This repository contains utilities to determine the parameters to use in a OO simulation based on the disease, simulation constraints, and estimated social mixing parameters:
- The spreadhseet (par-calculator.xlsx) that generates OO parameters given simulation features and pathogen.
- The R script (seir-analysis.Rmd) can be used to run plausible outcomes of OO simulations with the generated parameters from the spreadsheet under the assumption of a basic SEIR model. To use, plug the beta, gamma, and delta parameters generated by the parameter calculator in the sim.properties file (use the simulations/tb case as a template).
- The Python notebook (index_case_probs.ipynb) is useful to evaluate the probability of no index cases ocurring in an OO simulation given the desired number of index cases set in the parameters.
- Epi Cookbook: http://epirecip.es/epicookbook/
- POMP package: https://kingaa.github.io/pomp/
- Model-based Inference in Ecology and Epidemiology: http://kingaa.github.io/short-course/
- Simulation of stochastic dynamic models: https://kingaa.github.io/short-course/stochsim/stochsim.html
- Iterated filtering: principles and practice: http://kingaa.github.io/short-course/mif/mif.html
- Simulation-based Inference for Epidemiological Dynamics: https://kingaa.github.io/sbied/index.html