31:T4c2,md` # CDC Hospital Capacity Data **Update July 16th: It is unclear whether or not the CDC will be getting and publishing hospital data anymore, as the US Adminstration appears to have instructed that data collection be directed to a different office.** This notebook seeks to expose and explore hospital [capacity data from the US CDC](https://www.cdc.gov/nhsn/covid19/report-overview.html#anchor_1590010579051). I'm interested in thinking about what 'capacity' means, especially in terms of any excess load caused by COVID-19. Limitations: - Note that the data is delayed. Specifically, for the data you're looking at right now, the data ends on **${d3.timeFormat("%A %B %e")(mostRecentDate)}, or ${d3.timeDay.count(mostRecentDate, new Date())} days in the past.** - No effort here to understand seasonal patterns or typical capacity for a given state. Take broad trends with a grain of salt. - In some states, relatively few hospitals are reporting data. (See [Percentage of Facilities Reporting by State](https://www.cdc.gov/nhsn/covid19/report-overview.html#anchor_1590010344017)) This impacts accuracy of the data, though some statistical methods seem to be applied to provide a 95% confidence interval. `32:[] 2f:{"title":"CDC Hospital Capacity Data","cells":[{"id":0,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":130,"value":"viewof config = {\n const multiselect = (name, values) => {\n return html`\n \n `;\n };\n\n return form(html`\n \n `);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":157,"value":"{\n return vl\n .data(selectedData)\n .title(\"Percent of Inpatient Beds with COVID-19\")\n .encode(\n vl.color({legend:{orient:\"top\"}}).fieldN('statename'),\n vl.x().fieldT('normalizedCollectionDate').title(\"Date\"), \n )\n .layer(\n vl.markArea()\n .encode(\n vl.y().fieldQ('InBedsOccCOVID__Numbeds_UpCI').scale({domain:[0,100]}),\n vl.y2().fieldQ('InBedsOccCOVID__Numbeds_LoCI'),\n vl.opacity().value(0.2)\n ),\n vl.markLine()\n .encode(\n vl.y().fieldQ('InBedsOccCOVID__Numbeds_Est').scale({domain:[0,100]}).title(null).axis({labelExpr: \"join([datum.label,'%'],'')\"})\n )\n )\n .width(width)\n .height(width * 0.25)\n .autosize({type: 'fit-x', contains: 'padding'})\n .render();\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":183,"value":"{\n return vl\n .data(selectedData)\n .title(\"ICU Percent Occupancy (All Patients)\")\n .encode(\n vl.color({legend:null}).fieldN('statename'),\n vl.x().fieldT('normalizedCollectionDate').title(\"Date\"), \n )\n .layer(\n vl.markArea()\n .encode(\n vl.y().fieldQ('ICUBedsOccAnyPat__N_ICUBeds_UpCI').scale({domain:[0,100]}),\n vl.y2().fieldQ('ICUBedsOccAnyPat__N_ICUBeds_LoCI'),\n vl.opacity().value(0.2)\n ),\n vl.markLine()\n .encode(\n vl.y().fieldQ('ICUBedsOccAnyPat__N_ICUBeds_Est').scale({domain:[0,100]}).title(null).axis({labelExpr: \"join([datum.label,'%'],'')\"})\n )\n )\n .width(width)\n .height(width * 0.25)\n .autosize({type: 'fit-x', contains: 'padding'})\n .render();\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":87,"value":"md`# Plumbing`","pinned":false,"hidden":false,"mode":"ojs"},{"id":188,"value":"defaultStates = [\"United States\", \"New York\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":69,"value":"selectedData = stateDailyReports.filter(r => config.selectedStateNames.includes(r.statename))","pinned":false,"hidden":false,"mode":"ojs"},{"id":16,"value":"md`## Dependencies`","pinned":false,"hidden":false,"mode":"ojs"},{"id":13,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":45,"value":"md`The data file itself can be grabbed (at time of writing, early July 2020) from https://www.cdc.gov/nhsn/pdfs/covid19/covid19-NatEst.csv`","pinned":false,"hidden":false,"mode":"ojs"},{"id":206,"value":"table(stateDailyReports)","pinned":false,"hidden":false,"mode":"ojs"},{"id":6,"value":"rawCSV = d3.csv(\"https://www.cdc.gov/nhsn/pdfs/covid19/covid19-NatEst.csv\")\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":25,"value":"stateDailyReports = {\n let reports = rawCSV\n .slice(1);\n //.filter(r => r.statename !== \"United States\");\n \n reports\n .forEach(r => r.normalizedCollectionDate = dataDateParser(r.collectionDate));\n \n return reports\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":227,"value":"mostRecentDate = d3.max(stateDailyReports.map(r => r.normalizedCollectionDate))","pinned":false,"hidden":false,"mode":"ojs"},{"id":133,"value":"statenames = stateDailyReports.map(r => r.statename).reduce(\n (l,name) => { \n if (l.indexOf(name) === -1) {\n l.push(name);\n }\n return l;\n },\n []\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":11,"value":"headerIndex = rawCSV[0];","pinned":false,"hidden":false,"mode":"ojs"},{"id":73,"value":"dataDateParser = d3.timeParse(\"%d%b%Y\");","pinned":false,"hidden":false,"mode":"ojs"},{"id":20,"value":"md`### Libraries`","pinned":false,"hidden":false,"mode":"ojs"},{"id":204,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":62,"value":"import {autoSelect, select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":139,"value":"import { form } from \"@mbostock/form-input\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":40,"value":"import {vl} from '@vega/vega-lite-api'","pinned":false,"hidden":false,"mode":"ojs"},{"id":2,"value":"d3 = require(\"d3@5\")","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W32","stdlib":"1","titling":"auto"}

States - Pick a few