SARS-CoV-2-Viz/data-covid.js

// SARS-CoV-2-Viz
// Animated COVID case count visualization
// Copyright 2022 Edward L. Platt <ed@elplatt.com>

const covidUrl = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv";

// Parse covid tsv
function parseCovidData(tsv, onProgress) {
    let rows = tsv.split(/[\r\n]+/);
    let keys = rows[0].split("\t");
    let dates = keys.slice(11);

    // Initialize data array
    let dataForDay = [];
    for (const date of dates) {
	dataForDay.push([]);
    }
    
    // Iterate through non-header rows
    const rowCount = rows.length - 1;
    let percent = 0;
    for (const [index, row] of rows.slice(1).entries()) {

	onProgress("0 of ${rowCount} rows");
	const rowData = tsvRowToJSON(keys, row);

	// Only update progress when it has actually changed
	let newPercent = Math.floor(100 * index / rowCount);
	if (newPercent > percent) {
	    percent = newPercent;
	}   
	
	let FIPS = rowData.FIPS;
	if (typeof(FIPS) === "undefined") {
	    continue;
	}
	FIPS = FIPS.slice(0, FIPS.indexOf(".") || FIPS.length).padStart(5, "0");

 	let lastSeven = [];
	for (const [index, date] of dates.entries()) {
	    
	    const newCases = index == 0 ?
		  parseInt(rowData[date]) :
		  parseInt(rowData[date])
		  - parseInt(rowData[dates[index - 1]]);

	    // Update array for running average
	    if (lastSeven.length == 7) {
		lastSeven.shift();
	    }
	    lastSeven.push(newCases);
	    const mean = Math.round(
		lastSeven.reduce((x, y) => x + y) / lastSeven.length);
	    
	    dataForDay[index].push({
		FIPS: FIPS,
		date: date,
		count: newCases,
		sevenDayMean: mean
	    });
	}
    }
    onProgress("${rowCount} of ${rowCount}");
    
    // Calculate maximum case count for each day
    let maxSoFar = 0;
    for (const [day, date] of dates.entries()) {

	let dayMax = Math.max(
	    ...dataForDay[day].map(
		d => d.sevenDayMean));

	maxSoFar = Math.max(maxSoFar, dayMax);

	// Add data to each county for current day
	for (let [countyIndex, d] of dataForDay[day].entries()) {
	    d.dayMax = dayMax;
	    d.maxSoFar = maxSoFar;
	}
    }

    // Convert day's data from array to object keyed on FIPS
    return dataForDay.map(data => {
	const entries = new Map(data.map(d => [d.FIPS, d]));
	return Object.fromEntries(entries);
    });
}

async function getData(onProgress) {
    const content = await fetchWithProgress(covidUrl, onProgress);
    return content;
}

async function parseData(content, onProgress) {
    onProgress("initializing...");
    let tsv = csvToTSV(
	content,
	(progress) => onProgress("parsing csv: {$progress}"));
    let dataForDay = parseCovidData(
	tsv,
	(progress) => onProgress("building data structure: {$progress}"));
    onProgress("done");
    return dataForDay;
}

/*
  Add normalization data to each data element in dataForDay.

  Parameters
  dataForDay: [{FIPS_1: d1, FIPS_2: d2, ...}, ... ]
*/
function normalizeData(dataForDay, population) {
    let maxSoFar = 0;
    let maxSoFarPer100KCap = 0;
    let normalizedForDay = [];
    
    for (const [day, data] of dataForDay.entries()) {

	let normalized = {};
	
	// Add normalized counts
	for (let [FIPS, d] of Object.entries(data)) {
	    const countyPop = population[FIPS];
	    if (FIPS
		&& countyPop
		&& !Number.isNaN(countyPop)
		&& countyPop > 0) {
		d.sevenDayMeanPer100KCap = 100000 * d.sevenDayMean / countyPop;
		normalized[FIPS] = d;
	    }
	}

	// Calculate daily maxima
	let dayMax = Math.max(
	    ...Object.entries(normalized).map(
		(entry) => entry[1].sevenDayMean));
	let dayMaxPer100KCap = Math.max(
	    ...Object.entries(normalized).map(
		(entry) => entry[1].sevenDayMeanPer100KCap));

	maxSoFar = Math.max(maxSoFar, dayMax);
	maxSoFarPer100KCap = Math.max(maxSoFarPer100KCap, dayMaxPer100KCap);

	// Add data to each county for current day
	for (let [FIPS, d] of Object.entries(normalized)) {
	    d.dayMax = dayMax;
	    d.maxSoFar = maxSoFar;
	    d.dayMaxPer100KCap = dayMaxPer100KCap;
	    d.maxSoFarPer100KCap = maxSoFarPer100KCap;
	}

	// Add normalized datum to result
	normalizedForDay.push(normalized);
    }

    return normalizedForDay;
}