Compartmental epidemic models for forecasting and analysis of infectious disease pandemics: contributions from Ben Bolker, Jonathan Dushoff, David Earn, Morgan Kain, Michael Li, Irena Papst (in alphabetical order). Feedback is welcome at the issues list, or e-mail us.
The repository contains an R package and various workflows/analyses. You can fork/clone the repository (from here) and install locally or use
remotes::install_github("mac-theobio/McMasterPandemic") to install the package. You will need to first install the developer version of
remotes::install_github("bbolker/bbmle")) before installing
dockerfilefor details on Debian Linux)
make dependenciesor running
make doc-updateto update the
make pkgtestfrom the shell or
devtools::test()from within R). (Tests are also run on GitHub Actions; if you want to skip CI testing, e.g. for a trivial commit, put
[skip ci]somewhere in your commit message.) Please don’t make a habit of pushing without testing.
make styleor run
make style(or running
misc/macpan_lint.R) also creates a new file,
misc/lints.csv, which contains stylistic and other lints that
stylercannot automatically fix.
pkgdownsite using GitHub Actions: click “run workflow” on the link to rebuild.
MACPAN_TEST_LEVELenvironment (shell) variable. Many of the test files contain this code:
testLevel to a default value of 1 unless the environment variable is found. You can set this environment variable outside of your R session (e.g. via
export MACPAN_TEST_LEVEL=2 in a bash shell), or via
Sys.setenv(MACPAN_TEST_LEVEL=2) from within R. In principle this mechanism allows for a hierarchy of slowness; at present only 1 and >1 are distinguished.
The documentation is a little bit scattered right now, working on cleaning it up. In addition to the standard short descriptions of the functions (
help(package="McMasterPandemic")), stuff can be found:
model: design decisions and information for developers
calibration(very out of date)
farr: stuff on Farr’s law and phenomenological curve-fitting (very incomplete and likely to remain so for now)
testing_flow: incorporating testing dynamics (ditto)
McMasterReport.Rnw: this is a more or less up-to-date description of calibration to Ontario data
ontario_calibration_report.html: more technical and less up-to-date than the preceding document
TODO.md: active to-do list
More bits and pieces: