Data Scientist passionate with making colourful shapes appear and move on my computer screen.
Published
Edited
May 21, 2021
2 stars
n_steps = 300
experiments_parameters = ({
beta: [0.3, 0.3, 0.3],
gamma: [0.01],
theta: [0.001],
delta: [0.01],
initial_infected: [50],
initial_immune_perc: [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
})
/**
* - S: susceptible; can be infected
* - I: infected; can infect others, recover, or die
* - R: recovered; immune, can become susceptible again
* - D: dead
*/
class Society {
constructor(input_data, desease_data = null) {
this.pop_data = input_data;
this.historical = [];
this.historical.push(this.make_historical_entry());
for (const node of this.pop_data.nodes) {
node.status = "S";
}
if (!desease_data) {
this.desease_transmission_rate = desease_values[0][0];
this.desease_recovery_rate = desease_values[1][0];
this.desease_susceptibility_rate = desease_values[2][0];
this.desease_death_rate = desease_values[3][0];
} else {
this.desease_transmission_rate = desease_data.beta;
this.desease_recovery_rate = desease_data.gamma;
this.desease_susceptibility_rate = desease_data.theta;
this.desease_death_rate = desease_data.delta;
}
}
// the percentage of immune people will take priority if both n_immune_initial and n_immune_initial_perc are specified
init(
n_infected_initial = 1,
n_immune_initial = 0,
n_immune_initial_perc = null
) {
this.pop_data.nodes = underscore.shuffle(this.pop_data.nodes);
if (n_immune_initial_perc)
n_immune_initial = n_immune_initial_perc * this.pop_data.nodes.length;
for (const i in this.pop_data.nodes) {
if (i < n_infected_initial) {
this.pop_data.nodes[i].status = "I";
} else if (i < n_infected_initial + n_immune_initial) {
this.pop_data.nodes[i].status = "R";
} else {
this.pop_data.nodes[i].status = "S";
}
}
}
data() {
return this.pop_data;
}
update() {
this.historical.push(this.make_historical_entry());
for (const node of this.pop_data.nodes) {
if (node.status == "S") {
for (const link of this.pop_data.links) {
// link has this node
if (link.source == node || link.target == node) {
const other = link.source == node ? link.target : link.source;
if (other.status == "I") {
// linked node can infect
if (Math.random() < this.desease_transmission_rate) {
node.status = "I";
}
}
}
}
} else if (node.status == "I") {
if (Math.random() < this.desease_recovery_rate) {
node.status = "R";
} else if (Math.random() < this.desease_death_rate) {
node.status = "D";
}
} else if (node.status == "R") {
if (Math.random() < this.desease_susceptibility_rate) {
node.status = "S";
}
}
}
}
make_historical_entry() {
return {
t: this.historical.length,
deaths: this.perc_deaths(),
infected: this.perc_infected()
};
}
count_susceptibles() {
return this.pop_data.nodes.reduce(
(acc, cur) => (cur.status == "S" ? acc + 1 : acc),
0
);
}
perc_infected() {
return (
this.pop_data.nodes.reduce(
(acc, cur) => (cur.status == "I" ? acc + 1 : acc),
0
) / this.pop_data.nodes.length
);
}
perc_deaths() {
return (
this.pop_data.nodes.reduce(
(acc, cur) => (cur.status == "D" ? acc + 1 : acc),
0
) / this.pop_data.nodes.length
);
}
}
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Type JavaScript, then Shift-Enter. Ctrl-space for more options. Arrow ↑/↓ to switch modes.
map_color = function(status) {
if (status == 'S') return in_values[2][0];
if (status == 'I') return in_values[2][1];
if (status == 'R') return in_values[2][2];
if (status == 'D') return in_values[2][3];
}
society_example = new Society(initial_network)
init_btn = in_values[1][0]
initialize_example = {
init_btn;
society_example.init(in_values[0][0], in_values[0][1]);
}
step_btn = sim_values[0][0]
step_example = {
step_btn;
society_example.update();
}
function transform_data(list_of_edges) {
var nodes = [];
var links = list_of_edges.map(x => {
if (x.source == x.target) return null; // skip self-connections
// create nodes
if (!nodes.map(x => x.id).includes(x.source)) nodes.push({ id: x.source });
if (!nodes.map(x => x.id).includes(x.target)) nodes.push({ id: x.target });
return {
source: nodes.find(y => y.id == x.source),
target: nodes.find(y => y.id == x.target)
};
});
return { nodes: nodes, links: links };
}
input_net_csv = get_net(in_values[1][1])
// data from http://networkrepository.com/soc-dolphins.php
get_net = (key) => {
if (key == "test")
return [
{ source: 1, target: 2 },
{ source: 2, target: 3 },
{ source: 2, target: 4 },
{ source: 3, target: 4 },
{ source: 3, target: 5 },
{ source: 4, target: 6 },
{ source: 5, target: 7 }
];
if (key == "small")
return FileAttachment("ba_small@2.csv").csv({
typed: true
});
if (key == "big")
return FileAttachment("ba_big@2.csv").csv({
typed: true
});
}
initial_network = transform_data(input_net_csv)
height = 600
d3 = require("d3@6")
Inputs = require("@observablehq/inputs@0.7.21/dist/inputs.umd.min.js")
import { color } from "@jashkenas/inputs"
import { inputsGroup } from "@bumbeishvili/input-groups"
// https://stackoverflow.com/a/43053803/5599687
cartesian = (...a) =>
a.reduce((a, b) => a.flatMap((d) => b.map((e) => [d, e].flat())))
underscore = (await import("https://unpkg.com/underscore@1.10.1/modules/index-all.js"))
.default
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