Blog Archives

Occupancy model fit & AUC

July 30, 2013
By
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...

Read more »

Split violin plots

June 25, 2013
By
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...

Read more »

Bayesian model II regression

May 27, 2013
By
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...

Read more »

Modeling habitat diversity and species richness

April 20, 2013
By
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...

Read more »

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

April 20, 2013
By
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...

Read more »

Dynamic community occupancy modeling with R and JAGS

February 24, 2013
By
Dynamic community occupancy modeling with R and JAGS

This post is intended to provide a simple example of how to construct and make inferences on a multi-species multi-year occupancy model using R, JAGS, and the ‘rjags’ package. This is not intended to be a standalone tutorial on dynamic community occupancy modeling. Useful primary literature references include MacKenzie et al. (2002), Kery and Royle (2007), Royle and Kery...

Read more »

Multi-species dynamic occupancy model with R and JAGS

February 24, 2013
By
Multi-species dynamic occupancy model with R and JAGS

This post is intended to provide a simple example of how to construct and make inferences on a multi-species multi-year occupancy model using R, JAGS, and the ‘rjags’ package. This is not intended to be a standalone tutorial on dynamic community occupancy modeling. Useful primary literature references include MacKenzie et al. (2002), Kery and Royle (2007), Royle and Kery...

Read more »

Interactive two-host SIR model

February 20, 2013
By
Interactive two-host SIR model

This is an example of interfacing R, shiny, and deSolve to produce an interactive environment where users can explore model behavior by altering parameters in an easy to use GUI. The model tracks the number of susceptible, infectious, and recovered individuals in two co-occuring host species. The rates of change for each class are represented as a system of differential...

Read more »

Interactive two-host SIR model

February 20, 2013
By

This is an example of interfacing R, shiny, and deSolve to produce an interactive environment where users can explore model behavior by altering parameters in an easy to use GUI. The model tracks the number of susceptible, infectious, and recovered individuals in two co-occuring host species. The rates of change for each class are represented as a system of...

Read more »

Interactive stage-structured population model

February 16, 2013
By
Interactive stage-structured population model

This is an example of interfacing R and shiny to allow users to explore a biological model often encountered in an introductory ecology class. We are interested the growth of a population that is composed of multiple, discrete stages or age classes. Patrick H. Leslie provides an in-depth derivation of the model in his 1945 paper “On the...

Read more »