31:T1722,chart = { // Filter data to only be within the window selected in the brush chart const data_ = data.filter(d => ( +d.date > +brush.startDate && +d.date < +brush.endDate && systems.includes(d.system) )) const milestones_ = ( accompanyingData.includes('Annotations') ? milestones.filter(d => +d.date > +brush.startDate && +d.date < +brush.endDate) : [] ) // Returns a function to update a tooltip using data from the specified system const updateTooltip = (event, datum) => { const date = d3.utcDay.floor(datum.x) const fetchedData = data_.filter(d => +d.date === +date) event.currentTarget._tippy.setContent( d3.utcFormat('%-m/%d/%Y')(date) + '
' + fetchedData.map(d => `${capitalize(d.system)}: ${d3.format(',')(d.concentrationAvg)} cp/mL `).join('
') ) } // Render a plot const plot = Plot.plot({ y: { grid: true, type: scaleType, label: 'Copies/mL ↑', tickFormat: 's', domain: staticYAxis ? [ scaleType === 'log' ? d3.min(data, d => d.concentration) : 0, d3.max(data, d => d.ciHigh), ] : [ scaleType === 'log' ? d3.min(data_, d => d.concentration) : 0, d3.max(data_, d => d.ciHigh), ] }, color: { legend: true, domain: ['northern', 'southern'], tickFormat: t => `${capitalize(t)} System`, }, width: chartWidth, height: chartWidth / 1.6, marginRight: accompanyingData.includes('Annotations') ? 100 : 10, marks: [ // Milestones Marks (the ticks go up here to go behind everything else, but the text is at the bottom to go above) Plot.tickX(milestones_, { x: 'date', stroke: '#999', strokeDasharray: '4,2' }), // Daily Measurements accompanyingData.includes('Daily Measurements') ? Plot.dot(data_, { x: 'date', y: 'concentration', fill: 'system', opacity: 0.33, r: 2, }) : null, // Intervals accompanyingData.includes('Intervals') ? Plot.link(data_, { x1: 'date', x2: 'date', y1: 'ciLow', y2: 'ciHigh', strokeWidth: 3, stroke: 'system', opacity: 0.1, strokeLinecap: 'round', }) : null, // Average Intervals accompanyingData.includes('Average Intervals') ? Plot.areaY(data_,{ x: 'date', y1: 'avgHigh', y2: 'avgLow', fill: 'system', opacity: 0.15, }) : null, // 7-Day Average Line on( Plot.line(data_, { x: 'date', y: 'concentrationAvg', stroke: 'system', strokeWidth: 4 }), { // This updates the tooltip (added below) with inspector data for the point being hovered over pointermove: updateTooltip, pointerenter: updateTooltip, pointerdown: updateTooltip, } ), accompanyingData.includes('Annotations') ? [ Plot.dot( data_, Plot.selectMaxY({ x: 'date', y: 'concentrationAvg', fill: 'system', r: 5, stroke: '#FFF' }) ), Plot.text( data_, Plot.selectMaxY({ x: 'date', y: 'concentrationAvg', z: 'system', fill: '#000', strokeWidth: 3, stroke: '#FFF', text: (d, i, data) => { const sameSysData = data.filter(d_ => d.system === d_.system) return d3.format(',d')(d.concentrationAvg) + ' cp/Ml\n' + formatRatio(d.concentrationAvg / d3.min(sameSysData, d => d.concentrationAvg)) + ' min' }, dy: -12, textAnchor: 'start' }) ), // Min Plot.dot(data_, Plot.selectMinY({ x: 'date', y: 'concentrationAvg', fill: 'system', r: 5, stroke: '#FFF' })), Plot.text( data_, Plot.selectMinY({ x: 'date', y: 'concentrationAvg', z: 'system', fill: '#000', strokeWidth: 3, stroke: '#FFF', text: d => d3.format(',d')(d.concentrationAvg) + ' cp/Ml\n', dy: 12, textAnchor: 'start' }) ), // Curr Plot.dot(data_, Plot.selectMaxX({ x: 'date', y: 'concentrationAvg', fill: 'system', r: 5, stroke: '#FFF' })), Plot.text( data_, Plot.selectMaxX({ x: 'date', y: 'concentrationAvg', z: 'system', fill: '#000', strokeWidth: 3, stroke: '#FFF', text: d => { const sameSysData = data_.filter(d_ => d.system === d_.system) return `${formatRatio(d.concentrationAvg / d3.max(sameSysData, d => d.concentrationAvg))} peak` + '\n' + `${formatRatio(d.concentrationAvg / d3.min(sameSysData, d => d.concentrationAvg))} min` }, dx: 8, textAnchor: 'start' }) ), ] : null, // Milestone Text Plot.text(milestones_, { x: 'date', textAnchor: 'start', text: 'name', dx: -4, dy: 0, rotate: 90, frameAnchor: 'top', stroke: '#FFF', fill: '#333', strokeWidth: 4, }), ] }) // Change the paint order on text so the stroke shows up below the fill d3.select(plot).selectAll('text').attr('paint-order', 'stroke') // Make lines have crips edges d3.select(plot).selectAll('line').attr('shape-rendering', 'crispEdges') // Add tooltips showing inspector to the plot const tooltip = tippy(plot.querySelectorAll('[aria-label="line"] path'), { followCursor: true, allowHTML: true, theme: 'light', animation: 'fade', delay: [0, 200], }) return plot }32:T49c,viewof brush = { const data_ = data.filter(d => d.concentration) const plot = Plot.plot({ marginLeft: 0, marginRight: 0, marginTop: 0, y: { type: 'log', ticks: false }, x: { grid: true, ticks: 10 }, height: 80, width: width, marks: [ Plot.dot(data_, { x: 'date', y: 'concentration', fill: 'system', opacity: 0.4, r: 1.5 }), Plot.line(data_, { x: 'date', y: 'concentrationAvg', stroke: 'system', strokeWidth: 1.5 }), Plot.frame({ stroke: '#CCC' }) ] }) const xScale = plot.scale('x') const yScale = plot.scale('y') const brushed = ({ selection }) => { plot.value = { startDate: xScale.invert(selection[0]), endDate: xScale.invert(selection[1]) } plot.dispatchEvent(new Event('input'), { bubbles: true }) } const brush = d3.brushX() .extent([[xScale.range[0], yScale.range[1]], [xScale.range[1] + 1, yScale.range[0]]]) .on("start brush end", brushed) d3.select(plot) .append('g') .call(brush) .call( brush.move, [d3.utcDay.offset(d3.max(data_, d => d.date), -269), d3.utcDay.offset(d3.max(data_, d => d.date), 1)].map(xScale.apply) ) return plot }33:T463,mapAndLegend = htl.html`

${map.node()}

${Array.from(SYSTEMS_BY_TOWN).map(([system, towns]) => htl.html.fragment`

${capitalize(system)}

${t}

`)}

`34:T433,{ const data_ = data.filter(d => d.concentration !== null).sort((a, b) => a.date - b.date) return Plot.plot({ height: d3.utcYear.count( d3.utcYear.floor(d3.min(data_, d => d.date)), d3.utcYear.floor(d3.max(data_, d => d.date)) ) * 150, width: width, y: { type: scaleType, tickFormat: 's', grid: true, ticks: 3, domain: [100, 10000] }, x: { tickFormat: t => d3.timeFormat('%b %-d')(dateFromPct(t)) }, fy: { tickFormat: d => d.toFixed() }, facet: {data: data_, y: d => d3.utcDay.offset(d.date, 1).getFullYear() }, marks: [ Plot.link(data_, { x1: d => pctThroughYear(d.date), x2: d => pctThroughYear(d.date), y1: 'ciLow', y2: 'ciHigh', strokeWidth: 3, stroke: 'system', opacity: 0.25, strokeLinecap: 'round', }), Plot.line( data_, { x: d => pctThroughYear(d.date), y: 'concentrationAvg', stroke: 'system', strokeWidth: 3, } ), Plot.frame({ stroke: '#CCC' }), ], }) }35:T790,data = (await d3.csv(DATA_URL)).map(d => ({ northernVariant: parseVariantResults(d['Northern\rVariant\rResults']), southernVariant: parseVariantResults(d['Southern\rVariant Results']), ...d, date: d3.utcParse('%m/%d/%Y')(d['Sample Date']), southern: toIntOrNull(d['Southern\r(copies/mL)']), northern: toIntOrNull(d['Northern\r(copies/mL)']), southernAvg: toIntOrNull(d['Southern\r7 day avg']), northernAvg: toIntOrNull(d['Northern\r7 day avg']), })) .map(d => ({ ...d, southernLow: d.southern - toIntOrNull(d['Southern\rLow Confidence\rInterval']), northernLow: d.northern - toIntOrNull(d['Northern\rLow Confidence\rInterval']), southernHigh: d.southern + toIntOrNull(d['Southern\rHigh Confidence\rInterval']), northernHigh: d.northern + toIntOrNull(d['Northern\rHigh Confidence\rInterval']), })) .map((d, i, arr) => { const windowStart = Math.max(0, i - 7) const windowEnd = i const window = arr.slice(windowStart, windowEnd) return { ...d, southernLowAvg: d3.mean(window.filter(d => d.southernLow), d => d.southernLow), northernLowAvg: d3.mean(window.filter(d => d.northernLow), d => d.northernLow), southernHighAvg: d3.mean(window.filter(d => d.southernHigh), d => d.southernHigh), northernHighAvg: d3.mean(window.filter(d => d.northernHigh), d => d.northernHigh), } }) // Unfold the data so each system gets its own datapoints .map((d, i, arr) => ( [ { system: 'northern', date: d.date, concentration: d.northern, concentrationAvg: d.northernAvg, ciHigh: d.northernHigh, ciLow: d.northernLow, avgHigh: d.northernHighAvg, avgLow: d.northernLowAvg, }, { system: 'southern', date: d.date, concentration: d.southern, concentrationAvg: d.southernAvg, ciHigh: d.southernHigh, ciLow: d.southernLow, avgHigh: d.southernHighAvg, avgLow: d.southernLowAvg, } ] )) 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2f:{"title":"Boston-Area SARS-CoV-2 Wastewater Levels","cells":[{"id":0,"value":"# Boston-Area SARS-CoV-2 Wastewater Levels","pinned":false,"hidden":false,"mode":"md"},{"id":425,"value":"**Latest reading:**\n${d3.utcDay.count(latestDate(data), d3.utcDay.floor(new Date()))}\n${pluralize('day', d3.utcDay.count(latestDate(data), d3.utcDay.floor(new Date())))} ago,\n${d3.utcFormat('%-m/%-d/%Y')(latestDate(data))}\n${\n latestSiteUpdate ?\n htl.html.fragment`\n (${+latestDate(data) >= +latestSiteUpdate ?\n 'Up to date' :\n `Outdated, latest website data is from ${d3.utcFormat('%-m/%-d/%Y')(latestSiteUpdate)}`\n })\n ` : \n ''\n}","pinned":false,"hidden":false,"mode":"md"},{"id":415,"value":"> Samples are currently taken 3 - 7 times a week and analyzed by [Biobot Analytics](https://biobot.io), a wastewater epidemiology company. Data are updated as received by Biobot following an internal review process.\n>\n> — [Massachusetts Water Resources Authority](https://www.mwra.com/biobot/biobotdata.htm)","pinned":false,"hidden":false,"mode":"md"},{"id":93,"value":"viewof scaleType = Inputs.radio(['log', 'linear'], { label: 'Scale Type', value: 'log' })","pinned":false,"hidden":false,"mode":"ojs"},{"id":189,"value":"viewof systems = Inputs.checkbox([\"northern\", \"southern\"], { label: \"Systems\", value: ['northern', 'southern'] })","pinned":false,"hidden":false,"mode":"ojs"},{"id":1178,"value":"viewof accompanyingData = Inputs.checkbox(\n ['Daily Measurements', 'Intervals', 'Average Intervals', 'Annotations'],\n { label: 'Data', value: ['Daily Measurements', 'Intervals', 'Annotations'] }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1210,"value":"Lines represent a 7-day average and are always shown","pinned":false,"hidden":false,"mode":"html"},{"id":640,"value":"viewof staticYAxis = Inputs.toggle({label: \"Preserve y-axis over all time\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":656,"value":"Drag selection window to change date range (currently selected: ${d3.utcDay.count(brush.startDate, brush.endDate)} days):","pinned":false,"hidden":false,"mode":"md"},{"id":435,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":867,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":1712,"value":"## By Year","pinned":false,"hidden":false,"mode":"md"},{"id":1714,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":200,"value":"***\n\n## Implementation\n\nThe data comes from this [GitHub repo](https://github.com/harrislapiroff/mwra-wastewater-scraper), which I maintain. The code in the repo scrapes PDF from the MWRA website and converts the latest data to CSV. I run it whenever I notice the data is outdated.","pinned":false,"hidden":false,"mode":"md"},{"id":3,"value":"$35","pinned":true,"hidden":false,"mode":"ojs"},{"id":1701,"value":"data","pinned":true,"hidden":false,"mode":"ojs"},{"id":1319,"value":"milestones = holidays.inRange(...d3.extent(data, d => d.date)).map(h => ({\n ...h,\n date: d3.utcDay.floor(h.date), // Convert dates to UTC\n}))","pinned":true,"hidden":false,"mode":"ojs"},{"id":326,"value":"### Check most recent update\n\nThis bit checks the MWRA website to see if there's a more recent PDF than the data we have. If there is, [**@harrislapiroff**](https://observablehq.com/@harrislapiroff/) needs to convert it to CSV and upload to this notebook.","pinned":false,"hidden":false,"mode":"md"},{"id":339,"value":"RECENT_DATE_RE = /Biobot Data - samples submitted through (\\d{1,2}\\/\\d{1,2}\\/\\d{4})/","pinned":true,"hidden":false,"mode":"ojs"},{"id":330,"value":"mwra_page = (await fetch(CORS_PROXY + 'https://www.mwra.com/biobot/biobotdata.htm')).text()","pinned":true,"hidden":false,"mode":"ojs"},{"id":342,"value":"latestSiteUpdate = {\n try {\n return d3.utcParse('%m/%d/%Y')(mwra_page.match(RECENT_DATE_RE)[1])\n } catch {\n return null\n }\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":711,"value":"### Map","pinned":false,"hidden":false,"mode":"md"},{"id":725,"value":"TOWNS = FileAttachment(\"ma-towns-state-plane-topo-1.json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":732,"value":"SYSTEMS_BY_TOWN = new Map([\n ['northern', ['Wilmington', 'Reading', 'Bedford', 'Burlington', 'Woburn', 'Stoneham', 'Lexington', 'Winchester', 'Melrose', 'Arlington', 'Medford', 'Malden', 'Waltham', 'Belmont', 'Somerville', 'Everett', 'Revere', 'Chelsea', 'Watertown', 'Cambridge', 'Winthrop']],\n ['both', ['Newton', 'Boston', 'Brookline', 'Milton']],\n ['southern', ['Ashland', 'Framingham', 'Natick', 'Wellesley', 'Needham', 'Dedham', 'Quincy', 'Westwood', 'Canton', 'Randolph', 'Braintree', 'Weymouth', 'Hingham', 'Norwod', 'Canton', 'Walpole', 'Stoughton', 'Holbrook', 'Norwood']]\n])","pinned":true,"hidden":false,"mode":"ojs"},{"id":823,"value":"systemForTown = t => {\n const system = Array.from(SYSTEMS_BY_TOWN.entries())\n .find(([system, towns]) => towns.includes(t))\n\n if (!system) return null\n\n return system[0]\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":785,"value":"includedTowns = topojson.merge(\n TOWNS,\n TOWNS.objects.towns.geometries.filter(t => !!systemForTown(t.properties.TOWN2))\n)","pinned":true,"hidden":false,"mode":"ojs"},{"id":839,"value":"mapFillScale = (system, both, none) => {\n const colorScale = chart.scale('color')\n const color = colorScale.apply(system)\n if (color) return color\n\n if (system === 'both') return both\n \n return none\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":903,"value":"colorScale = chart.scale('color')","pinned":true,"hidden":false,"mode":"ojs"},{"id":900,"value":"bothTexture = textures.lines()\n .size(8)\n .strokeWidth(2.5)\n .stroke(colorScale.range[0])\n .background(colorScale.range[1])","pinned":true,"hidden":false,"mode":"ojs"},{"id":718,"value":"map = {\n const mapWidth = Math.min(600, width)\n const map = d3.select(DOM.svg(mapWidth, mapWidth))\n map.attr('style', 'max-width: 100%')\n\n const reprojection = d3.geoIdentity().fitExtent([[20, 20], [mapWidth - 20, mapWidth - 20]],includedTowns)\n const path = d3.geoPath(reprojection)\n\n map.call(bothTexture)\n\n const townShapes = map.append('g')\n .selectAll()\n .data(topojson.feature(TOWNS, TOWNS.objects.towns).features)\n .join('path')\n .attr('d', path)\n .attr('fill', d => mapFillScale(systemForTown(d.properties.TOWN2), bothTexture.url(), '#EEE'))\n .attr('stroke', '#FFF')\n \n return map\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":369,"value":"### Utils","pinned":false,"hidden":false,"mode":"md"},{"id":703,"value":"Given the entire dataset, find the most recent date for which data exists:","pinned":false,"hidden":false,"mode":"md"},{"id":374,"value":"latestDate = data => data.filter(d => !!d.concentrationAvg).slice(-1)[0].date","pinned":true,"hidden":false,"mode":"ojs"},{"id":932,"value":"Capitalize the first char of a string:","pinned":false,"hidden":false,"mode":"md"},{"id":207,"value":"capitalize = s => s.substring(0, 1).toUpperCase() + s.substring(1)","pinned":true,"hidden":false,"mode":"ojs"},{"id":936,"value":"Convert a string to a number (or null, if it's an empty string):","pinned":false,"hidden":false,"mode":"md"},{"id":34,"value":"toIntOrNull = d => d === \"\" ? null : +d","pinned":true,"hidden":false,"mode":"ojs"},{"id":948,"value":"Pluralize a word conditionally, based on a provided count:","pinned":false,"hidden":false,"mode":"md"},{"id":940,"value":"pluralize = (word, count, plural) => count === 1 ? word : (plural || word + 's')","pinned":true,"hidden":false,"mode":"ojs"},{"id":1050,"value":"parseVariantResults = str => {\n if (str === '') return\n const [variant, pctStr] = str.split('\\r')\n return { [variant]: +pctStr.substring(0, pctStr.length - 1) / 100 }\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":1416,"value":"Format a ratio as \"N× higher/lower\":","pinned":false,"hidden":false,"mode":"md"},{"id":1419,"value":"formatRatio = (n, formats = {}) => {\n const { numberFormat, lowerFormat, higherFormat, exactString } = Object.assign({}, {\n numberFormat: d3.format('d'),\n higherFormat: n => `↑${n}× over`,\n lowerFormat: n => `↓${n}× below`,\n exactString: 'At'\n }, formats)\n if (n < 0) throw('Ratio cannot be smaller than 0')\n if (n < 1) return lowerFormat(numberFormat(1 / n))\n if (n > 1) return higherFormat(numberFormat(n))\n return exactString\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":1487,"value":"chartWidth = Math.max(width, 600)","pinned":false,"hidden":false,"mode":"ojs"},{"id":241,"value":"***\n\n## Appendix","pinned":false,"hidden":false,"mode":"md"},{"id":245,"value":"import {on} from \"@fil/plot-onclick-experimental-plugin\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":846,"value":"textures = require('textures@1.2.3')","pinned":false,"hidden":false,"mode":"ojs"},{"id":254,"value":"tippy = require('tippy.js@6.3.7')","pinned":false,"hidden":false,"mode":"ojs"},{"id":1839,"value":"holidays = import('https://cdn.skypack.dev/@18f/us-federal-holidays@4.0.0?min')","pinned":true,"hidden":false,"mode":"ojs"},{"id":306,"value":"","pinned":false,"hidden":false,"mode":"html"},{"id":332,"value":"CORS_PROXY = 'https://corsproxy.harrislapiroff.com/'","pinned":false,"hidden":false,"mode":"ojs"},{"id":1307,"value":"DATA_URL = `https://raw.githubusercontent.com/harrislapiroff/mwra-wastewater-scraper/main/output/latest.csv?cachebreaker=${d3.timeFormat('%Y-%m-%d')(new Date())}`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1726,"value":"pctThroughYear = (date) => {\n const year = date.getFullYear()\n const isLeapYear = (0 == year % 4) && (0 != year % 100) || (0 == year % 400)\n return d3.utcDay.count(d3.utcYear.floor(date), d3.utcDay.ceil(date)) / (isLeapYear ? 366 :365)\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":1779,"value":"dateFromPct = (pct) => {\n const dayOfYear = pct * 365 // will be slightly inaccurate for leap years, fine for our purposes\n return d3.utcDay.offset(d3.utcYear.floor(new Date()), dayOfYear)\n}","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W36","stdlib":"1","titling":"auto"}