2c:null 2d:["$","title",null,{"children":"SARS-CoV-2 concentrations measured in NYC Wastewater by Sewersheds | BetaNYC | Observable"}] 32:Tfd6,{ const container = html`

`; const height = 650; const svg = d3 .select(container) .append("svg") .attr("viewBox", [0, 0, width, height]); //legend svg .append("g") .attr("transform", "translate(20,20)") .append(() => Legend(sample_scale, { title: `${ options.type === "raw" ? "Concentration N1 Copies/L" : "Per capita N1 copies per day per population" } - Sample Date ${d3.utcFormat("%Y-%m-%d")(nearestDayWithData)}`, ticks: 4, tickFormat: ".2s" }) ); //projection paths const projection = d3 .geoTransverseMercator() .rotate([50, 0, 15]) .fitExtent( [ [10, 10], [width, height] ], sewer_sheds ); const path = d3.geoPath(projection); const g = svg.append("g"); //basemap svg .selectAll(".shoreline") .data(shoreline.features) .enter() .append("path") .attr("d", path) .attr("fill", "none") .style("stroke", "#eee"); const sheds = svg .append("g") .selectAll(".shed-base") .data(sewer_sheds.features) .enter() .append("path") .classed("shed-base", true) .attr("d", path) .attr("stroke", "white") .attr("stroke-width", 0.4) .attr("fill", (d) => { const id = d.properties.Sewershed; const find = shed_samples.find((i) => i.id === id); if (!find || !find.name) return "#eee"; if (options.type === "raw") return sample_scale(find.concentration); if (options.type === "per") return sample_scale(find.concentrationPerPop); }); //interactive layer const div = d3.select(container).append("div").classed("tooltip", true); const tooltip = new Tooltip(div); let selectedShed = null; const shedsMouseOver = svg .append("g") .selectAll(".shed-base") .data(sewer_sheds.features) .enter() .append("path") .classed("shed-base", true) .attr("d", path) .attr("fill", "rgba(0,0,0,0)") .attr("stroke", "#191919") .attr("stroke-width", 0) .on("mouseover", function (event, d) { const id = d.properties.Sewershed; if (id && id !== "NA") { tooltip.display(d, tooltipContents); d3.select(this).style("stroke", "black").style("stroke-width", 1.3); selectedShed = id; //update plants .attr("fill", (d) => { const id = d.properties.wpcp; return id === selectedShed ? "black" : "#777"; }) .attr("r", (d) => { const id = d.properties.wpcp; return id === selectedShed ? 6 : 4; }); } }) .on("mouseout", function () { tooltip.hide(); d3.select(this).style("stroke", "black").style("stroke-width", 0); selectedShed = null; plants.attr("fill", "#777").attr("r", 4); }) .on("mousemove", (event) => { tooltip.move(event); }); //plant points for reference const plants = svg .append("g") .selectAll("circle") .data(wwtp.features) .enter() .append("circle") .attr("transform", function (d) { const [lon, lat] = d.geometry.coordinates; let point = projection([lon, lat]); return `translate(${point[0]},${point[1]})`; }) .attr("stroke-width", 2) .attr("stroke", "white") .attr("fill", (d) => { const id = d.properties.wpcp; return id === selectedShed ? "black" : "#777"; }) .attr("r", 4); return container; }33:[{"id":"5f4eb23a4b159964c0b42a965b5894aa17c24686e7f46083a3b5ee89b64113fb03544be1f0d3d0ab3507a3d470dee464be1acd2ce439b6dd1556b5bd001a2bd1","href":"https://static.observableusercontent.com/files/5f4eb23a4b159964c0b42a965b5894aa17c24686e7f46083a3b5ee89b64113fb03544be1f0d3d0ab3507a3d470dee464be1acd2ce439b6dd1556b5bd001a2bd1","name":"noaa-hydro-shoreline-25m-v1.geojson","type":"application/geo+json","lastModified":1647103702350.436,"size":319538},{"id":"23ee7d504a0344f32694cf2d151b1b7837da2be18a0d36f2f511b39063805538c190fbf64a169b4ac5bf22347eebfefbf99afdbc3a86e8dd2d285124f22a0cd7","href":"https://static.observableusercontent.com/files/23ee7d504a0344f32694cf2d151b1b7837da2be18a0d36f2f511b39063805538c190fbf64a169b4ac5bf22347eebfefbf99afdbc3a86e8dd2d285124f22a0cd7","name":"wwtp@1.geojson","type":"application/geo+json","lastModified":1647122270362.864,"size":5055},{"id":"2e4eb5df9e047c11b33eb88d47ba90534f1fef9991b899ff39e444d12caf3c4f8ba89283192a25ae607b73756a92bb29750fbe6a868f0daf44824f8037c01f67","href":"https://static.observableusercontent.com/files/2e4eb5df9e047c11b33eb88d47ba90534f1fef9991b899ff39e444d12caf3c4f8ba89283192a25ae607b73756a92bb29750fbe6a868f0daf44824f8037c01f67","name":"sewersheds@4.geojson","type":"application/geo+json","lastModified":1647147308960.847,"size":158955},{"id":"9cc46f1018c87a21c8f9bf05718fd97757990c2c289e9355f2713b2f907703fed01760aa06104893ea83a93cab2feb76e6644e12b633e7ced22a83c9a499fb7c","href":"https://static.observableusercontent.com/files/9cc46f1018c87a21c8f9bf05718fd97757990c2c289e9355f2713b2f907703fed01760aa06104893ea83a93cab2feb76e6644e12b633e7ced22a83c9a499fb7c","name":"SARS-CoV-2_concentrations_measured_in_NYC_Wastewater.csv","type":"text/csv","lastModified":1705619941347.651,"size":373692}] 30:{"id":"e3cc2917c0c69121","slug":"sars-cov-2-concentrations-measured-in-nyc-wastewater-by-sew","title":"SARS-CoV-2 concentrations measured in NYC Wastewater by Sewersheds","thumbnail":"cb105beb6b0115c0b26c0dc7c418ce974f43264da12fe273e48e0835126e7954","access_level":"public","create_time":"$D2022-03-12T15:44:41.537Z","update_time":"$D2022-06-14T19:01:54.329Z","view_time":null,"first_public_time":"$D2022-03-12T19:58:34.309Z","fork":false,"stars":1,"starred":false,"owner":{"type":"team","id":"6056c9907da84bd4","login":"betanyc","name":"BetaNYC","avatar_url":"https://avatars-next.observableusercontent.com/8e6d78f21df3c658c180a93a099938214f753f20e2bc46f10a162c9d35e419d1","tier":"pro_2024"},"version":993,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"215e59083f0e53f8","login":"zhik","name":"Zhi Keng He","avatar_url":"https://avatars-next.observableusercontent.com/1921c3cb8ffa82cde953aa4417dc8b601dbd05384629c1f8ecf0544be068a204","tier":null}],"members":[{"type":"team","id":"6056c9907da84bd4","login":"betanyc","name":"BetaNYC","avatar_url":"https://avatars-next.observableusercontent.com/8e6d78f21df3c658c180a93a099938214f753f20e2bc46f10a162c9d35e419d1","tier":"pro_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"SARS-CoV-2 concentrations measured in NYC Wastewater by Sewersheds","cells":[{"id":0,"value":"# SARS-CoV-2 concentrations measured in NYC Wastewater by Sewersheds\nRead more about the dataset [here.](https://data.cityofnewyork.us/Health/SARS-CoV-2-concentrations-measured-in-NYC-Wastewat/f7dc-2q9f)\n\nRead a more comprehensive analysis of the relationships [here.](https://pubs.rsc.org/en/content/articlelanding/2022/EW/d1ew00747e)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":657,"value":"## How does the SARS-CoV-2 wastewater concentrations compare to cases (7-day average)?\n*Note: Wastewater concentrations data starts in 08/31/2020. Samples are collected biweekly.*","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":911,"value":"TimeAxis({ ...time_chart_options })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":833,"value":"{\n const concentrations_by_date = samples.reduce((total, row) => {\n const date = row.Date;\n const dt = row.sampleDate;\n const value = row.concentration;\n\n if (typeof value === \"undefined\") return total;\n\n //check if date exist\n let find = total.find((t) => t.date === date);\n if (find) {\n find.values.push(value);\n } else {\n total.push({ date, dt, values: [value] });\n }\n return total;\n }, []);\n\n const avgs = concentrations_by_date.map(({ dt, values }) => ({\n date: dt,\n value: d3.sum(values)\n }));\n\n return TimeChart(avgs, {\n ...time_chart_options,\n title: \"Concentration totals (N1 Copies/L)\"\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":890,"value":"TimeChart(\n case_by_day.map(({ dt, ALL_CASE_COUNT_7DAY_AVG }) => ({\n date: dt,\n value: ALL_CASE_COUNT_7DAY_AVG\n })),\n {\n ...time_chart_options,\n title: \"7-day avg cases\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":820,"value":"### A closer look (Sept 2020 - Current)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":746,"value":"Plot.plot({\n width: width,\n x: {\n type: \"utc\",\n grid: true,\n domain: [new Date(\"2020-09-01\"), new Date()]\n },\n y: {\n tickFormat: \".2s\",\n label: \"↑ Concentration N1 Copies/L at each Treatment Plant\"\n },\n marks: [\n Plot.line(samples, {\n x: \"Date\",\n y: \"concentration\",\n z: \"WRRF Name\",\n curve: \"bump-x\",\n strokeOpacity: 0.3\n })\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":688,"value":"Plot.plot({\n width,\n x: {\n type: \"utc\",\n grid: true,\n domain: [new Date(\"2020-09-01\"), new Date()]\n },\n marks: [\n Plot.areaY(case_by_day, {\n x: \"Date\",\n y: \"ALL_CASE_COUNT_7DAY_AVG\",\n fill: \"rgba(255,76,76,0.6)\"\n })\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":653,"value":"## Map!","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":244,"value":"viewof nthDay = {\n return Inputs.range([0, duration], {\n step: 1,\n label: \"Quick Sample Date Picker\",\n value: duration\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":424,"value":"viewof options = form(html`

SARS-CoV-2 Volume in Wastewater

\n \n Concentration SARS-CoV-2 gene target (N1 Copies/L)\n \n \n\n Per capita SARS-CoV-2 load (N1 copies per day per population)\n\n

\n\n

\nThe measure of the SARS-CoV-2 RNA concentration is provided in units of Copies/L (i.e., copy number of the viral RNA virus per liter of wastewater analyzed), is the concentration of the N1 region of the virus’ RNA genome (this targeted sequence is the same as one of the two sequences targeted in the clinical assays developed and approved by the Center for Disease Control (CDC) and used for clinical testing in the USA).\n`)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":521,"value":"{\n //if the domain is all zeros then the sample data is too small\n const domain = sample_scale.domain();\n const domain_all_zero = domain.every((i) => i === 0);\n const error_message = `

${\n domain_all_zero && options.type === \"per\"\n ? \"*Numbers for per capita measurement are too small* Try switching over to concentration.\"\n : \"\"\n }

`;\n return html`\nHover for details.

${error_message}`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":51,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":33,"value":"### Data sources:\n\n- SARS-CoV-2 concentrations measured in NYC Wastewater from [NYC DEP via #NYCOpenData](https://data.cityofnewyork.us/Health/SARS-CoV-2-concentrations-measured-in-NYC-Wastewat/f7dc-2q9f)\n- Wastewater Treatment Plants and Sewersheds from [Open Sewer Atlas](https://openseweratlas.tumblr.com/data)\n\n#### Code from:\n- https://observablehq.com/@dmaynard/date-range-inputs\n- https://observablehq.com/@benoldenburg/nyc-transit-turnstile-change-2019-2020\n- https://observablehq.com/@zhik/manhattan-zipcode-evictions-and-covid-cases","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":565,"value":"\n#### Todo\n- Make a graphic to show the change in concentration (so it is clear what N1 Copies/ L means)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":329,"value":"#### Vars:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":914,"value":"time_chart_options = ({\n interval: d3.timeDay.every(1),\n start: new Date(2012, 10, 1),\n stop: extent[1]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":974,"value":"function tooltipContents(d) {\n //lookup\n const id = d.properties.Sewershed;\n\n const find = shed_samples.find((i) => i.id === id);\n\n if (find) {\n const { name, concentration, concentrationPerPop } = find;\n\n const format = d3.format(\",\");\n\n if (!name) {\n return `

${id}

No data for this date

`;\n }\n\n return `

${name}

Sample Date: ${\n find[\"Sample Date\"]\n }

Concentration SARS-CoV-2 gene target (N1 Copies/L): ${format(\n concentration\n )}

Per capita SARS-CoV-2 load\n(N1 copies per day per population): ${format(\n concentrationPerPop\n )}

Annotation: ${find.Annotation}

`;\n } else {\n return `

No data for this shed.

`;\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":271,"value":"nearestDayWithData = {\n const selectedDate = time_scale.invert(nthDay);\n //find closest date\n\n const unique_dates = [\n ...new Set(samples_dates.map((d) => d3.utcFormat(\"%Y-%m-%d\")(d)))\n ].map((d) => d3.timeParse(\"%Y-%m-%d\")(d));\n\n //get difference for dates\n const diff = unique_dates.map((d) => [d, Math.abs(d - selectedDate)]);\n\n //sort\n const sorted = diff.sort((a, b) => a[1] > b[1]);\n\n return sorted[0][0];\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":314,"value":"samples_dates = samples.map((i) => i.sampleDate)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":283,"value":"extent = {\n return d3.extent(samples_dates);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":280,"value":"duration = d3.timeDay.count(...extent)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":275,"value":"time_scale = {\n return d3.scaleTime().domain(extent).range([0, duration]);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":144,"value":"sample_scale = {\n const raw_values = shed_samples\n .filter((i) => typeof i.concentration !== \"undefined\")\n .map((i) => i.concentration);\n\n const per_values = shed_samples\n .filter((i) => typeof i.concentrationPerPop !== \"undefined\")\n .map((i) => i.concentrationPerPop);\n\n const values = options.type === \"raw\" ? raw_values : per_values;\n\n return d3.scaleSequentialQuantile(d3.interpolateOranges).domain(values);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":126,"value":"shed_samples = {\n //for each shed get the latest sample\n const latest = sewer_sheds.features.map((shed) => {\n const id = shed.properties[\"Sewershed\"];\n const find = samples.filter(\n (sample) =>\n sample[\"WRRF Abbreviation\"] === id &&\n d3.utcFormat(\"%Y-%m-%d\")(nearestDayWithData) ===\n d3.utcFormat(\"%Y-%m-%d\")(sample.sampleDate)\n );\n\n if (find.length) {\n const latest = find[0];\n\n latest.name = latest[\"WRRF Name\"];\n return { id, ...latest };\n }\n return { id };\n });\n\n return latest;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":318,"value":"#### Dataset imports:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":6,"value":"samples = {\n const file = await fetch(\n \"https://data.cityofnewyork.us/api/views/f7dc-2q9f/rows.csv?accessType=DOWNLOAD\"\n );\n\n const rows = d3.csvParse(await file.text());\n\n //convert 'Sample Date' and 'Test date' to dt objects\n return rows.map((row) => {\n function formatDate(dt) {\n return d3.timeParse(\"%m/%d/%Y\")(dt);\n }\n\n row.sampleDate = formatDate(row[\"Sample Date\"]);\n row.testDate = formatDate(row[\"Test date\"]);\n\n row.concentration = +row[\n \"Concentration SARS-CoV-2 gene target (N1 Copies/L) \"\n ];\n row.concentrationPerPop = +row[\n \"Per capita SARS-CoV-2 load (N1 copies per day per population)\"\n ];\n row.pop = +row[\"Population Served, estimated \"];\n\n row.Date = d3.utcFormat(\"%Y-%m-%d\")(row.sampleDate);\n return row;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":41,"value":"sewer_sheds = await FileAttachment(\"sewersheds@4.geojson\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"value":"wwtp = FileAttachment(\"wwtp@1.geojson\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":113,"value":"shoreline = await FileAttachment(\"noaa-hydro-shoreline-25m-v1.geojson\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":664,"value":"case_by_day = {\n const file = await fetch(\n \"https://raw.githubusercontent.com/nychealth/coronavirus-data/master/trends/cases-by-day.csv\"\n );\n const rows = d3.csvParse(await file.text());\n\n rows.map((row) => {\n const dt = d3.timeParse(\"%m/%d/%Y\")(row.date_of_interest);\n row[\"dt\"] = dt;\n row[\"Date\"] = d3.utcFormat(\"%Y-%m-%d\")(dt);\n return row;\n });\n\n return rows;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":324,"value":"#### Library imports:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":428,"value":"function formValue(form) {\n const object = {};\n for (const input of form.elements) {\n if (input.disabled || !input.hasAttribute(\"name\")) continue;\n let value = input.value;\n switch (input.type) {\n case \"range\":\n case \"number\": {\n value = input.valueAsNumber;\n break;\n }\n case \"date\": {\n value = input.valueAsDate;\n break;\n }\n case \"radio\": {\n if (!input.checked) continue;\n break;\n }\n case \"checkbox\": {\n if (input.checked) value = true;\n else if (input.name in object) continue;\n else value = false;\n break;\n }\n case \"file\": {\n value = input.multiple ? input.files : input.files[0];\n break;\n }\n case \"select-multiple\": {\n value = Array.from(input.selectedOptions, (option) => option.value);\n break;\n }\n }\n object[input.name] = value;\n }\n return object;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":426,"value":"function form(form) {\n const container = html`
${form}`;\n form.addEventListener(\"submit\", (event) => event.preventDefault());\n form.addEventListener(\"change\", () => {\n container.dispatchEvent(new CustomEvent(\"input\"));\n });\n form.addEventListener(\"input\", () => (container.value = formValue(form)));\n container.value = formValue(form);\n return container;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":147,"value":"import { Legend } from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":150,"value":"import { Tooltip } from \"@clhenrick/tooltip-component\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":830,"value":"import { TimeChart, TimeAxis } from \"@observablehq/timechart\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 31:"$30:body"