MetaCast

A package for broadCASTing epidemiological and ecological models over META-populations.

Summary

MetaCast is a python package for broadcasting epidemiological and ecological ODE based models over metapopulations (structured populations). Users first define a function describing the subpopulation model. MetaCast's users then define the dimensions of metapopulations that this subpopulation is broadcast over. These dimensions can be flexibly defined allowing for multiple dimensions and migration (flows) of populations between subpopulations. In addition to the metapopulation suite MetaCast has several features. A multinomial seeder allows users to randomly select infected stages to place an infected population in based on the occupancy time of infected states. MetaCast's event queue suite can handle discrete events within simulations, such as movement of populations between compartments and changes in parameter values. Sensitivity analysis can be done in MetaCast using parallelisable Latin Hypercube Sampling and Partial Rank Correlation Coefficient functions. All of this makes MetaCast an ideal package not only for modelling metapopulations but for wider scenario analysis.

Installation

Requirements

Python 3.10 and pip. Package requirements:

• numpy >= 1.26.3
• pandas >= 2.1.4
• scipy >= 1.11.4
• pingouin >= 0.5.4
• tqdm >= 4.66.1
• dask >= 2024.2.1
• distributed >= 2024.2.1

For running demonstration jupyter notebooks

• bokeh >= 3.3.4
• seaborn >= 0.13.2
• jupyter >= 1.0.0

Installing via pip

Note this should also install required packages.

pip install metacast

Usage

See jupyter notebooks in demonstration directory of the projects GitGub repository: https://github.com/m-d-grunnill/MetaCast/tree/main/demonstrations

Documentation

https://metacast.readthedocs.io/en/latest/index.html

Citation & Paper

Grunnill et al., (2024). MetaCast: A package for broadCASTing epidemiological and ecological models over META-populations.. Journal of Open Source Software, 9(99), 6851, https://doi.org/10.21105/joss.06851

Contributing

If you wish to contribute to this project please see the CONTRIBUTING.md file.