the bazaar, and the SNAFU principle

I've recently been exploring foundational ideas of Free and Open-Source Software (FOSS) culture, and I've found them relevant not only for software development, but also for academia. Here is something that I picked up for inspiration: If you have no idea who Richard Stallman is, I recommend his TEDx talk … Continue reading

## On Theory in Ecology – Reading Marquet et al. (2014)

Marquet et al. have essay in Bioscience entitled “On theory in ecology”, with the main message being we need more good theory; I agree 100%. The paper also presents an overview of important ecological theories and some good points about why theory is important. Notable one: “Theory, etymologically, comes from … Continue reading

## The man in the academic arena

Lately I went through a couple of ordinary academic failures. I had one manuscript rejected in three statistical journals in a row. I had another one rejected in Science, PNAS and PLoS Biology in a prompt sequence. Interestingly, among all of the six submissions only Science actually sent it out … Continue reading

## Center for Theoretical Study, Prague: more intense than ivy league

I have recently been lucky to relocate from Yale to Center for Theoretical Study in Prague, Czech Republic. The institute brings together philosophers, mathematicians, physicists, sociologists, economists, biologists and others; it is similar to Santa Fe Institute or Princeton Institute for Advanced Study, and its aim is to stimulate interdisciplinary … Continue reading

## Species Distribution Models on the right track. Finally.

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 … Continue reading

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

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 … Continue reading

## Tailoring univariate probability distributions

This post shows how to build a custom univariate distribution in R from scratch, so that you end up with the essential functions: a probability density function, cumulative distribution function, quantile function and random number generator. In the beginning all you need is an equation of the probability density function, … Continue reading