epid-814-materials

Readings

• Compartmental Models and DAGs - Discussion paper

• Firth’s Penalized Likelihood - Heinze & Schemper, 2002

• ggplot tutorials

  • Nice, comprehensive ggplot tutorial

  • Another tutorial, and an introductory course on datacamp

  • Mapping with ggplot

• Some nice posts on Bayesian stuff

  • Overview of Metropolis & MCMC

  • Also this one

  • Overview of conjugate priors

• Andrew’s overview of thinking about linear algebra, the next generation matrix, and R0

  • A linear algebraic approach to understanding the basic reproduction number (Andrew Brouwer)
• MCMC, Bayesian estimation, etc (more to be added here soon)

  • Markov Chain Monte Carlo: an introduction for epidemiologists

  • Custom distributions in Stan

• Useful info on the BayesianTools R package

  • BayesianTools on CRAN

  • Some vignettes from the package documentation - includes tutorial examples and illustrates how to use different sampling methods.

  • A nice, short blog post with a quick introduction

  • More vignettes](https://rdrr.io/cran/BayesianTools/f/vignettes/BayesianTools.Rmd)

• Latin Hypercube Sampling and Sensitivity Analysis

  • Marino et al., 2008

  • Morris and Mitchell, 1995

• Useful Agent Based Modeling Resources