Principal Web Developer at Freedom of the Press Foundation
Published
Edited
Aug 25, 2020
6 stars
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How many SARS-CoV-2 tests are we running in the U.S.?
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Coronavirus
usData = (await fetch('https://corsproxy.harrislapiroff.com/https://covidtracking.com/api/v1/us/daily.json')).json()
statesData = (await fetch('https://corsproxy.harrislapiroff.com/https://covidtracking.com/api/v1/states/daily.json')).json()
annotateData = (data, movingAverageN) => {
data.sort((a, b) => a.date - b.date)
return data.map((d, i, a) => {
const startIdx = i < movingAverageN ? 0 : i + 1 - movingAverageN
const dataToAverage = a.slice(startIdx, i + 1)
return {
...d,
positiveIncreaseSMA: average(dataToAverage.map(getPosTestCount)),
negativeIncreaseSMA: average(dataToAverage.map(getNegTestCount)),
totalIncreaseSMA: average(dataToAverage.map(getTestCount)),
}
})
}
activeData = annotateData(
dataFilter === 'ALL' ? usData : statesData.filter(d => d.state === dataFilter),
MOVING_AVERAGE_N
).filter(d => getDate(d) >= DATA_START_DATE)
height = width * .618
xScale = d3.scaleTime()
.domain([DATA_START_DATE, d3.max(usData, getDate)])
.range([margin.left, width - margin.right])
yScale = d3.scaleLinear()
.domain([0, d3.max(activeData, getTestCount)])
.range([height - margin.bottom, margin.top])
.nice()
xAxis = g => g.attr('transform', `translate(0, ${height - margin.bottom})`)
.call(
d3.axisBottom(xScale)
.ticks(width > 400 ? 15 : 5) // Fewer ticks for smaller screen
.tickFormat(d3.timeFormat(width > 400 ? '%b %d' : '%m/%d')) // Concise dates for smaller screen
)
yAxis = g => g.attr('transform', `translate(${margin.left}, 0)`)
.attr('class', 'grid')
.call(
d3.axisLeft(yScale)
.ticks(5)
.tickSize(-width + margin.left + margin.right)
)
.call(g => g.select('.domain').remove())
totalTestsSMALine = d3.area()
.defined(d => !isNaN(getPosSMA(d)))
.x(d => xScale(getDate(d)))
.y1(d => yScale(getTotalSMA(d)))
.y0(d => yScale(getPosSMA(d)) - 1)
posTestsSMALine = d3.area()
.defined(d => !isNaN(getPosSMA(d)))
.x(d => xScale(getDate(d)))
.y1(d => yScale(getPosSMA(d)))
.y0(d => yScale(0))
addInteractivity = (
xScale, // d3 scale
yScale, // d3 scale
g // d3 svg
) => {
const line = g.append('g')
.append('line')
.attr('stroke', 'rgba(0, 0, 0, 0.5)')
.attr('stroke-width', 1)
.attr('x1', 100)
.attr('y1', yScale.range()[0])
.attr('x2', 100)
.attr('y2', yScale.range()[1])
.attr('opacity', 0)
// We're "cheat" a little at interactivity by leveraging Obervable's views functionality
// We start by setting the value of the DOM node to null and then update it according to mouse events
const node = g.node()
node.value = null
const inputEvent = new CustomEvent("input")
g.on('mouseover', function() {
line.attr('opacity', 1)
})
g.on('mouseout', function() {
line.attr('opacity', 0)
node.value = null
node.dispatchEvent(inputEvent)
})
g.on('mousemove', function() {
const mouse = d3.mouse(this)
const xDomainVal = xScale.invert(mouse[0])
// Add 12 hours and clip off the time to round to the nearest midnight
const xDomainValRounded = (new Date(+xDomainVal + 43200000)).setHours(0, 0, 0, 0)
const xRangeVal = xScale.clamp(true)(xDomainValRounded)
// Offset position by 0.5 to get a pixel aligned line
line.attr('x1', xRangeVal + 0.5)
.attr('x2', xRangeVal + 0.5)
node.value = new Date(xDomainValRounded)
node.dispatchEvent(inputEvent)
})
}
testChart = {
const svg = d3.select(DOM.svg(width, height))
svg.append('g').call(yAxis)
const lineConfig = [
{
d: totalTestsSMALine,
fill: TOTAL_COLOR,
stroke: 'none',
},
{
d: posTestsSMALine,
fill: POS_COLOR,
stroke: 'none',
},
]
lineConfig.forEach(conf => {
const line = svg.append('path').datum(activeData)
Object.entries(conf).forEach(([k, v]) => line.attr(k, v))
})
// x-axis has to go after lines so it stacks on top of them
svg.append('g').call(xAxis)
.style('text-anchor', 'end')
.selectAll('text')
.attr('y', 8)
.attr('x', -6)
.attr('transform', 'rotate(-45)')
svg.call(
addInteractivity.bind(
this,
xScale,
yScale,
)
)
return svg
}
posPerYScale = d3.scaleLinear()
.domain([0, 1]).nice()
.range([height - margin.bottom, margin.top])
posPerYAxis = g => g.attr('transform', `translate(${margin.left}, 0)`)
.attr('class', 'grid')
.call(
d3.axisLeft(posPerYScale)
.ticks(10)
.tickFormat(d3.format(".0%"))
.tickSize(-width + margin.left + margin.right)
)
.call(g => g.select('.domain').remove())
posPerLine = d3.line()
.defined(d => !isNaN(getPosPerTest(d)))
.x(d => xScale(getDate(d)))
.y(d => posPerYScale(getPosPerTest(d)))
posPerSMALine = d3.line()
.defined(d => !isNaN(getPosPerTestSMA(d)))
.x(d => xScale(getDate(d)))
.y(d => posPerYScale(getPosPerTestSMA(d)))
posPerTestChart = {
const svg = d3.select(DOM.svg(width, height))
svg.append('g').call(xAxis)
.style('text-anchor', 'end')
.selectAll('text')
.attr('y', 8)
.attr('x', -6)
.attr('transform', 'rotate(-45)')
svg.append('g').call(posPerYAxis)
svg.append('path')
.datum(activeData)
.attr('d', posPerSMALine)
.attr('fill', 'none')
.attr('stroke', POS_COLOR)
.attr('stroke-width', FOREGROUND_WIDTH)
.attr('stroke-dasharray', FOREGROUND_DASH)
svg.call(
addInteractivity.bind(
this,
xScale,
yScale,
)
)
return svg
}
STATE_CHART_WIDTH = width > 600 ? '33%' : '100%'
html`<style type="text/css">
.state-charts-grid {
display: flex;
flex-direction: ${width > 600 ? 'row' : 'column'};
flex-wrap: wrap;
}
.state-charts-grid > * {
flex-basis: ${STATE_CHART_WIDTH};
margin-bottom: 15px;
}
.chart-label {
font-family: sans-serif;
font-weight: bold;
font-size: 12px;
text-transform: uppercase;
letter-spacing: .05em;
text-align: center;
}
</style>`
stateChart = (stateAbbr, width, highlight = 'total') => {
const height = Math.floor(width / 1.618)
const margin = {left: 40, right: 40, top: 10, bottom: 20}
const stateData = annotateData(
statesData.filter(d => d.state === stateAbbr),
MOVING_AVERAGE_N
)
if (stateData.length === 0) return null
const xScale = d3.scaleTime()
.domain([DATA_START_DATE, d3.max(usData, getDate)])
.range([margin.left, width - margin.right])
// Let's make a line for number of tests
const yScaleTotals = d3.scaleLinear()
.domain([0, d3.max(stateData, getTotalSMA)])
.range([height - margin.bottom, margin.top])
.nice()
const testLine = d3.line()
.defined(d => !isNaN(getTotalSMA(d)))
.x(d => xScale(getDate(d)))
.y(d => yScaleTotals(getTotalSMA(d)))
// Let's make a line for positives as a percentage of tsts
const yScalePercentage = d3.scaleLinear()
.domain([0, 1])
.range([height - margin.bottom, margin.top])
.nice()
const posPerTestLine = d3.line()
.defined(d => !isNaN(getPosPerTestSMA(d)))
.x(d => xScale(getDate(d)))
.y(d => yScalePercentage(getPosPerTestSMA(d)))
// Now generate the chart HTML and SVG
const wrapper = d3.select(html`<div class="state-chart"></div>`)
const svg = wrapper.append('svg')
.attr('width', width)
.attr('height', height)
// Add the name underneath the chart
wrapper.append('div')
.attr('class', 'chart-label')
.html(US_STATES[stateAbbr])
// Add the x-axis
svg.append('g')
.attr('transform', `translate(0, ${height - margin.bottom})`)
.call(
d3.axisBottom(xScale)
.ticks(width > 400 ? 5 : 3) // Fewer ticks for smaller screen
.tickFormat(d3.timeFormat(width > 400 ? '%b %d' : '%m/%d')) // Concise dates for smaller screen
.tickSize(5)
)
// Add y-axes
svg.append('g')
.attr('class', 'grid')
.attr('transform', `translate(${margin.left}, 0)`)
.call(
d3.axisLeft(highlight == 'total' ? yScaleTotals : yScalePercentage)
.ticks(5)
.tickFormat(highlight == 'total' ? d3.format('.2s') : d3.format('.0%'))
.tickSize(-width + margin.left + margin.right)
)
.call(g => g.select('.domain').remove())
// Add the test total data
svg.append('path')
.datum(stateData)
.attr('d', testLine)
.attr('fill', 'none')
.attr('stroke', TOTAL_COLOR)
.attr('stroke-width', highlight === 'total' ? 2 : 1)
.attr('stroke-dasharray', highlight === 'total' ? FOREGROUND_DASH : BACKGROUND_DASH)
// Add the pos per test data
svg.append('path')
.datum(stateData)
.attr('d', posPerTestLine)
.attr('fill', 'none')
.attr('stroke', POS_COLOR)
.attr('stroke-width', highlight === 'percentage' ? 2 : 1)
.attr('stroke-dasharray', highlight === 'percentage' ? FOREGROUND_DASH : BACKGROUND_DASH)
const finalPoint = stateData[stateData.length - 1]
const finalPointTotal = getTotalSMA(finalPoint)
svg.append('text')
.attr('x', width - margin.right + 5)
.attr('y', yScaleTotals(finalPointTotal))
.attr('font-family', 'sans-serif')
.attr('font-size', 12)
.attr('font-weight', 'bold')
.attr('fill', TOTAL_COLOR)
.attr('dominant-baseline', 'middle')
.attr('opacity', highlight === 'total' ? 1 : 0.25)
.text(d3.format('.2s')(finalPointTotal))
const finalPointPosPercentage = getPosPerTestSMA(finalPoint)
svg.append('text')
.attr('x', width - margin.right + 5)
.attr('y', yScalePercentage(finalPointPosPercentage))
.attr('font-family', 'sans-serif')
.attr('font-size', 12)
.attr('font-weight', 'bold')
.attr('fill', POS_COLOR)
.attr('dominant-baseline', 'middle')
.attr('opacity', highlight === 'percentage' ? 1 : 0.25)
.text(d3.format('.0%')(finalPointPosPercentage))
return wrapper.node()
}
html`
<style type="text/css">
.grid line {
stroke: #E5E5E5;
}
.grid .tick:first-of-type {
display: none;
}
</style>
`
getPosPerTest = d => {
const testCount = getTestCount(d)
if (testCount < MIN_TESTS_FOR_PERCENTAGE) return NaN // If test count is too low to return a useful %age
return getPosTestCount(d) / testCount
}
getPosPerTestSMA = d => {
const testCountSMA = getTotalSMA(d)
if (testCountSMA < MIN_TESTS_FOR_PERCENTAGE) return NaN // If test count is too low to return a useful %age
return getPosSMA(d) / testCountSMA
}
getPointByDate = (data, date) => data.filter(d => date.getTime() == getDate(d).getTime())[0]
FOREGROUND_WIDTH = width > 600 ? 4 : 1
BACKGROUND_WIDTH = width > 600 ? 1.5 : 1
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