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.
- index.md, index.html: Landing page
- acknowledge.md, acknowledge.html: Acknowledgements
- syllabus.md, syllabus.html: Course syllabus
- welcome.md, welcome.html: Course introduction slides
- EDTsyllabus.Rmd, EDTsyllabus.html: Course syllabus with timezone offset
- 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
- header.tex: General latex preamble commands
- beamer.tex: Latex beamer preamble commands
- logo.jpg: SBIED logo
- packages.R: code for loading needed packages
- CLUSTER-kinglab.R: example
CLUSTER.Rfile for site-specific cluster setup - setup.Rmd, setup.Rnw: knitr child documents for R-markdown and R-noweb documents, respectively
- 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
- quiz: Quiz materials
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.
At last count, the archives amount to about 129MB. About 123MB of this is six files in the polio lesson, in which large amounts of redundant information are stored.
The following is a log of compilations.
- Full compilation refers to compilation following the deletion of all archives. Full compilation generates the complete set of archives.
- Finishing compilation refers to compilation with all archives in place, but with the re-Making of all documents.
| Type | Completion date | Time required | CPUs available |
|---|---|---|---|
| finishing | 2021-07-20 | 11min | 36 |
| full | 2021-07-21 | 488min | 250 |
| polio level 3 | 2021-07-21 | 150min | 250 |
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