Bayesian ANOVA: Powerful inference with within-group sample size of 1

By | March 9, 2017

1 Objective 2 The data 3 Fixed-effects ANOVA in JAGS 4 Relaxing the assumption of constant variance 5 Conclusion This post is inspired by a question by Dylan Craven that he raised during my Bayesian stats course. 1 Objective My aim here is to demonstrate that, in Bayesian setting, one can make powerful inference about… Read More »

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 »

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 »

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 »

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 »

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 »

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

By | June 26, 2015

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. The book has a wide… 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 »

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 »

Bayesian PCA

By | January 5, 2015

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. Rationale of bPCA Here is… 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 »