Nature, in Code

A Spatial Model of Inbreeding

When individuals mate with genetically similar individuals, inbreeding is the consequence. In this stochastic, individual-based spatial simulation, individuals can only mate with their immediate local neighbors.

RELOAD SIMULATION

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 p = 0.5;
var grid = [];
var max_mating_distance = 1; // change to 50 for global mating
var A1A1 = 0;
var A1A2 = 0;
var A2A2 = 0;
var generation_counter = 0;

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) {
			var random_number = Math.random();
			if (random_number < p*p) {
		        grid[i][ii] = "A1A1";
				A1A1 = A1A1 + 1;
			}
			else if (random_number > 1 - (1-p) * (1-p)) {
				grid[i][ii] = "A2A2";
				A2A2 = A2A2 + 1;
			}
			else {
				grid[i][ii] = "A1A2";
				A1A2 = A1A2 + 1;
			}
		}
	}
	console.log(A1A1, A1A2, A2A2);
}

init_grid();

draw_grid(grid);

function simulate_and_visualize() {
	run_generation();
	update_grid(grid);
}
setInterval(simulate_and_visualize, 100);

function run_generation() {
	var temp_grid = [];
	for (var i = 0; i < grid_length; i = i + 1) {
		temp_grid[i] = [];
		for (var ii = 0; ii < grid_length; ii = ii + 1) {
			var mating_partner = pick_mating_partner(i,ii);
			temp_grid[i][ii] = get_offspring(grid[i][ii],mating_partner);
		}
	}
	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];
		}
	}
	print_data();
	generation_counter = generation_counter + 1;
}

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

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 pick_mating_partner(i, ii) {
	var j   = get_random_int(i-max_mating_distance, i+max_mating_distance);
	var jj  = get_random_int(ii-max_mating_distance, ii+max_mating_distance);
	j  = get_bounded_index(j);
	jj = get_bounded_index(jj);
	return grid[j][jj];
}

function get_offspring(parent1, parent2) {
	var p1 = parent1;
	var p2 = parent2;
	if (p1 == "A1A1" && p2 == "A1A1") {
		return "A1A1";
	}
	else if ((p1 == "A1A1" && p2 == "A1A2") || (p1 == "A1A2" && p2 == "A1A1")) {
		if (Math.random() < 0.5) {
			return "A1A1";
		}
		else {
			return "A1A2";
		}
	}
	else if ((p1 == "A1A1" && p2 == "A2A2") || (p1 == "A2A2" && p2 == "A1A1")) {
		return "A1A2";
	}
	else if (p1 == "A1A2" && p2 == "A1A2") {
		var random_number = Math.random();
		if (random_number < 0.25) {
			return "A1A1";
		}
		else if (random_number > 0.75){
			return "A2A2";
		}
		else {
			return "A1A2";
		}
	}
	else if ((p1 == "A1A2" && p2 == "A2A2") || (p1 == "A2A2" && p2 == "A1A2")) {
		if (Math.random() < 0.5) {
			return "A1A2";
		}
		else {
			return "A2A2";
		}
	}
	else if (p1 == "A2A2" && p2 == "A2A2") {
		return "A2A2";
	}
 }
 
 function print_data() {
	A1A1 = 0;
	A1A2 = 0;
	A2A2 = 0;
	for (var i = 0; i < grid_length; i = i + 1) {
		for (var ii = 0; ii < grid_length; ii = ii + 1) {
			if (grid[i][ii] == "A1A1") {
				A1A1 = A1A1 + 1;
			}
			else if (grid[i][ii] == "A1A2") {
				A1A2 = A1A2 + 1;
			}
			else {
				A2A2 = A2A2 + 1;
			}
		}
	}
	console.log("generation " + generation_counter + ":");
	console.log(A1A1, A1A2, A2A2);
	var N = A1A1 + A1A2 + A2A2;
	var h_o = A1A2 / N;
	var p = ((2 * A1A1) + A1A2) / (2 * N);
	var h_e = 2 * p * (1-p);
	var F = (h_e - h_o) / h_e;
	console.log("F = " + F);
}
			

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