This repo contains code for investigating the potential efficacy of vaccination allocation for a disease interactively via a streamlit app using a next generation matrix approach.
- Enable poetry with
poetry install - To run the app:
make, which callsstreamlit run scripts/widget.py
- Build and tag the image:
podman build -t ngm . - Run the container:
podman run -p 8501:8501 --rm ngm - Note the port 8501 is hard-coded in the
Dockerfile - In a browser, visit:
http://localhost:8501/
The build and run process can also be executed using the build_container and run_container targets in the included Makefile.
This repo contains code to apply the next-generation method of Diekman et al. (1990) to calculate R0 for an SIR model with 3 risk groups and flexible inputs for varying vaccine allocation to each group.
The next-generation matrix approach (NGM) is described in docs/ngm.md.
The documentation is best viewed off of GitHub, either by opening in VSCode and using the built in markdown preview or by building with mkdocs using mkdocs serve (this requires installing mkdocs).
Vaccination is assumed to be all or nothing -- each individual's immunity is determined by a coin flip with probability of being immune equal to the vaccine efficacy.
The widget is designed to let users modify vaccine allocation choices, measures of between- and within-group spread, population composition, and see how this effects
Specific inputs to and outputs from the widget are documented therein.
Diekmann O, Heesterbeek JA, Metz JA. On the definition and the computation of the basic reproduction ratio R0 in models for infectious diseases in heterogeneous populations. J Math Biol. 1990;28(4):365-82. doi: 10.1007/BF00178324. PMID: 2117040.
Diekmann O, Heesterbeek JA, Roberts MG. The construction of next-generation matrices for compartmental epidemic models. J R Soc Interface. 2010 Jun 6;7(47):873-85. doi: 10.1098/rsif.2009.0386. Epub 2009 Nov 5. PMID: 19892718; PMCID: PMC2871801.
van den Driessche P, Watmough J. Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. Math Biosci. 2002 Nov-Dec;180:29-48. doi: 10.1016/s0025-5564(02)00108-6. PMID: 12387915.
- Paige Miller [email protected]
- Scott Olesen [email protected]
- Andy Magee [email protected]
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