These are notes, scripts, and quarto files from a short course given by Spencer J. Fox and Qianying Lin at Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID), starting from 2024. All codes and notes are adapted from a previous version developed by Aaron King and Ed Ionides. From the course page published based on the current repo, panels lead to topics corresponding to sessions in the course. Within each panel, R scripts and the corresponding dataset are included to reproduce results discussed in course. These scripts help students understand, digest, explore, and modify the models, results, and analyses out of their interest and curiosity.
The codes require, at a minimum, R version 4.2 and pomp version 5.2 Windows users must also have the appropriate version of Rtools installed.
Several other packages are required to perform data manipulation, visualization, and analyses:
- tidyverse
- reshape2
- ggplot2
- cowplot
- foreach
- doFuture / doParallel
- microbenchmark
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