31:T421,NYT2array = async function(theData) { const combineNytCovid = function(tocombine){ let thisState = { "Country/Region": tocombine[0]["Country/Region"], fips: tocombine[0]["fips"], dates: tocombine.map(x=>x.date), cases: tocombine.map(x=>parseFloat(x.cases)), deaths: tocombine.map(x=>parseFloat(x.deaths)), recovered: new Array(tocombine.length).fill(0), } return thisState } let shrinking = theData.slice() let aggregated = [] while(shrinking.length>0){ // outer loop, for each county let tocombine = [shrinking.shift()] let thiscountry = tocombine[0]["Country/Region"] while(true){ // inner loop, look for each match let countries = shrinking.map(x=>x["Country/Region"]) let hit = countries.findIndex(x => x == thiscountry) if(hit==-1){ break } else { tocombine.push(shrinking.splice(hit,1)[0]) } } aggregated.push(combineNytCovid(tocombine.slice())) } return aggregated }32:T8f7,addCalculatedStats = async function(aCovidArray) { return aCovidArray.map(function(oneCountry) { oneCountry = JSON.parse(JSON.stringify(oneCountry)) // smooth our the raw data oneCountry["cases"] = smooth(oneCountry["cases"],toSmooth).map(x=>Math.round(x)) oneCountry["deaths"] = smooth(oneCountry["deaths"],toSmooth).map(x=>Math.round(x)) oneCountry["recovered"] = smooth(oneCountry["recovered"],toSmooth).map(x=>Math.round(x)) // clean up dates oneCountry.dates = oneCountry.dates.map(function(x) { let thisDay = new Date(x); let stringDay = thisDay.toLocaleDateString("en-US") stringDay = stringDay.substring(0,stringDay.length) return stringDay } ) // define active cases as the remainder after subtracting deaths and recoveries oneCountry["active"] = oneCountry["cases"].map(function (num, idx) { return num - oneCountry["recovered"][idx] - oneCountry["deaths"][idx] } ) // define new cases as the difference between today and yesterday oneCountry["newCases"] = [oneCountry["cases"][0]] for(let i = 1;ix[1]))) let minY = Math.min(...(data.map(x=>x[1]))) let newvalue = Math.min(Math.max(minY,estimate[1]),maxY) //console.log('max: ' + maxY +' min: ' + minY +' new: ' + newvalue) result[i] = newvalue } return result }34:[] 2f:{"title":"COVID cases and deaths","cells":[{"id":2541,"value":"md`# COVID cases and deaths\n## on the same graph`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1043,"value":"md`## Data source\nState data are derived from [The New York Times](https://github.com/nytimes/covid-19-data). Check below the plot for timestamps on the last modifications from each github repo. Check the bottom of this notebook for a list of libraries used.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2474,"value":"md`## Figure 1. \n### Deaths and cases`\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":2147,"value":"md`I'm showing new cases and new deaths on the same graph. Why do some states seem proportionate, and other states seem uncoupled?`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1278,"value":"shownDiv = {\n\n var layout = {\n width:\"100%\",\n height:600,\n grid: {rows: 1, columns: 1, pattern: 'independent'},\n yaxis: {\n domain: [0.2, 1],\n anchor: 'x1',\n title: \"New cases\",\n type: whichScale,\n },\n yaxis2: { \n domain: [0.2, 1],\n anchor: 'x1',\n title: \"New deaths\",\n type: whichScale,\n overlaying: 'y',\n side: 'right'\n },\n title: 'New Deaths & New Cases',\n xaxis: { title: 'Date',\n domain: [0.1, .9],},\n };\n\n const div = DOM.element('div1')\n Plotly.newPlot(div, thePlotTraces,layout);\n return div\n}\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":4384,"value":"viewof whichScale = radio({\n title: \"Scale\",\n options: [\"linear\",\"log\"],\n value: \"linear\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":4381,"value":"viewof checkStates = select({\n description: 'always show these locations',\n options: [...(selectionList.map(x=>x[\"name\"]))].sort(),\n value:[\"New York\",\"Florida\",\"US total\"],\n multiple: true,\n size:10\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":4389,"value":"viewof toSmooth = radio({\n options: [\n { label: 'Show raw data', value: 0},\n { label: 'Apply smoothing', value: 1},\n ],\n value: 1\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2351,"value":"md`### NYT commit log:`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2348,"value":"table(modTableNYT)","pinned":false,"hidden":false,"mode":"ojs"},{"id":25,"value":"md`# Backend`","pinned":false,"hidden":false,"mode":"ojs"},{"id":568,"value":"md`## Data pulling`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1867,"value":"md`### Raw data into array of JSON`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2241,"value":"pullNYTcovid = async function(url) {\n let rawTxt = await (await fetch(url)).text()\n let rawArray = rawTxt.split(/\\r\\n|\\n/g).map(x=>mysplit(x))\n // trailing blank\n if((rawArray.slice(-1)[0].length==1)&isNaN(rawArray.slice(-1)[0][0])){ \n rawArray=rawArray.slice(0,-1)\n }\n let header = rawArray[0]\n console.log(rawArray.slice(0,2))\n rawArray = rawArray.slice(1) \n let jsonVec = rawArray.map(function(x) {\n let m = new Object()\n for (let i = 0; i < header.length; i++) {\n m[header[i]] = x[i] \n }\n return(m)\n })\n return(jsonVec)\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":2242,"value":"NYTdata = await pullNYTcovid(\"https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1990,"value":"md`### Combine by state and merge cases, deaths, recovered`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2269,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":2273,"value":"NYTArray = {\n let theData = NYTdata\n theData = theData.map(function(x){\n let y = JSON.parse(JSON.stringify(x))\n y[\"Country/Region\"] = y.state\n return y\n }) \n return await NYT2array(theData)\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":4421,"value":"USsummed = {\n let initialValue = JSON.parse(JSON.stringify(NYTArray[0]))\n initialValue[\"Country/Region\"] = \"US total\"\n initialValue[\"fips\"] = 0\n initialValue[\"cases\"] = initialValue[\"cases\"].map(x=>0)\n initialValue[\"deaths\"] = initialValue[\"deaths\"].map(x=>0)\n initialValue[\"recovered\"] = initialValue[\"recovered\"].map(x=>0)\n let mergeFun = function(ax,ay,bx,by) {\n let ai = 0\n let bi = 0\n while(ai < ax.length){\n if(ax[ai]==bx[bi]){\n ay[ai] = ay[ai] + by[bi]\n ai++\n bi++\n } else {\n ai++\n }\n }\n return ay\n }\n let summerCallback = function( acc, cur ) {\n acc[\"cases\"] = mergeFun(acc[\"dates\"],acc[\"cases\"],cur[\"dates\"],cur[\"cases\"])\n acc[\"deaths\"] = mergeFun(acc[\"dates\"],acc[\"deaths\"],cur[\"dates\"],cur[\"deaths\"])\n acc[\"recovered\"] = mergeFun(acc[\"dates\"],acc[\"recovered\"],cur[\"dates\"],cur[\"recovered\"])\n return acc\n }\n let summedUS = NYTArray.reduce(summerCallback,initialValue)\n\n return [summedUS]\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1992,"value":"md`### Add calculated stats: new, active, rates`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1965,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":2281,"value":"combinedStateData = await addCalculatedStats(NYTArray) ","pinned":false,"hidden":false,"mode":"ojs"},{"id":4458,"value":"combinedUSData = await addCalculatedStats(USsummed) ","pinned":false,"hidden":false,"mode":"ojs"},{"id":4442,"value":"combinedAllData = [...combinedStateData,...combinedUSData]","pinned":false,"hidden":false,"mode":"ojs"},{"id":570,"value":"md`## Prepare for plotting`","pinned":false,"hidden":false,"mode":"ojs"},{"id":364,"value":"covidToTraceShifted = function(covid,isShifted,thisCaseSync,thisVariable) {\n \n let trace = new Object()\n trace.y = covid[thisVariable]\n if(isShifted){\n let dayshift = trace.y.findIndex(x=>x>Math.pow(10,thisCaseSync))\n if(dayshift==-1){\n dayshift = trace.y.length\n } else if (dayshift <= 1){\n } else {\n dayshift = dayshift - 1 + (Math.pow(10,thisCaseSync) - trace.y[dayshift-1])/(trace.y[dayshift]-trace.y[dayshift-1])\n }\n trace.x = Array.from(trace.y.keys()).map(x=>x-dayshift)\n } else {\n trace.x = Array.from(covid[\"dates\"])\n }\n trace.mode = 'lines'\n trace.name = covid[\"Country/Region\"]+\" \"+thisVariable\n if(covid[\"Country/Region\"]==\"US\"){\n trace.line = {\n width: 4,\n color: 'rgb(0, 0, 255S)'\n }\n\n }\n return trace\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1702,"value":"makePlotFromArray = function(covidArray,caseFilter,thisVariable,yaxis) {\n let theData = covidArray\n \n theData = theData.filter(x=> caseFilter.includes(x[\"Country/Region\"]))\n\n let theTrace = theData.map(function(x) {\n let ATrace = covidToTraceShifted(x,false,0,thisVariable)\n ATrace.yaxis = yaxis\n return ATrace\n })\n\n return theTrace\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1385,"value":"thePlotTraces = {\n let casesTrace = makePlotFromArray(combinedAllData,checkStates,'newCases','y')\n let deathsTrace = makePlotFromArray(combinedAllData,checkStates,'newDeaths','y2')\n return [...casesTrace,...deathsTrace]\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":3219,"value":"selectionList = {\n let maxCases = combinedAllData.map(function(x){return {name: x[\"Country/Region\"],\n max: Math.max(...(x.cases)),}\n })\n maxCases.keys\n return maxCases\n}\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":2019,"value":"md`## String parsing`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2010,"value":"mysplit = function(x) {\n if(x[0]==\",\"){\n x = \" \" + x\n }\nlet odd = x.split(/,\"|\",|\"/)\nlet bigx = []\nfor(let i = 0; imysplit(x))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2633,"value":"md`## Smoothing functions`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2636,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":2643,"value":"smoothDiv = {\n \n let x = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]\n let y = [0,0,1,0,0,0,5,9,4,17,17,17,17,19,19,19,19,19,10,0,0,0,0]\n let yhat = smooth(y,toSmooth)\n let smoothPlotData = []\n \n let trace = new Object()\n trace.y = y\n trace.x = x\n trace.mode = 'markers'\n trace.name = 'original'\n smoothPlotData.push(trace)\n \n trace = new Object()\n trace.y = yhat\n trace.x = x\n trace.mode = 'lines'\n trace.name = 'smooth'\n smoothPlotData.push(trace)\n \n const div = DOM.element('div1')\n Plotly.newPlot(div, smoothPlotData);\n return div\n}\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":11,"value":"md`# Libraries\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1083,"value":"md`## User inputs\nhttps://observablehq.com/@jashkenas/inputs`","pinned":false,"hidden":false,"mode":"ojs"},{"id":951,"value":"import {slider} from \"@jashkenas/inputs\"\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":1215,"value":"import {checkbox} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1270,"value":"import {radio} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":3172,"value":"import {select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1079,"value":"md`## Pretty table and git data\nhttps://observablehq.com/@tmcw/tables`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2337,"value":"modTableNYT = {\n let result = await (await fetch(\"https://api.github.com/repos/nytimes/covid-19-data/commits?path=us-states.csv\") ).json()\n let myTable = []\n for(let i = 0; i<3 ; i++){\n let thisresult = result[i]\n \n let mydate = thisresult.commit.committer.date\n let myActualDate = new Date(mydate)\n let prettyDate = myActualDate.toString()\n \n let out = new Object()\n out.timestamp = prettyDate\n out.comment = thisresult.commit.message\n myTable.push(out)\n }\n return myTable\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1066,"value":"import {table} from \"@tmcw/tables@513\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1081,"value":"md`## Plotly!\nhttps://cdn.plot.ly/plotly-latest.min.js`","pinned":false,"hidden":false,"mode":"ojs"},{"id":37,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":2666,"value":"md`## Regression!\nhttps://github.com/Tom-Alexander/regression-js`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2748,"value":"regression = require('https://unpkg.com/regression@2.0.1/dist/regression.js')","pinned":false,"hidden":false,"mode":"ojs"},{"id":2536,"value":"md`## Editors note\nFingers crossed that it won't end up like my [old notebook](https://observablehq.com/@rmoffitt/covid)`","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W34","stdlib":"1","titling":"auto"}