Ecology

Introduction to Bayesian Methods guest lecture

October 18, 2012 | Corey Chivers

This is a talk I gave this week in Advanced Biostatistics at McGill. The goal was to provide an gentle introduction to Bayesian methodology and to demonstrate how it is used for inference and prediction. There is a link to an accompanying R script in the slides [Read more...]

Continuous dispersal on a discrete lattice

September 27, 2012 | Corey Chivers

Dispersal is a key process in many domains, and particularly in ecology. Individuals move in space, and this movement can be modelled as a random process following some kernel. The dispersal kernel is simply a probability distribution describing the distance travelled in a given time frame. Since space is continuous, ... [Read more...]

Dynamical systems: Mapping chaos with R

July 13, 2012 | Corey Chivers

Chaos. Hectic, seemingly unpredictable, complex dynamics. In a word: fun. I usually stick to the warm and fuzzy world of stochasticity and probability distributions, but this post will be (almost) entirely devoid of randomness. While chaotic dynamics are entirely deterministic, their sensitivity to initial conditions can trick the observer into ... [Read more...]

Recology is 1 yr old…

December 23, 2011 | Scott Chamberlain

This blog has lasted a whole year already. Thanks for reading and commenting. There are a couple of announcements:Less blogging: I hope to put in many more years blogging here, but in full disclosure, I am blogging for Journal of Ecology no...

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Plotting grouped data vs time with error bars in R

October 31, 2011 | Daniel Hocking

This is my first blog since joiningR-bloggers. I’m quite excited to be part of this group and apologize if I boreany experienced R users with my basic blogs for learning R or offendprogrammers with my inefficient, sloppy coding. Hopefully writing for...

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Two new rOpenSci R packages are on CRAN

October 27, 2011 | Scott Chamberlain

Carl Boettiger, a graduate student at UC Davis, just got two packages on CRAN. One is treebase, which which handshakes with the Treebase API. The other is rfishbase, which connects with the Fishbase, although I believe just scrapes XML cont...

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Two-sex demographic models in R

October 26, 2011 | Scott Chamberlain

Tom Miller (a prof here at Rice) and Brian Inouye have a paper out in Ecology (paper, appendices) that confronts two-sex models of dispersal with empirical data.They conducted the first confrontation of two-sex demographic models with empirical data on...

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Generating sets of permutations

October 21, 2011 | ucfagls

In previous posts I discussed how to generate a single permutation from a fully-randomised or restricted permutation design using shuffle(). Here I want to briefly mention the shuffleSet() function and illustrate it’s usage. Every time you call shuffle() it has to interpret the … Continue reading → [Read more...]

Phylogenetic community structure: PGLMMs

October 13, 2011 | Scott Chamberlain

So, I've blogged about this topic before, way back on 5 Jan this year.Matt Helmus, a postdoc in the Wootton lab at the University of Chicago, published a paper with Anthony Ives in Ecological Monographs this year (abstract here). The paper addres...

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permute: a package for generating restricted permutations

October 4, 2011 | ucfagls

Multivariate ordination methods are commonly used in ecology to investigate patterns in species composition in space or time. Constrained ordination methods such as redundancy analysis (RDA) and canonical correspondence analysis (CCA) are effectively just multiple regressions, but we lack the … Continue reading → [Read more...]

rnpn: An R interface for the National Phenology Network

August 31, 2011 | Scott Chamberlain

The team at rOpenSci and I have been working on a wrapper for the USA National Phenology Network API. The following is a demo of some of the current possibilities. We will have more functions down the road. Get the publicly available code, and contribu...

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(#ESA11) rOpenSci: a collaborative effort to develop R-based tools for facilitating Open Science

August 8, 2011 | Scott Chamberlain

Our development team would like to announce the launch of rOpenSci. As the title states, this project aims to create R packages to make open science more available to researchers. http://ropensci.org/ What this means is t... [Read more...]

Model Validation: Interpreting Residual Plots

July 18, 2011 | Daniel Hocking

When conducting any statistical analysis it is important to evaluate how well the model fits the data and that the data meet the assumptions of the model. There are numerous ways to do this and a variety of statistical tests to evaluate deviations from model assumptions. However, there is little ...

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GLMM Hell

July 7, 2011 | Daniel Hocking

I have been starting to analyze some data I have of repeated counts of salamanders from 5 plots over 4 years. I am trying to develop a predictive model of salamander nighttime surface activity as a function of weather variables. The repeated counting l...

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iEvoBio 2011 Synopsis

June 22, 2011 | Scott Chamberlain

We just wrapped up the 2011 iEvoBio meeting. It was awesome! If you didn't go this year or last year, definitely think about going next year.Here is a list of the cool projects that were discussed at the meeting (apologies if I left some out):Vistrails...

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Troubling news for the teaching of evolution

February 9, 2011 | Scott Chamberlain

A recent survey reported in Science ("Defeating Creationism in the Courtroom, but not in the Classroom"), suggests that high school teachers are not teaching evolution to the fullest extent, say, that grammar is being taught in the English c...

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R and Google Visualization API: Fish harvests

January 17, 2011 | Scott Chamberlain

I recently gathered fish harvest data from the U.S. National Oceanic and Atmospheric Administarion (NOAA), which I downloaded from Infochimps. The data is fish harvest by weight and value, by species for 21 years, from 1985 to 2005. Here is a link to a google document of the data I used below: ...

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Another boring blog

December 2, 2010 | Daniel Hocking

I recently decided to create two blogs as outlets for my research. The first (The Richness of Life) focuses more on the organisms I work with as an ecologist and my general interest as a student of natural history. This blog on Quantitative...

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A (fast!) null model of bipartite networks

September 12, 2010 | Timothée

One of the challenges for ecologists working with trophic/interaction networks is to understand their organization. One of the possible approaches is to compare them across a random model, with more or less constraints, in order to estimate the departure from randomness. To this effect, null models have been developed. ... [Read more...]

10w2170, Banff

September 11, 2010 | xi'an

Yesterday night, we started the Hierarchical Bayesian Methods in Ecology workshop by trading stories. Everyone involved in the programme discussed his/her favourite dataset and corresponding expectations from the course. I found the exchange most interesting, like the one we had two years ago in Gran Paradiso, because of the ... [Read more...]

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Ecology

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