This model simulates a multivariant SEIR epidemic with cross immunity between variants, a preimmune population and an ongoing vaccination campain, the later is untested.
A tutorial for this simulator is available on youtube: https://youtu.be/XX-6VUYhGvk
Please cite: Haschka, T., Vergu, E., Roche, B. et al. Retrospective analysis of SARS-CoV-2 omicron invasion over delta in French regions in 2021–22: a status-based multi-variant model. BMC Infect Dis 22, 815 (2022). https://doi.org/10.1186/s12879-022-07821-5
In order to use this program you need a c compilier and lapack libraries, i.e. http://www.netlib.org/lapack/
gcc -O3 -march=native execute_model.c epidemic.c rkf.c parser.c -lm -llapack -o execute-model
Performing an epidemic simulation requires a prepared input file in keyword-value format. An example can be found in example.input. The simulator generates trajectories written to standard out in tab seperated format. The first column referes to the simulation time, follwing by the S I E R compartments. Depending on how many age classes, variants you simulate you will encounter multiple columns.
./execute-model sample.input
should yield an epidemic trajectory. An a description of the model implemented as well as of the input files parameters is found in documentation/doc.pdf
This is experimental and was only developed for in house in modelling the SARS-CoV-2 epedemic.
First compile the fit program:
gcc -O3 -march=native fit-model.c epidemic.c rkf.c parser.c -lm -llapack -o fit-model
You can then fit to the example data:
fit-model fit-sample.input fit-sample.table fit-sample.out