The avatar for @nstrayer
Nick Strayer
Engineer on the Shiny team at RStudio. Biostats Ph.D. from Vanderbilt.
Published
Edited
May 11, 2020
6 forks
58 stars
Coronavirus
Andy's Walgreens COVID-19 Tracker TrackerBelgium Vaccination Tracker - Progress of the vaccination campaignVaccination against covid-19 in France500,000 COVID-19 DeathsCovid-19 vaccinations: BubblesTime Spiral with a COVID DemoCOVID MasksGrid Cartogram component with live COVID demos (plus a MapEditor)The US COVID SyringeCOVID-19 DKCOVID-19 World Community Mobility Report by GoogleCOVID 19Chicago COVID ZIP SparklinesThe COVID Syringeభారతదేశంలో కోవిడ్-19SVG DataGrid with many features and a live COVID Dashboard demoThe spread of Covid-19 in New MexicoHeatmap of COVID-19 Confirmed Cases by Age over Time in JapanThe CoViD-19 ReportCovid19 WorldwideMassachusetts Coronavirus Cases by TownChoropleth map about Covid19 in FranceWell ordered coronavirus heatmaps for US and the WorldCOVID-19 Racial/Ethnic Mortality AnalysisProPublica's COVID Arrow MapClustering students to slow virus spread inside schoolsCOVID-19 in the USAWho Is Wearing Masks in the U.S.Covid-19 Viz RoundupCoronavirus StatsThe Covid-19 Crisis' Impact on the Number of US Flight PassengersCOVID-19 Daily New CasesCOVID-19 CasesCOVID–19 Bubble Chart with D3 RenderCoronavirus Deaths by Race / EthnicityHow many SARS-CoV-2 tests are we running in the U.S.?COVID-19 Onset vs. ConfirmationPeaks in confirmed daily deaths due to COVID-19 so farCOVID-19 in the U.S.Recreating John Burn-Murdoch’s Coronavirus trackerTracking COVID-19 Cases in VietnamCOVID-19 in NYC by Zip Code & IncomeVisualizing the Network Meta-Analysis of Covid-19 Studiesxkcd COVID-19 spread sketchCOVID-19's deaths in EuropeCovid-19 (corona virus) deaths per 1,000,000 peopleCOVID-19 Bubble map or spike map? (Twitter debate)A Timeline of Shelter-in-PlaceWhere’s that $2 trillion going?Estimating SARS-COV-2 infectionsCODAVIM - CountySARS-CoV-2 Epi CurveCOVID-19 Curves (U.S.)COVID-19 Cases by CountyCOVID-19 world growth rate
A graphical experiment of exponential spread
COVID-19 by US countyCOVID-19 Confirmed vs. New cases"Live" Logistic Coronavirus Death CounterInfografiche: COVID-19 in ItaliaCoronavirus (COVID-19) GlobeBar Chart Race, COVID-19 outbreak Worldwide to 24th March 2020US Coronavirus testing by statesUnited States Coronavirus Daily Cases Map (COVID-19)COVID-19 Numbers by State, Side by SideRecreating NYT U.S. Cases MapCOVID-19 in Washington stateCOVID-19 outbreak in maps and chartsCOVID-19 Spreading trendsRestaurants during COVID-19 social distancingCOVID-19 Countries Trajectories in 3DStates that aren't reporting aspects of their COVID-19 testing processNextstrain Prototyping - Issue 817Reviewing COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxivCoronavirus worldwide evolutionCovid-19 New Cases PunchcardCovid-19 cases per district in Germany.COVID-19 Cases, Deaths, and Recoveries (Select Country)Quarantine NowEmissions in WuhanCOVID-19(nCOV-2019) Outbreak in S.KoreaMovement of population between provinces in 2019-nCoVComparing COVID-19 GrowthCovid-19 derived chartCoronavirus Trends (COVID-19)Netherlands Coronavirus Daily Cases Map (COVID-19)Map and timeline of Corona outbreakSARS-CoV-2 Phylogenetic TreeCoronavirus data (covid-19)Visualizing the Logic of Exponential Viral SpreadItaly Coronavirus Daily Cases Map (COVID-19)COVID-19 Fatality Rate
Also listed in…
simulations
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sim
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sim_results = sim.run_simulation(simulation_parameters, initial_infections)
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sim = setup_infection_sim_full(data_gen_parameters)
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function setup_infection_sim_full(data_params){
// Generate network data
const {nodes, edges, node_quadtree} = generate_network_data(
data_params.num_nodes.val,
build_poisson_mixture([
{mean: data_params.avg_num_edges.val, size: 1 - data_params.prop_popular_nodes.val},
{mean: data_params.avg_num_edges_pop.val, size: data_params.prop_popular_nodes.val}
])
);

function* run_simulation(sim_params, initial_infections = [], sim_speed = 1){

let time = 1;
const hist = [{
total_infections: initial_infections.length,
new_infections: initial_infections,
n_new: initial_infections.length,
potential_infectors: initial_infections.length,
time: time++
}];

// Reset all nodes before starting
nodes.forEach(node => {
node.infected = false;
node.inactive = false;
node.time_infected = -1;
node.uninfected_neighbors = [...node.neighbors];
});

// Setup the initial infecting nodes
initial_infections.forEach(id => {
const node = nodes[id];
node.infected = true;
node.time_infected = time;

// Create an array of potential neighbors to infect, make sure to not include already infected nodes
node.uninfected_neighbors = node.neighbors.filter(n => !(initial_infections.includes(n.id)));
});

// State vectors that keep track of what nodes are in what states
const potential_infectors = new Set(initial_infections);
const infections = new Set(initial_infections);

while(potential_infectors.size > 0 && infections.size < nodes.length) {
const no_longer_infecting = [];
const new_infections = new Set();

const expose_node = node => {
const was_infected = Math.random() < sim_params.prob_of_infect.val;
if(was_infected) new_infections.add(node.id);
};

potential_infectors.forEach(id => {
const node = nodes[id];

// Exposes all the node's neighbors
node.uninfected_neighbors.forEach(expose_node);

// Does this node randomly expose a "long edge"?
const has_long_edge = Math.random() < sim_params.prob_of_long_edge.val;
if (has_long_edge){
const random_node = nodes[Math.floor(Math.random() * nodes.length)];
const is_infectable = !(random_node.id === node.id || random_node.infected);
if(is_infectable) expose_node(random_node);
}

// Will node no longer be infections at the next time point?
if(time >= node.time_infected + sim_params.contagious_period.val) no_longer_infecting.push(id);
});

const set_inactive = id => {
nodes[id].inactive = true;
potential_infectors.delete(id);
}

// Remove nodes neighbors infected or have been infected for time period from potential infectors
no_longer_infecting.forEach(set_inactive);

// Run through newly infected nodes and set to infected
new_infections.forEach( id => {
infections.add(id);

const node = nodes[id];
node.infected = true;
node.time_infected = time;

// Create an array of potential neighbors to infect, make sure to not include already infected nodes
node.uninfected_neighbors = node.neighbors.filter(n => !(n.infected || new_infections.has(n.id)));

// Node can only infect others if it has neighbors that are not already infected
if(node.uninfected_neighbors.length !== 0) potential_infectors.add(id);

// Go to all of this node's neighbors and remove itself from their list of nodes they could infect
node.neighbors.forEach(neighbor => {
neighbor.uninfected_neighbors = neighbor.uninfected_neighbors.filter(n => n.id !== id);

if(neighbor.uninfected_neighbors.length == 0) set_inactive(neighbor.id);
});
});

// Update state history
hist.push({total_infections: infections.size,
new_infections: [...new_infections],
n_new: new_infections.size,
potential_infectors: potential_infectors.size,
time: time});

yield Promises.tick(sim_speed, {ids: [...infections],
history: hist,
timestep: time++,
running: true,
settings: sim_params,
status: "running"});
}
yield Promises.tick(sim_speed, {ids: [...infections],
history: hist,
timestep: hist.length,
settings: sim_params,
status: hist.length == 1 ? "waiting": "finished"});
}

return {nodes,
edges,
node_quadtree,
run_simulation,
settings: data_params};
}
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colors = {
const early_infection = "#990000";
const late_infection = "#fc8d59";
const infected = "#e41a1c";
const healthy = "#377eb8";
const safe_edge = "#d9d9d9";
const interactive = "#2690ce";
const inactive = change_brightness(infected, -1);
const newly_infected = change_brightness(infected, 1);
const danger_edge = d3.interpolateHslLong(safe_edge, infected)(0.5);
const inactive_edge = d3.interpolateHslLong(safe_edge, inactive)(0.1);
return {infected,
inactive,
newly_infected,
healthy,
safe_edge,
inactive_edge,
danger_edge,
interactive,
early_infection,
late_infection};
}
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mutable data_gen_parameters = ({
num_nodes: {
val: 3000,
min: 1000,
max: 15001,
step: 100,
int: true,
},
avg_num_edges: {
val: 8,
min: 1,
max: 25,
step: 0.1,
},
avg_num_edges_pop: {
val: 25,
min: 10,
max: 100,
step: 0.1,
},
prop_popular_nodes: {
val: 0.2,
min: 0,
max: 1,
step: 0.01,
percent: true,
}
});
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mutable simulation_parameters = ({
prob_of_infect: {
val: 0.15,
min: 0.01,
max: 0.99,
start: 0.15,
step: 0.01,
},
prob_of_long_edge:
{
val: 0,
min: 0,
max: 0.2,
start: 0,
step: 0.005,
},
contagious_period: {
val: 10,
min: 1,
max: 30,
start: 10,
step: 1,
int: true,
}
});
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