Solves a stochastic SEIR model for disease progression. SanSEIR reproduces the results presented in the paper

Yao Yu Yeo, Yao-Rui Yeo, Wan-Jin Yeo, A Computational Model for Estimating the Progression of the COVID-19 Cases in the US West and East Coasts, MedRxiv, https://doi.org/10.1101/2020.03.24.20043026

Sample results based on the inputs of Yeo et al. are given in the yeo-etal directory.

To build with gfortran simply:

make

You will need to modify the Makefile if you use a different FORTRAN compiler. Once you have sanseir build, to run simply pass the input file (in FORTRAN namelist format) as an argument

cd yeo-etal/usa
../../sanseir.exe usa.inp

This generates an ensemble of 50 runs with output files called output.*, scaled.*, rates.*.

These can be plotted using gnuplot. For example, to plot the cummulative deaths

gnuplot
plot for [i=1:50] file=sprintf("output.%d",i) file using 1:12 w l lt 'grey' title ""

There are a number of gnuplot scripts for making typical plots in the plot directory.

For example, to make the West Coast plot shown at the bottom of this page, do the following

cd yeo-etal/west
../../sanseir.exe west.inp
gnuplot
load "../../plot/all-infected.com"

S. Scott Collis\