These are notes from a short course given by Ed Ionides and Aaron King at the Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID). From the main page, links lead to pages on a number of specific topics, culminating in four case studies that exemplify the methods and raise key issues. For each such page, there is a corresponding R script, which contains the codes needed to recapitulate the calculations. This script is a starting point for students to follow, explore, and modify the analysis according to their own curiosity and interest.
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.
The prep directory contains scripts that will install other needed
packages and test the user’s installation.
The following R packages are needed to build the materials, but are not used in the materials:
- revealjs
- diagram
- mapproj
The contacts lesson requires
panelPomp. An installation
script is provided there.
A Github Action checks that these installations and actions succeed on a variety of current and legacy platforms:
- index.md, index.html: Landing page
- acknowledge.md, acknowledge.html: Acknowledgements
- subdirectories:
- prep: Lesson 0, on preparing for the course
- intro: Lesson 1
- stochsim: Lesson 2
- pfilter: Lesson 3
- mif: Lesson 4
- measles: Lesson 5
- polio: Lesson 6
- ebola: Lesson 7
- contacts: Lesson 8
- od: Lesson from an earlier version of the course
- misc: Miscellaneous lessons
- _includes: latex, HTML, R files included in other files
- graphics: figures in various formats
- LICENSE.md: Full text of license
- TODO.md: To-do list
- Makefile, rules.mk: GNU Make files
- sbied.bib: Bibliography database
- jss.bst, jss.csl: Bibliography style files
- CLUSTER.R: example
CLUSTER.Rfile for site-specific cluster setup
Full compilation of all the materials can be accomplished by running
make in the root directory. This requires substantial resources. For
this reason, the most expensive computations are archived using the
facilities provided for the purpose in pomp. Compilation with these
archives in place requires much less time than does compilation from
scratch. The following gives an indication of the size of the archives
and the time required for their computation on a linux cluster with
250 cpus.
| directory | size (kB) | time (min) |
|---|---|---|
| measles/results | 340 | 224.0 |
| mif/results | 2244 | 67.6 |
| polio/results | 41687 | 65.6 |
| polio/initial-values-exercise/results | 41635 | 64.3 |
| polio/starting-values-exercise/results | 41687 | 64.2 |
| contacts/results | 206 | 13.7 |
| pfilter/results | 142 | 13.2 |
| polio/runlevel2/results | 3266 | 4.8 |
| polio/runlevel1/results | 612 | 0.8 |
| ebola/results | 2259 | 0.4 |
The archives amount to about 131 MB. About 126 MB of this is associated with the polio lesson, in which large amounts of redundant information are stored.
Full compilation, i.e., rebuilding the complete set of materials following deletion of all archives, requires about 534 min on a 250-processor cluster. Full compilation regenerates the complete set of archives. A finishing compilation, i.e., rebuilding with all archives in place, but with the re-Making of all documents, requires about 12 min on a 64-cpu workstation.
This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). Under its terms, you are free to:
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- Adapt — remix, transform, and build upon the material
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- No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.
The licensor cannot revoke these freedoms as long as you follow the license terms.