Everything you might have been afraid to ask about implementing models with discrete parameters in Stan. Written for ecologists that know BUGS, JAGS, or NIMBLE, and want to use Stan. Provides an example by marginalizing over partly observed presence/absence states in a simple occupancy model.
A high-level overview, an example, and a call to action.
Migrating from Jekyll to distill, with some reflections on the past 6 years.
Gaussian processes that scale to larger data.
In-class activities to teach design matrices from multiple perspectives.
10 books I wish I had entering graduate school.
A series of introductory R videos.
How to visualize spatial neighbors using ggplot2, spdep, and sf.
TLDR: scripting plots is more reproducible and efficient long term
Partial pooling and the best NBA free throw shooters of all time.
Dynamic multi-year occupancy models, marginalizing over latent occurrence states.
Computing the proportion of land cover types using R and the raster package.
A guest post by Joe Mihaljevic.
Exploring how correlation among covariates inflates uncertainty in coefficient estmates.
Using spike and slab priors to shrink coefficients toward zero.
Fitting a Bayesian ZOIB regression model in JAGS.
Fitting a Bayesian regression with covariate uncertainty.
A short description of the post.
A homemade Metropolis algorithm animation using R and the animation package.
How to propage posterior uncertainty to R-squared in R and JAGS.
One quick way to improve reporting of interaction effects in linear models.
Comparing distributions with split violin plots in R.
Fitting a regression model with uncertainty in the explanatory variable.
Experimenting with an agent based model of habitat diversity and species richness in R.
Creating an interactive two host SIR model in R and shiny.
Building an interactive stage-structured population model in R with shiny.
Multi-species, multi-timestep occupancy model in R and JAGS
If you see mistakes or want to suggest changes, please create an issue on the source repository.
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/mbjoseph/mbjoseph.github.io, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".