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 »

Is natural history more fundamental than statistics?

By | March 11, 2016

A couple of weeks ago at iDiv I had an exchange with Jonathan Chase about the importance of natural history, and whether it is more fundamental than statistics. Jon was arguing for fundamental importance of natural history, I disagreed. To quote Jon quoting Evelyn Hutchinson: A quote Hutchinson wrote in 1975 about the importance of… 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 »

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 »

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 »

12 nifty tips for scientists who use computers

By | February 16, 2015

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 you use R studio, then… 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 »