# Category Archives: Uncategorized

## Introduction to maximum likelihood and Bayesian statistics for ecologists (1-3 March 2017, iDiv)

By | February 27, 2017

The course is full. Here is syllabus with instructions. Complete raw codes (Markdown and R) and materials see the course's GitHub repository. DAY 1 Introduction: Course contents, pros and cons of Bayes, necessary skills. Normal distribution: Introducing likelihood on the Normal example. Poisson distribution: Likelihood maximization. Probability mass function. AIC and deviance. The Bayesian way… Read More »

## Reproducible art with R

By | July 27, 2016

This is my tribute to the fantastic R package spatstat. All the artwork was 100% done in R, the source code is here. Click the images for hi-res (6000 x 4000) versions. License: This is a public domain work. Feel free to do absolutely whatever you want with the code or the images, there are… Read More »

## Logarithmic axes with linear gridlines in basic R plots

By | July 18, 2016

I like Mathematica’s and Matlab’s log-log plots with logarithmic axes and linear tickmarks (and gridlines). In a way, they enable to imagine both multiplication and addition in a single figure. They also enable to more exactly visually connect data points with values. I haven’t found a simple ‘one-liner’ that’d do such plots in R. In… Read More »

## Big-data spatio-temporal analyses using open source GIS software (29 June - 1 July, iDiv, Leipzig)

By | March 23, 2016

The course is full. We are organizing a 3 day intensive course on open-source GIS high-performance analytical methods, with Giuseppe Amatulli (Yale University) as the main teacher, and Petr Keil (iDiv) as a teaching assistant. Date and place: 29 June - 1 July 2016, 'Red Queen' room, iDiv, Leipzig, Germany. Summary Over the past decade… 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 »

## Light diversity: obscuring the observed species

By | October 2, 2015

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 of species ‘dark diversity’. So… Read More »

## What did Novak Djokovic really smell?

By | August 17, 2015

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 getting dizzy.” And later: “You… Read More »

## Typesetting beautiful conference posters with Tickzposter

By | June 11, 2015

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 the code. Sounds insane at… Read More »

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

By | June 1, 2015

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 of function F at x… Read More »

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

By | May 18, 2015

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, ultimately, journal referees -- a… Read More »

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

By | April 15, 2015

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 that this simple analogy can… Read More »

## Bayesian Biostatistics 2015

By | February 1, 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 1 Introduction: Course contents, pros… Read More »

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

By | November 21, 2014

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 on Free software, free society.… Read More »

## The man in the academic arena

By | October 20, 2014

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 for review (and then rejected).… Read More »

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

By | October 8, 2014

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 approaches to science, encouraging new… 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 »

## Tailoring univariate probability distributions

By | June 26, 2014

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, from which everyting else can… Read More »

## A suggestion to Windows-based users of R: It may be time to relocate

By | June 17, 2014

Do you remember the time when you switched from graphical statistical software to R? I did it eight years ago, and I had hard time doing even a simple regression analysis without constantly searching for help, it was a pain. In desperation I frequently cheated and went back to Statistica for the familiar window-ish feeling.… Read More »

## Bayesian Biostatistics 2014

By | February 2, 2014

This post contains materials for Bayesian stats course that I taught between 2-4 Feb 2014 at Faculty of Science, Charles University, Prague, Czech Republic. There were around 40 participants. The complete materials and their source codes (Markdown and R) are on a GitHub repository. The lectures can also be accessed directly as follows (I recommend… 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 »

## Fast Conway's game of life in R

By | November 26, 2012

Here I demonstrate a simple way to code Conway's game of life (GoL) in R and to produce the animation above. Cellular automata in R are usually painfully slow if you iterate through all grid cells in an array. A couple of years ago my friend Martin Weiser came with an idea to avoid the… Read More »

## Protected: Secret lesson

By | October 16, 2012

There is no excerpt because this is a protected post.

## On American competition

By | October 9, 2012

'Play hard and good things will happen.' (motto on the wall of Yale gym) An obvious aspect of US culture is the omnipresent accent on competition, ambitions and achievements. A common misconception is that America 'is all about money'. This is inaccurate – it is not money that matters. It is achievement, which can be… Read More »

## Large datasets in OpenBUGS: Buffer overflow?

By | August 30, 2012

I recently made an attempt to run MCMC sampling in OpenBUGS using a large dataset and a spatially explicit occupancy model. Here I report some potentially interesting speed and memory issues that I noticed. Model and Data I won't go into technical details of my model as it is not the main focus of this… Read More »