Publications by Maxwell B. Joseph
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 use of ...
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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 ...
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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...
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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...
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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 a...
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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 col...
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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...
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Split violin plots
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 are crossed with groups 1 and 2, with N=1000. 1 2 3 4 5 6 7 8 9 # Simul...
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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 Applicat...
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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 exampl...
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