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For more background, see [the CA DPH Site](https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/COVID-19/COVID-Variants.aspx). The data here was taken from that page on 2022-01-01, current as of 2021-12-30.\n\n_Note that this is based on the ${total_sequenced.toLocaleString()} cases which have been sequenced, not the total cases._","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":461,"value":"viewof vscale = slider({\n min: 300,\n max: 2000,\n step: 1,\n value: 500,\n format: \"\",\n description: \"Vertical Size. Increase to see minor variants.\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":6,"value":"box(md`In order of appearance in CA:\n${Swatches({\n color: colors\n})}\n${showPlot(prevalence)}`)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":803,"value":"These are ordered in order of appearance at a level of >0.05% in sequenced tests. The ones that win out over the long term are not always the first to appear.\n\nOther regions will have differing patterns. Prevalence depends not just on how infective a variant is, but how, when, and where it is introduced. A strain introduced in a highly-connected susceptible population will have an advantage over one introduced in a setting with fewer opportunities to spread. Social distancing and masks remain important tools. Remember, we still aren't vaccinating young children, and far too many are ending up in the hospital.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":807,"value":"The CA DPH reports:\n\n${status.split(\"\\n\").map(s => s.trim()).map(s => `> ${s}`)}","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":580,"value":"md`\n\nCases out of a total of ${total_sequenced.toLocaleString()} sequenced and reported to date:\n

\n${md`\n| Variant | Designation | Cases | Notes |\n| ------- | ----------- | ----- | ----- |\n${appearance\n .map(\n (v) =>\n `|${[\n `**${v}**`,\n variants[v].designation.replace(\"\\n\", \" \"),\n variants[v].cases.toLocaleString(),\n `

${variants[v].notes?.replace(\"\\n\", \" \") ?? \"\"}

` ??\n \"\"\n ].join(\"|\")}|`\n )\n .join(\"\\n\")}\n`}\n${footnote}\n

\n\nThe usual caveats apply about potential selection bias in how the samples to sequence were chosen.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":419,"value":"## Appendix\n\nImplementation Details; you may ignore the stuff below unless you're interested in how this works.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":516,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":319,"value":"// The colors we consider.\ncolor_scheme = [...d3.schemeCategory10, ...d3.schemePastel1]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":451,"value":"showPlot = (data) =>\n Plot.plot({\n caption: \"Covid Variant Predominance\",\n style: {\n \"max-width\": width - 7\n },\n width: width,\n height: vscale,\n \"margin-left\": \"0px\",\n \"margin-bottom\": \"0px\",\n color: {\n range: colors.range(),\n domain: colors.domain()\n },\n y: {\n tickFormat: \"%\",\n label: \"%\"\n },\n marks: [\n Plot.areaY(data, {\n x: \"month\",\n y: \"fraction\",\n fill: \"variant\",\n title: (d) => `${d.variant}\nDesignation: ${variants[d.variant].designation}\nTotal cases: ${variants[\n d.variant\n ].cases.toLocaleString()} out of ${total_sequenced.toLocaleString()} sequenced`,\n curve: \"catmull-rom\",\n order: appearance\n })\n ]\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":91,"value":"// The raw HTML data from the attachment.\nhtmlData = new DOMParser().parseFromString(\n await FileAttachment(\"Tracking Variants@6.html\").text(),\n \"text/html\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":65,"value":"// Find the tables; there are three of them.\ntables = d3.select(htmlData).selectAll(\"table\").nodes()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":472,"value":"concernTable = tables[0]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":475,"value":"interestTable = tables[1]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":464,"value":"prevalenceTable = tables[2]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":192,"value":"// Parse our main table. Clean up non-breaking spaces and any spurious whitespace.\n// TH tags are text, TD are numbers, more-or-less. Parser can be supplied.\nparsePrevalenceTable = (table, parse = (s) => s) => {\n const ar = Array.from(table.querySelectorAll(\"tr\")).map((e) =>\n Array.from(e.querySelectorAll(\"td,th\")).map((e) =>\n e.tagName === \"TH\"\n ? e.textContent.replace(/[\\u200b]/g, \"\").trim()\n : parse(e.textContent.replace(/[\\u200b]/g, \"\").trim())\n )\n );\n const head = ar.shift();\n return ar.flatMap((row) => {\n const month = parseMonth(row.shift().trim());\n return [\n {\n month,\n variant: \"Other\",\n fraction: 1 - sum(...row.map((i) => i / 100))\n },\n ...row.map((c, i) => ({\n month,\n variant: head[i + 1],\n fraction: c / 100\n }))\n ];\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":491,"value":"// Parse the variants tables. Clean up non-breaking spaces and any spurious whitespace.\n// TH tags are text, TD are data, more-or-less. Parser can be supplied.\nparseVariantTable = (table, type) => {\n const ar = Array.from(table.querySelectorAll(\"tr\")).map((e) =>\n Array.from(e.querySelectorAll(\"td,th\")).map((e) =>\n e.textContent.replace(/[\\u200b]/g, \"\").trim()\n )\n );\n // Strip header\n ar.shift();\n const variantData = ar.map((row, i) => ({\n type,\n variant: row[1],\n designation: row[0],\n cases: Number(row[2].replace(/,/g, \"\")),\n ...(notes[row[1]] && { notes: notes[row[1]] })\n }));\n return [...variantData];\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":502,"value":"total_sequenced = Number(/([0-9,]+)\\ssamples/.exec(status)[1].replace(/,/g, \"\"))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":498,"value":"variants = {\n const concern = parseVariantTable(concernTable, \"concern\");\n const interest = parseVariantTable(interestTable, \"interest\");\n const cases = (v) => v.cases;\n const table = [\n {\n type: \"other\",\n variant: \"Other\",\n designation: \"N/A\",\n cases:\n total_sequenced - sum(...concern.map(cases), ...interest.map(cases)),\n ...(notes[\"Other\"] && { notes: notes[\"Other\"] })\n },\n {\n type: \"concern\",\n variant: \"Omicron\",\n designation: \"B.1.1.529\",\n cases: \"1+\",\n notes: notes.Omicron\n },\n ...concern,\n ...interest\n ]\n .map((v) =>\n v.variant === \"Not available\" ? [v.designation, v] : [v.variant, v]\n )\n .reduce(keyReducer, {});\n return table;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":604,"value":"keyReducer = (acc, [key, v]) => ((acc[key] = v), acc)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":584,"value":"notes = d3\n .select(htmlData)\n .selectAll(\".article-content li\")\n .nodes()\n .map((n) => n.textContent)\n .filter((t) =>\n t.trim().match(/^[A-Z][.]\\d+|([a-zA-Z]+)\\s+\$[A-Z](?:[.]\\d+)+\$/)\n )\n .map((t) => [\n /\$([a-zA-Z]+)\$/.exec(t)?.[1] ??\n /^([a-zA-Z]+)\\s+\$[A-Z](?:[.]\\d+)+\$/.exec(t)?.[1] ??\n /^([A-Z](?:[.]\\d+)+)/.exec(t)?.[1],\n t\n ])\n .reduce(keyReducer, {\n Other:\n \"Includes all strains not designated _Variant of Interest_ or _Variant of Concern_.\"\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":710,"value":"findText = (s, t = (t) => t, e = (e) => e.textContent) => {\n const r = [];\n const p = t instanceof RegExp ? (txt) => t.test(txt) : t;\n d3.select(htmlData)\n .selectAll(s)\n .each(\n withThis((n) => {\n return p(n.textContent) && r.push(e(n));\n })\n );\n return r;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":750,"value":"find1Text = (s, t, e) => {\n const r = findText(s, t, e);\n switch (r.length) {\n case 0:\n return undefined;\n case 1:\n return r[0];\n default:\n throw new Error(`Multiple returns in find1Text ${s}`);\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":741,"value":"footnote = find1Text(\"table.ms-rteTable-default+span > span\", /^\\*includes/i)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":778,"value":"status = find1Text(\n \"h2\",\n /^How much sequencing/,\n (e) => e.nextSibling.textContent\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":732,"value":"withThis = (fn) => {\n function withThis(...args) {\n fn.call(this, this, ...args);\n }\n return withThis;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":269,"value":"// Add up a set of numbers\nsum = (...ar) => ar.reduce((acc, v) => acc + v, 0)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":386,"value":"// Put a box around the content\nbox = (content, tag = \"group-box\") =>\n // Wrap a box around a group of displays.\n html`

${content}

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":826,"value":"parsePercent = (e) => Number(e.replace(/%$/, \"\"))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":203,"value":"// Our main dataset in tidy form.\nprevalence = parsePrevalenceTable(prevalenceTable, parsePercent)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":356,"value":"// The variants in order of appearance (in quantities that round to 0.1% or greater).\nappearance = [\n ...Object.keys(\n prevalence.reduce(\n (acc, v) => (v.fraction && (acc[v.variant] = true), acc),\n {}\n )\n ),\n \"Omicron\"\n]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":280,"value":"// Turn English-specific months into months that sort properly.\nparseMonth = (s) => {\n const match = /^(\\d\\d)-([a-z]{3,4})$/i.exec(s);\n const [y, m] = [match?.[1], match?.[2]];\n return `${y}-${(months[m] + 1).toString().padStart(2, \"0\")}`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":278,"value":"months = ({\n Jan: 0,\n Feb: 1,\n Mar: 2,\n Apr: 3,\n May: 4,\n Jun: 5,\n Jul: 6,\n Aug: 7,\n Sep: 8,\n Sept: 8,\n Oct: 9,\n Nov: 10,\n Dec: 11\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":296,"value":"// Sometimes useful for debugging.\ntryEv = (f) => {\n try {\n return f();\n } catch (e) {\n return e.message;\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":322,"value":"// The mapping between variant and color\ncolors = d3.scaleOrdinal(appearance, color_scheme)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":316,"value":"import { swatches as Swatches } from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":391,"value":"import { slider } from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"1"}} 31:"$30:body"