md`## Simulation code`
simulation_results = {
rerun_simulation;
const states = [];
states[0] = initialize_simulation(edge_list(graph));
for(let timestep = 1; timestep < timesteps; timestep++) {
states[timestep] = tick_simulation(states[timestep - 1], edge_list(graph));
}
return states;
}
initialize_simulation = function(edge_list) {
const state = {
node_states: [],
time_in_state: [],
infection_pathways: []
};
// Set all nodes to susceptible
for(let i = 0; i < edge_list.length; i++) {
state.node_states[i] = STATES.SUSCEPTIBLE;
state.time_in_state[i] = 0;
}
// Pick random nodes to be infected
const shuffled = Array.from({length: N}, (_, i) => i).sort(() => 0.5 - Math.random());
const selected = shuffled.slice(0, num_infected_initialization);
for(let index in selected) {
state.node_states[index] = STATES.INFECTED;
state.time_in_state[index] = 0;
}
return state;
}
tick_simulation = function(state, edge_list) {
const new_state = { node_states: state.node_states.slice(0),
time_in_state: state.time_in_state.slice(0),
infection_pathways: []};
// Update time spent in state
for(let i = 0; i < edge_list.length; i++) {
new_state.time_in_state[i] = state.time_in_state[i] + 1;
}
// Loop through each individual
for(let i = 0; i < edge_list.length; i++) {
if(state.node_states[i] == STATES.INFECTED) {
// If they have been infected for N timesteps, set them back to susceptible
if(state.time_in_state[i] == time_infected) {
new_state.node_states[i] = STATES.RECOVERED;
new_state.time_in_state[i] = 0;
}
// If they are still infected, infect their neighbors
for(let j = 0; j < edge_list[i].length; j++) {
if(state.node_states[edge_list[i][j]] == STATES.SUSCEPTIBLE && Math.random() < infection_probability) {
new_state.node_states[edge_list[i][j]] = STATES.INFECTED;
new_state.time_in_state[edge_list[i][j]] = 0;
new_state.infection_pathways.push({
source: i,
target: edge_list[i][j]
});
}
}
}
if(state.node_states[i] == STATES.RECOVERED && state.time_in_state[i] == time_recovered) {
new_state.node_states[i] = STATES.SUSCEPTIBLE;
new_state.time_in_state[i] = 0;
}
}
return new_state;
}
STATES = ({
SUSCEPTIBLE: 0,
INFECTED: 1,
RECOVERED: 2
});
color = (node_state) => {
if(node_state == STATES.INFECTED) return palette.pomegranate;
if(node_state == STATES.RECOVERED) return palette.belize_hole;
if(node_state == STATES.SUSCEPTIBLE) return palette.concrete;
}
import {Scrubber} from "@mbostock/scrubber"
import { palette } from "@herbps10/flat-ui-colors"
Purpose-built for displays of data
Observable is your go-to platform for exploring data and creating expressive data visualizations. Use reactive JavaScript notebooks for prototyping and a collaborative canvas for visual data exploration and dashboard creation.
