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.

#### 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.