Blog Archives

R and my divorce from Word

October 30, 2013
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R and my divorce from Word

Being in grad school, I do a lot of scholarly writing that requires associated or embedded R analyses, figures, and tables, plus bibliographies. Microsoft Word makes this unnecessarily difficult. Many tools are now available to break free from the tyranny of Word. The ones I like involve writing an article in markdown format, integrating all data preparation,...

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How heavy is the Siberut macaque? A Bayesian phylogenetic approach

September 30, 2013
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How heavy is the Siberut macaque? A Bayesian phylogenetic approach

Among-species comparisons can include phylogenetic information to account for non-independence arising from shared evolutionary history. Often, phylogenetic topologies and branch lengths are not known exactly, but are estimated with uncertainty. This uncertainty can be accounted for using methods recently described in a neat paper called Bayesian models for comparative analysis integrating phylogenetic uncertainty by Villemereuil et...

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Animating the Metropolis algorithm

September 8, 2013
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Animating the Metropolis algorithm

The Metropolis algorithm, and its generalization (Metropolis-Hastings algorithm) provide elegant methods for obtaining sequences of random samples from complex probability distributions. When I first read about modern MCMC methods, I had trouble visualizing the convergence of Markov chains in higher dimensional cases. So, I thought I might put together a visualization in a two-dimensional case. I’ll use...

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Quantifying uncertainty around R-squared for generalized linear mixed models

August 22, 2013
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Quantifying uncertainty around R-squared for generalized linear mixed models

People love $R^2$. As such, when Nakagawa and Schielzeth published an article in the journal Methods in Ecology and Evolution earlier this year, ecologists (amid increasing use of generalized linear mixed models (GLMMs)) rejoiced. Now there’s an R function that automates $R^2$ calculations for GLMMs fit with the lme4 package. $R^2$ is usually reported as a...

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Clarifying vague interactions

August 18, 2013
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Clarifying vague interactions

For some reason, authors occasionally present linear model results with vague or unintelligible interaction effects. One way to be vague when presenting interaction effects is to provide only a table of model coefficients, including no information on the range of covariate values observed, and no plots to aid in interpretation. Here’s an example: Suppose you have discovered a statistically significant...

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Occupancy model fit & AUC

July 30, 2013
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Occupancy model fit & AUC

Occupancy models are used to understand species distributions while accounting for imperfect detection. In this post, I’ll demonstrate a method to evaluate the performance of occupancy models based on the area under a receiver operating characteristic curve (AUC), as published last year by Elise Zipkin and colleagues in Ecological Applications. Suppose we are to fit a multi-year occupancy...

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Split violin plots

June 25, 2013
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Split violin plots

(This article was first published on Ecology in silico, and kindly contributed to R-bloggers) Violin plots are useful for comparing distributions. When data are grouped by a factor with two levels (e.g. males and females), you can split the violins in half to see the difference between groups. Consider a 2 x 2 factorial experiment: treatments A and B...

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Bayesian model II regression

May 27, 2013
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Bayesian model II regression

Regression is a mainstay of ecological and evolutionary data analysis. For example, a disease ecologist may use body size (e.g. a weight from a scale with measurement error) to predict infection. Classical linear regression assumes no error in covariates; they are known exactly. This is rarely the case in ecology, and ignoring error in covariates can bias regression coefficient...

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Modeling habitat diversity and species richness

April 20, 2013
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Modeling habitat diversity and species richness

How does habitat diversity affect species richness? Perhaps intuition suggests that habitat diversity increases species richness by facilitating niche or resource partitioning among species. But, for a fixed area, as habitat heterogeneity increases, the area that can be allocated to each habitat type decreases. In a recent paper, Allouche and colleagues (2012) provide a theoretical and empirical treatment...

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Agent-based modeling in R – habitat diversity and species richness

April 20, 2013
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Agent-based modeling in R – habitat diversity and species richness

How does habitat diversity affect species richness? Perhaps intuition suggests that habitat diversity increases species richness by facilitating niche or resource partitioning among species. But, for a fixed area, as habitat heterogeneity increases, the area that can be allocated to each habitat type decreases. In a recent paper, Allouche and colleagues (2012) provide a theoretical and empirical treatment...

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