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 »

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 »

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 »

Spatial autocorrelation of errors in JAGS

By | February 10, 2014

In the core of kriging, Generalized-Least Squares (GLS) and geostatistics lies the multivariate normal (MVN) distribution – a generalization of normal distribution to two or more dimensions, with the option of having non-independent variances (i.e. autocorrelation). In this post I will show: (i) how to use exponential decay and the multivariate normal distribution to simulate… 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 »

Poisson regression fitted by glm(), maximum likelihood, and MCMC

By | October 30, 2013

The goal of this post is to demonstrate how a simple statistical model (Poisson log-linear regression) can be fitted using three different approaches. I want to demonstrate that both frequentists and Bayesians use the same models, and that it is the fitting procedure and the inference that differs. This is also for those who understand… Read More »