McMasterPandemic
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.
Installation
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("bbolker/McMasterPandemic")
to install the package. You will need to first install the developer version of bbmle
(remotes::install_github("bbolker/bbmle")
) before installing McMasterPandemic
.
For developers
- to re-install the package, including re-building and incorporating vignettes, use
make build
- If you modify function arguments, you should change the roxygen documentation accordingly. If you change the roxygen documentation, please use
make doc-update
to update the.Rd
files. - please test/check the package periodically as you go (use
make pkgcheck
andmake pkgtest
from the shell ordevtools::check()
anddevtools::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. - Code that is used in the refactoring process should go in the top-level refactor folder.
Documentation
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:
- in the vignettes (look at the source code in the [vignettes] directory or
vignette(<title>, package="McMasterPandemic")
)getting_started
model
: design decisions and information for developerscalibration
(very out of date)farr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 dataontario_calibration_report.html
: more technical and less up-to-date than the preceding documentTODO.md
: active to-do list- issues list on github
More bits and pieces: notes/refactor.Rmd
, testing.md
, reimplementation.md
DISCLAIMER
All use of this package is at your own risk. Quantitative forecasts are only as good as their parameter estimates.