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base_rate.js
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base_rate.js
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/*
TODO
# Add textbox to enter percentages
# Add switch for test result
# When switch is on "positive", make the negative circles dim
# Escape quotes and apostrophes in input, test bugs
# Add formulas
*/
require.config({
paths: {
d3src: 'https://d3js.org',
slider: 'https://unpkg.com/[email protected]/dist/d3-simple-slider.min'
},
map: {
'*': {
'd3': 'd3src/d3.v7.min',
'd3-timer': 'd3src/d3-timer.v3.min',
'd3-interpolate': 'd3src/d3-interpolate.v3.min',
'd3-color': 'd3src/d3-color.v3.min',
'd3-time': 'd3src/d3-time.v3.min',
'd3-format': 'd3src/d3-format.v3.min',
'd3-time-format': 'd3src/d3-time-format.v4.min',
'd3-array': 'd3src/d3-array.v3.min',
'd3-axis': 'd3src/d3-axis.v3.min',
'd3-dispatch': 'd3src/d3-dispatch.v3.min',
'd3-drag': 'd3src/d3-drag.v3.min',
'd3-ease': 'd3src/d3-ease.v3.min',
'd3-scale': 'd3src/d3-scale.v4.min',
'd3-selection': 'd3src/d3-selection.v3.min',
'd3-transition': 'd3src/d3-transition.v3.min'
}
}
})
var total = 1000
var prior = 0.5
var true_pos = 0.5
var true_neg = 0.5
var graphic_width = 850
var test_result = 0 // 0: unset, 1: pos, -1: neg
const pos_col = '#ffa600' // yellow orange
const neg_col = '#003f5c' // dark blue
const pos_col_dim = '#ffe4b3'
const neg_col_dim = '#b3e7ff'
function drawSlider1(d3, slider, svg) {
let g = svg.append('g').attr('transform', 'translate(39, 20)')
let s = slider.sliderBottom()
g.call(
s.min(0).max(1)
.width(200)
.tickFormat(d3.format('.1%'))
.tickValues([0, 0.25, 0.5, 0.75, 1])
.default(.5)
.on('onchange', val => {
true_pos = val
drawCircles(d3, d3.select('#circles'))
legendText(d3, d3.select('#legend'))
d3.select('#input1').property('value', d3.format('.1f')(val * 100))
})
)
return s
}
function drawSlider2(d3, slider, svg) {
let g = svg.append('g').attr('transform', 'translate(39, 20)')
let s = slider.sliderBottom()
g.call(
s.min(0).max(1)
.width(200)
.tickFormat(d3.format('.1%'))
.tickValues([0, 0.25, 0.5, 0.75, 1])
.default(.5)
.on('onchange', val => {
prior = val
drawCircles(d3, d3.select('#circles'))
legendText(d3, d3.select('#legend'))
d3.select('#input2').property('value', d3.format('.1f')(val * 100))
})
)
return s
}
function drawSlider3(d3, slider, svg) {
let g = svg.append('g').attr('transform', 'translate(39, 20)')
let s = slider.sliderBottom()
g.call(
s.min(0).max(1)
.width(200)
.tickFormat(d3.format('.1%'))
.tickValues([0, 0.25, 0.5, 0.75, 1])
.default(.5)
.on('onchange', val => {
true_neg = 1 - val
drawCircles(d3, d3.select('#circles'))
legendText(d3, d3.select('#legend'))
d3.select('#input3').property('value', d3.format('.1f')(val * 100))
})
)
return s
}
function drawCircles(d3, g, transition=false) {
let col_len = 25
let d = 17
let data = []
for (let i = 0; i < total; i++) {
let r = 6
let pos_neg_split = Math.round(total * prior)
let is_pos = i < pos_neg_split
let is_test_pos = is_pos ? i < Math.round(total * prior * true_pos) : i >= pos_neg_split + Math.round(total * (1-prior) * true_neg)
let x = is_pos ? ((i / col_len) >> 0) * d + 20 : graphic_width - 20 - (((i - pos_neg_split) / col_len) >> 0) * d
let y = is_pos ? (i % col_len) * d + 20 : ((i - pos_neg_split) % col_len * d + 20)
let fill
let stroke
if (test_result == 0) {
fill = is_pos ? pos_col : neg_col
stroke = is_test_pos ? pos_col : neg_col
} else if (test_result == 1) {
fill = is_pos ? (is_test_pos ? pos_col : pos_col_dim) : (is_test_pos ? neg_col : neg_col_dim)
stroke = is_test_pos ? pos_col : neg_col_dim
} else if (test_result == -1) {
fill = is_pos ? (is_test_pos ? pos_col_dim : pos_col) : (is_test_pos ? neg_col_dim : neg_col)
stroke = is_test_pos ? pos_col_dim : neg_col
}
data[i] = [x, y, r, fill, stroke]
}
if (transition) {
g.selectAll('circle')
.data(data)
.join('circle')
.transition(d3.transition().duration(100).ease(d3.easeLinear))
.attr('cx', function(d, i) {
return d[0]
})
.attr('cy', function(d, i) {
return d[1]
})
.attr('r', function(d, i) {
return d[2]
})
.attr('fill', function(d, i) {
return d[3]
})
.attr('stroke', function(d, i) {
return d[4]
})
.attr('stroke-width', 2.2)
} else {
g.selectAll('circle')
.data(data)
.join('circle')
.attr('cx', function(d, i) {
return d[0]
})
.attr('cy', function(d, i) {
return d[1]
})
.attr('r', function(d, i) {
return d[2]
})
.attr('fill', function(d, i) {
return d[3]
})
.attr('stroke', function(d, i) {
return d[4]
})
.attr('stroke-width', 2.2)
}
}
function drawLegend(d3, g) {
let y = 500
let r = 8
let stroke_width = 2.2/6*8
g.append('text')
.attr('id', 'total_text')
.attr('x', graphic_width/2)
.attr('y', y-24)
.attr('text-anchor', 'middle')
.text('Out of ' + total + ', there are...')
g.append('circle')
.attr('cx', 50)
.attr('cy', y)
.attr('r', r)
.attr('fill', pos_col)
.attr('stroke', pos_col)
.attr('stroke-width', stroke_width)
g.append('circle')
.attr('cx', 250)
.attr('cy', y)
.attr('r', r)
.attr('fill', pos_col)
.attr('stroke', neg_col)
.attr('stroke-width', stroke_width)
g.append('circle')
.attr('cx', 450)
.attr('cy', y)
.attr('r', r)
.attr('fill', neg_col)
.attr('stroke', pos_col)
.attr('stroke-width', stroke_width)
g.append('circle')
.attr('cx', 650)
.attr('cy', y)
.attr('r', r)
.attr('fill', neg_col)
.attr('stroke', neg_col)
.attr('stroke-width', stroke_width)
}
function ppv() {
return prior * true_pos / (prior * true_pos + (1-prior) * (1-true_neg))
}
function npv() {
return (1-prior) * true_neg / ((1-prior) * true_neg + prior * (1-true_pos))
}
function legendText(d3, g) {
let y = 506
let a = Math.round(total * prior * true_pos)
let b = Math.round(total * prior * (1-true_pos))
let c = Math.round(total * (1-prior) * (1-true_neg))
let d = Math.round(total * (1-prior) * true_neg)
let data = [
['true_pos_text', 65, y, a + ((a == 1) ? ' true positive' : ' true positives'), 1],
['false_neg_text', 265, y, b + ((b == 1) ? ' false negative' : ' false negatives'), 1],
['false_pos_text', 465, y, c + ((c == 1) ? ' false positive' : ' false positives'), 1],
['true_neg_text', 665, y, d + ((d == 1) ? ' true negative' : ' true negatives'), 1],
]
let ppv_npv = ['ppv_npv', 230, y+64, '', 0]
if (test_result == 1) {
let val = ppv()
ppv_npv[3] = isNaN(val) ? 'Nothing tested positive!' : d3.format('.1%')(ppv()) + ' of those who tested positive are true positives'
ppv_npv[4] = 1
} else if (test_result == -1) {
let val = npv()
ppv_npv[3] = isNaN(val) ? 'Nothing tested negative!' : d3.format('.1%')(npv()) + ' of those who tested negative are true negatives'
ppv_npv[4] = 1
} else {
if (!d3.select('#ppv_npv').empty()) {
ppv_npv[3] = d3.select('#ppv_npv').text()
}
}
data.push(ppv_npv)
g.selectAll('.legend_text')
.data(data)
.join('text')
.attr('id', function(d, i) {
return d[0]
})
.attr('class', 'legend_text')
.attr('x', function(d, i) {
return d[1]
})
.attr('y', function(d, i) {
return d[2]
})
.text(function(d, i) {
return d[3]
})
.transition(d3.transition().duration(100).ease(d3.easeLinear))
.style('opacity', function(d, i) {
return d[4]
})
}
function chooseResult(d3, g) {
let x = 400
let y = 540
g.append('text')
.text('Actual test result:')
.attr('x', x-150)
.attr('y', y)
g.append('rect')
.attr('id', 'pos_button')
.attr('x', x-12)
.attr('y', y-18)
.attr('width', 80)
.attr('height', 25)
.attr('rx', 5)
.attr('ry', 5)
.attr('fill', '#f1f1f1')
.attr('stroke-width', 2.5)
.on('mouseover', function(d) {
d3.select('#pos_button').attr('fill', pos_col_dim)
d3.select('#pos_button_text').attr('fill', '#000')
}).on('mousedown', function() {
if (test_result == 1) {
test_result = 0
d3.select('#pos_button').attr('stroke', 'none')
} else if (test_result == 0) {
test_result = 1
d3.select('#pos_button').attr('stroke', pos_col)
} else if (test_result == -1) {
test_result = 1
d3.select('#pos_button').attr('stroke', pos_col)
d3.select('#neg_button').attr('stroke', 'none')
d3.select('#neg_button_text').attr('fill', '#777')
}
drawCircles(d3, d3.select('#circles'), true)
legendText(d3, d3.select('#legend'))
}).on('mouseleave', function(d) {
d3.select('#pos_button').attr('fill', '#f1f1f1')
if (test_result != 1) {
d3.select('#pos_button_text').attr('fill', '#777')
}
})
g.append('text')
.attr('id', 'pos_button_text')
.text('Positive')
.attr('x', x)
.attr('y', y)
.attr('pointer-events', 'none')
.attr('fill', '#777')
x = 490
g.append('rect')
.attr('id', 'neg_button')
.attr('x', x-9)
.attr('y', y-18)
.attr('width', 80)
.attr('height', 25)
.attr('rx', 5)
.attr('ry', 5)
.attr('fill', '#f1f1f1')
.attr('stroke-width', 2.5)
.on('mouseover', function(d) {
d3.select('#neg_button').attr('fill', neg_col_dim)
d3.select('#neg_button_text').attr('fill', '#000')
}).on('mousedown', function() {
if (test_result == 1) {
test_result = -1
d3.select('#neg_button').attr('stroke', neg_col)
d3.select('#pos_button').attr('stroke', 'none')
d3.select('#pos_button_text').attr('fill', '#777')
} else if (test_result == 0) {
test_result = -1
d3.select('#neg_button').attr('stroke', neg_col)
} else if (test_result == -1) {
test_result = 0
d3.select('#neg_button').attr('stroke', 'none')
}
drawCircles(d3, d3.select('#circles'), true)
legendText(d3, d3.select('#legend'))
}).on('mouseleave', function(d) {
d3.select('#neg_button').attr('fill', '#f1f1f1')
if (test_result != -1) {
d3.select('#neg_button_text').attr('fill', '#777')
}
})
g.append('text')
.attr('id', 'neg_button_text')
.text('Negative')
.attr('x', x)
.attr('y', y)
.attr('pointer-events', 'none')
.attr('fill', '#777')
}
function onInput(d3) {
let q1_text = document.getElementById('q1').value
let q2_text = document.getElementById('q2').value
let command = 'toJS("' + q1_text + '","' + q2_text + '")'
IPython.notebook.kernel.execute(command)
}
function makeTooltip(d3, container, element, f) {
element
.on('mouseover', function(d) {
d3.json('base_rate.json').then(function(e) {
let t = f(e)
if (t != '') {
d3.select('#my_tooltip').text(t)
.transition(d3.transition().duration(100).ease(d3.easeLinear))
.style('opacity', 1)
}
})
}).on('mousemove', function(d) {
d3.select('#my_tooltip')
.style('left', (d3.pointer(d, container)[0]-24) + 'px')
.style('top', (d3.pointer(d, container)[1]+20) + 'px')
}).on('mouseleave', function(d) {
d3.select('#my_tooltip')
.transition(d3.transition().duration(100).ease(d3.easeLinear))
.style('opacity', 0)
})
}
function validatePercentage(val) {
return /^(100|(\d|\d\d)(|\.\d*))$/.test(val)
}
require.undef('viz')
define('viz', ['d3', 'slider'], function(d3, slider) {
function draw(container) {
d3.select(container).append('div').attr('id', 'questions')
d3.select(container).append('div').attr('id', 'my_tooltip')
d3.select('#questions').append('label').attr('for', 'q1').text('What is the question you are trying to answer?').style('margin-right', '20px')
d3.select('#questions').append('input').attr('type', 'text').attr('id', 'q1').attr('name', 'q1').attr('placeholder', 'e.g. Do I have Covid? Is Jack the killer?').style('width', '500px')
d3.select('#q1').on('input', function() {
onInput(d3)
})
d3.select('#questions').append('br')
d3.select('#questions').append('label').attr('for', 'q2').text('What is the test you are performing?').style('margin-right', '20px')
d3.select('#questions').append('input').attr('type', 'text').attr('id', 'q2').attr('name', 'q2').attr('placeholder', 'e.g. PCR test').style('width', '200px')
d3.select('#q2').on('input', function() {
onInput(d3)
})
onInput(d3)
d3.select(container).append('div').attr('id', 'sliders')
d3.select('#sliders').append('div').attr('id', 'slider1')
d3.select('#sliders').append('div').attr('id', 'slider2')
d3.select('#sliders').append('div').attr('id', 'slider3')
let sl1 = d3.select('#slider1').append('span').attr('class', 'slider_label').text('True positive rate:')
let s1_input = d3.select('#slider1').append('input')
.attr('id', 'input1')
.attr('class', 'pc_input')
.attr('type', 'number')
.attr('step', 0.1)
.attr('value', true_pos * 100)
d3.select('#slider1').append('span').attr('class', 'slider_label').text('%')
makeTooltip(d3, container, sl1, (e) => {return 'If ' + e.statement + ', how likely would the ' + e.test + ' correctly turn up positive?'})
let sl2 = d3.select('#slider2').append('span').attr('class', 'slider_label').text('Prior probability:')
let s2_input = d3.select('#slider2').append('input')
.attr('id', 'input2')
.attr('class', 'pc_input')
.attr('type', 'number')
.attr('step', 0.1)
.attr('value', prior * 100)
d3.select('#slider2').append('span').attr('class', 'slider_label').text('%')
makeTooltip(d3, container, sl2, (e) => {return 'Before performing any tests, what is the prior probability that ' + e.statement + '?'})
let sl3 = d3.select('#slider3').append('span').attr('class', 'slider_label').text('False positive rate:')
let s3_input = d3.select('#slider3').append('input')
.attr('id', 'input3')
.attr('class', 'pc_input')
.attr('type', 'number')
.attr('step', 0.1)
.attr('value', (1 - true_neg) * 100)
d3.select('#slider3').append('span').attr('class', 'slider_label').text('%')
makeTooltip(d3, container, sl3, (e) => {return 'If ' + e.statement_neg + ', how likely would the ' + e.test + ' incorrectly turn up positive?'})
let svg_slider1 = d3.select('#slider1').append('svg').attr('width', '280px').attr('height', '70px')
let s1 = drawSlider1(d3, slider, svg_slider1)
s1_input.on('input', function() {
let val = document.getElementById('input1').value
if (validatePercentage(val)) {
true_pos = String(val / 100)
s1.silentValue(val / 100)
drawCircles(d3, d3.select('#circles'))
legendText(d3, d3.select('#legend'))
d3.select('#input1').transition(d3.transition().duration(100).ease(d3.easeLinear)).style('background-color', '#fff')
} else {
d3.select('#input1').transition(d3.transition().duration(100).ease(d3.easeLinear)).style('background-color', '#ffcdd2')
}
})
let svg_slider2 = d3.select('#slider2').append('svg').attr('width', '280px').attr('height', '70px')
let s2 = drawSlider2(d3, slider, svg_slider2)
s2_input.on('input', function() {
let val = document.getElementById('input2').value
if (validatePercentage(val)) {
prior = String(val / 100)
s2.silentValue(val / 100)
drawCircles(d3, d3.select('#circles'))
legendText(d3, d3.select('#legend'))
d3.select('#input2').transition(d3.transition().duration(100).ease(d3.easeLinear)).style('background-color', '#fff')
} else {
d3.select('#input2').transition(d3.transition().duration(100).ease(d3.easeLinear)).style('background-color', '#ffcdd2')
}
})
let svg_slider3 = d3.select('#slider3').append('svg').attr('width', '280px').attr('height', '70px')
let s3 = drawSlider3(d3, slider, svg_slider3)
s3_input.on('input', function() {
let val = document.getElementById('input3').value
if (validatePercentage(val)) {
true_neg = 1 - String(val / 100)
s3.silentValue(val / 100)
drawCircles(d3, d3.select('#circles'))
legendText(d3, d3.select('#legend'))
d3.select('#input3').transition(d3.transition().duration(100).ease(d3.easeLinear)).style('background-color', '#fff')
} else {
d3.select('#input3').transition(d3.transition().duration(100).ease(d3.easeLinear)).style('background-color', '#ffcdd2')
}
})
d3.select(container).append('div').attr('id', 'graphic')
d3.select('#graphic').append('svg').attr('width', graphic_width).attr('height', '600px')
let g_circles = d3.select('#graphic svg').append('g').attr('id', 'circles')
let g_legend = d3.select('#graphic svg').append('g').attr('id', 'legend')
drawCircles(d3, g_circles)
drawLegend(d3, g_legend)
legendText(d3, g_legend)
chooseResult(d3, g_legend)
let ppv_npv_text = d3.select('#ppv_npv')
makeTooltip(d3, container, ppv_npv_text, (e) => {
if (test_result == 1) {
return 'Given that the ' + e.test + ' came back positive, the probability that ' + e.statement + ' is ' + d3.format('.1%')(ppv()) + '.'
} else if (test_result == -1) {
return 'Given that the ' + e.test + ' came back negative, the probability that ' + e.statement_neg + ' is ' + d3.format('.1%')(npv()) + '.'
} else {
return ''
}
})
}
return draw
})
// element.append('Loaded 🎉')