Nature, in Code

Epidemics: A Spatial Simulation

This is a spatial simulation of an epidemic using the SIR (susceptible, infected, recovered) model. It uses the following color code:

susceptible
infected
recovered

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Code

var grid_length = 75;
// Note that grid_length in the book is 100.
// I reduced it here for smooth performance on mobile devices.
var grid = [];
var temp_grid = [];
var beta = 0.05;
var gamma = 0.1;

function get_random_int(min, max) {
	return Math.floor(Math.random() * (max - min + 1)) + min;
}

function init_grid() {
	for (var i = 0; i < grid_length; i = i + 1) {
		grid[i] = [];
		for (var ii = 0; ii < grid_length; ii = ii + 1) {
		   grid[i][ii] = "S";
		}
	}
	grid[get_random_int(0,grid_length-1)][get_random_int(0,grid_length-1)] = "I";
}

init_grid();

draw_grid(grid,["S","#dcdcdc","I","#c82605","R","#6fc041"]);

function simulate_and_visualize() {
	run_time_step();
	update_grid(grid,["S","#dcdcdc","I","#c82605","R","#6fc041"]);
}

setInterval(simulate_and_visualize, 50);

function run_time_step() {
	for (var i = 0; i < grid_length; i = i + 1) {
		temp_grid[i] = [];
		for (var ii = 0; ii < grid_length; ii = ii + 1) {
			temp_grid[i][ii] = grid[i][ii];
		}
	}
	for (i = 0; i < grid_length; i = i + 1) {
		for (ii = 0; ii < grid_length; ii = ii + 1) {
			if (grid[i][ii] == "I") {
				expose_neighbors(i,ii);
				try_recovery(i,ii);
			}
		}
	}
	for (i = 0; i < grid_length; i = i + 1) {
		for (ii = 0; ii < grid_length; ii = ii + 1) {
			grid[i][ii] = temp_grid[i][ii];
		}
	}
}

function expose_neighbors(i,ii) {
	for (var n_i = i-1; n_i <= i+1; n_i = n_i + 1) {
		for (var n_ii = ii-1; n_ii <= ii+1; n_ii = n_ii + 1) {
			if (n_i == i && n_ii == ii) {
				continue;
			}
			try_infection(get_bounded_index(n_i),get_bounded_index(n_ii));
		}
	}
}

function get_bounded_index(index) {
	var bounded_index = index;
	if (index < 0) {
		bounded_index = index + grid_length;
	}
	if (index >= grid_length) {
		bounded_index = index - grid_length;
	}
	return bounded_index;
}

function try_infection(i,ii) {
	if (grid[i][ii] == "S") {
		if (Math.random() < beta) {
			temp_grid[i][ii] = "I";
		}
	}
}

function try_recovery(i,ii) {
	if (grid[i][ii] == "I") {
		if (Math.random() < gamma) {
		   temp_grid[i][ii] = "R";
		}
	}
}			
			

Note: the draw_grid and update_grid functions are built with D3.js and can be found here.