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cases2.html
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<!DOCTYPE html>
<meta charset="utf-8">
<title>EBOV outbreak</title>
<link rel="stylesheet" type="text/css" href="css/dc.css"/>
<link rel="stylesheet" href="css/leaflet.css"/>
<link rel="stylesheet" href="css/MarkerCluster.css"/>
<link rel="stylesheet" href="css/MarkerCluster.Default.css"/>
<style>
body {
font-family: Helvetica, Arial, sans-serif;
width: 900px;
}
footer {
padding: 2em 0 1em 0;
font-size: 12px;
}
h1 {
font-size: 96px;
margin-top: .3em;
margin-bottom: 0;
}
h1 + h2 {
margin-top: 0;
}
h2 {
font-weight: 100;
font-size: 28px;
}
h1, h2 {
font-family: Helvetica, Arial, sans-serif;
text-rendering: optimizeLegibility;
}
#body > p {
line-height: 1.5em;
width: 640px;
text-rendering: optimizeLegibility;
}
#charts {
padding: 10px 0;
display: block;
}
#lists {
display: block;
}
.dc-chart {
margin-bottom: 20px;
float: none;
}
#map .selected path {
stroke: none;
fill-opacity: 1;
}
#map .deselected path {
stroke: none;
fill-opacity: .5;
}
.dc-chart g.row text {
fill: black;
font-family: Helvetica, Arial, sans-serif;
font-size: 11px;
cursor: pointer;
}
.reset {
padding-left: 1em;
font-size: smaller;
color: #aaa;
}
.reset-all {
color: #aaa;
}
.axis path, .axis line {
fill: none;
stroke: #000;
shape-rendering: crispEdges;
}
.axis text {
font: 10px;
}
.title {
font-weight: 200;
font-size: 14px;
}
.brush rect.extent {
fill: steelblue;
fill-opacity: .125;
}
.brush .resize path {
fill: #eee;
stroke: #666;
}
#time-chart {
width: 900px;
height: 240px;
}
#time-chart .bar {
fill: teal;
}
#cumulative-chart {
width: 900px;
height: 320px;
}
#location-chart {
width: 280px;
height: 180px;
}
#death-chart {
width: 180px;
height: 180px;
}
#case-list .month {
margin-bottom: .4em;
font-size: 14px;
}
#case-list .individual {
margin-left: 100px;
padding-left: 10px;
line-height: 1.5em;
background: #eee;
width: 780px;
margin-bottom: 1px;
font-size: 12px;
}
#case-list-header .header {
margin: 0px;
padding: 0px;
margin-left: 100px;
padding-left: 10px;
width: 780px;
font-size: 14px;
}
#case-list .individual div {
display: inline-block;
white-space: nowrap;
overflow: hidden;
text-overflow: ellipsis;
}
#case-list-header .header div {
display: inline-block;
white-space: nowrap;
overflow: hidden;
text-overflow: ellipsis;
}
div.onset,
div.death {
width: 60px;
padding-right: 10px;
text-align: left;
}
div.age,
div.gender {
width: 40px;
padding-right: 10px;
text-align: left;
}
div.province,
div.city {
width: 100px;
padding-right: 10px;
text-align: left;
}
div.notes {
color: #999;
width: 260px;
padding-right: 10px;
text-align: left;
font: 10px;
}
#data-count {
text-align: right;
width: 850px;
margin-top: 10px;
margin-right: 15px;
font-size: 14px;
}
#data-count .filter-count {
color: #3182bd;
font-weight: 400;
}
#data-count .total-count {
color: #3182bd;
font-weight: 400;
}
.inline-div {
display: inline-block;
}
.align-top {
vertical-align: top;
}
.align-bottom {
vertical-align: bottom;
}
.block-div {
display: block;
}
</style>
<style type="text/css">
svg {
display: block;
}
circle {
fill: brown;
fill-opacity: .5;
stroke: #fff;
}
circle:hover {
fill: red;
fill-opacity: 1;
stroke: #fff;
}
#province path {
fill: steelblue;
fill-opacity: 0.25;
stroke: #fff;
stroke-width: 1.5px;
vector-effect: non-scaling-stroke;
}
.info {
width: 200px;
padding: 6px 8px;
font: 14px/16px Helvetica, Arial, sans-serif;
background: white;
background: rgba(255, 255, 255, 0.8);
box-shadow: 0 0 15px rgba(0, 0, 0, 0.2);
border-radius: 5px;
}
.info h4 {
margin: 0 0 5px;
color: #777;
}
.legend {
width: 80px;
line-height: 18px;
color: #555;
}
.legend i {
width: 18px;
height: 18px;
float: left;
margin-right: 8px;
opacity: 0.7;
}
#map {
width: 900px;
height: 320px;
}
</style>
<div id="body">
<div>
<div id="data-count" class="title">
<span class="filter-count"></span> selected out of <span class="total-count"></span> cases | <a
class="reset-all title"
href="javascript:dc.filterAll(); dc.renderAll();">reset all</a>
</div>
</div>
<div id="charts">
<!--<div>-->
<!--<div id="data-count1" class="title">-->
<!--<span class="filter-count"></span> selected out of <span class="total-count"></span> cases | <a-->
<!--class="reset-all title"-->
<!--href="javascript:dc.filterAll(); renderAll();">reset all</a>-->
<!--</div>-->
<!--</div>-->
<div class="block-div">
<div id="location-chart" class="dc-chart align-bottom inline-div">
<span class="title" class="inline-div">Cases by Location</span>
<a class="reset title" href="javascript:locationChart.filterAll();dc.redrawAll();"
style="display: none;">reset</a>
</div>
<div id="death-chart" class="dc-chart align-bottom inline-div">
<span class="title">By Outcome</span>
<a class="reset title" href="javascript:deathChart.filterAll();dc.redrawAll();"
style="display: none;">reset</a>
</div>
<div id="map" class="inline-div align-bottom inline-div"></div>
</div>
<div id="time-chart" class="dc-chart">
<span class="title">New cases per week</span>
<a class="reset title" href="javascript:timeChart.filterAll();dc.redrawAll();"
style="display: none;">reset</a>
</div>
<div id="cumulative-chart" class="dc-chart">
<span class="title">Cases Cumulative</span>
<a class="reset title" href="javascript:cumulativeChart.filterAll();dc.redrawAll();" style="display: none;">reset</a>
</div>
</div>
<!--
<div id="lists" class="block-div">
<div id="case-list-header">
<div class="header title">
<div class="onset">Date</div>
<div class="death">Death</div>
<div class="age">Age</div>
<div class="gender">Gender</div>
<div class="province">Province</div>
<div class="city">City</div>
</div>
</div>
<div id="case-list" class="list"></div>
</div>
-->
<!--
<footer>
<span style="float:right;">
Released under the <a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache License 2.0</a>.
</span>
Uses <a href="http://squareup.com">Square, Inc.</a>
</footer>
-->
</div>
<script src="js/crossfilter.min.js"></script>
<script src="js/d3.min.js"></script>
<script src="js/d3.geo.projection.v0.min.js"></script>
<script src="js/colorbrewer.js"></script>
<script src="js/dc.js"></script>
<script src="js/queue.min.js"></script>
<script src="js/leaflet.js"></script>
<script src="js/leaflet.markercluster.js"></script>
<script src="js/utils.js"></script>
<!--
<script src="crossfilter.v1.min.js"></script>
<script src="d3.v3.min.js"></script>
-->
<script>
var map = dc.geoChoroplethChart("#map");
var timeChart = dc.barChart("#time-chart");
var cumulativeChart = dc.lineChart("#cumulative-chart");
var locationChart = dc.rowChart("#location-chart");
var deathChart = dc.rowChart("#death-chart");
dc.constants.EVENT_DELAY = 0;
queue()
.defer(d3.json, "data/countries_50m.json")
// .defer(d3.json, "data/locations.json")
.defer(d3.csv, "data/cases.csv")
.await(ready);
function ready(error, countryData, /*locationData, */caseData) {
if (error) return console.log("there was an error loading the data: " + error);
// Various formatters.
var formatNumber = d3.format(",d"),
formatPercent = d3.format(".1%"),
formatDate = d3.time.format("%Y-%m-%d"),
formatPrettyDate = d3.time.format("%d %b"),
formatMonth = d3.time.format("%b %Y");
var cases = [];
var deaths = [];
var countries = [];
var locations = [];
var nestByDate = d3.nest()
.key(function (d) {
return d3.time.month(d.date);
});
// Create a list of countries from the GeoJSON doc...
countryData.features.forEach(function (d) {
var c = {
name: d.properties.name,
cumulative: []
};
countries.push(c);
});
for (i = 0; i < caseData.length; i++) {
var d = caseData[i];
d.index = i;
if (d.location.length == 0) {
if (d.date != null) {
d.date = formatDate.parse(d.date);
}
var found = false;
countries.forEach(function (country) {
if (d.country == country.name) {
d['country'] = country;
var c = {
date: d.date,
cases: d.cases_cumulative,
deaths: d.deaths_cumulative,
confirmedCases: d.cases_cumulative_confirmed,
confirmedDeaths: d.deaths_cumulative_confirmed
};
var last = country.cumulative[country.cumulative.length - 1];
if (c.cases.length === 0) {
c.cases = (last ? last.cases : 0);
}
if (c.deaths.length === 0) {
c.deaths = (last ? last.deaths : 0);
}
if (c.confirmedCases.length === 0) {
c.confirmedCases = (last ? last.confirmedCases : 0);
}
if (c.confirmedDeaths.length === 0) {
c.confirmedDeaths = (last ? last.confirmedDeaths : 0);
}
// cast to integer
c.cases = +c.cases;
c.deaths = +c.deaths;
c.confirmedCases = +c.confirmedCases;
c.confirmedDeaths = +c.confirmedDeaths;
country.cumulative.push(c);
found = true;
}
});
if (!found) {
console.log("Country not found: " + d.country);
d.country = null;
}
// if (d.location.length > 0) {
// locationDate.forEach(function (location) {
// if (d.location == location.name) {
// d['location'] = location;
// found = true;
// }
// });
// if (!found) console.log("Location not found: " + d.location);
// }
// if (!found) d.location = null;
found = false;
}
}
countries.forEach(function (d, i) {
// iterate through the cumulative list for each country looking for drops
// in the cumulative counts (presumably due to re-evaluation of cases). Feed
// these back to previous counts.
for (i = d.cumulative.length - 1; i > 0; i--) {
var d2 = d.cumulative[i];
var prev = d.cumulative[i - 1];
if (prev.cases > d2.cases) {
prev.cases = d2.cases;
}
if (prev.deaths > d2.deaths) {
prev.deaths = d2.deaths;
}
if (prev.confirmedCases > d2.confirmedCases) {
console.log("Unexpected drop in confirmed cases, " + d.name + ", " + d2.date);
prev.confirmedCases = d2.confirmedCases;
}
if (prev.confirmedDeaths > d2.confirmedDeaths) {
console.log("Unexpected drop in confirmed deaths, " + d.name + ", " + d2.date);
prev.confirmedDeaths = d2.confirmedDeaths;
}
}
// create items for each new case and death
for (i = 1; i < d.cumulative.length; i++) {
var d2 = d.cumulative[i];
var prev = d.cumulative[i - 1];
var caseCount = d2.cases - prev.cases;
var deathCount = d2.deaths - prev.deaths;
var confirmedCaseCount = d2.confirmedCases - prev.confirmedCases;
var confirmedDeathCount = d2.confirmedDeaths - prev.confirmedDeaths;
for (j = 0; j < caseCount; j++) {
var c = {
date: d2.date,
country: d,
location: null,
isDead: (j <= deathCount)
}
cases.push(c);
}
last = d2;
}
});
// Create the crossfilter for the relevant dimensions and groups.
var crossFilter = crossfilter(cases),
filteredCases = crossFilter.groupAll(),
allCases = crossFilter.dimension(function (d) {
return d;
}),
dateFilter = crossFilter.dimension(function (d) {
return d.date;
}),
dateGroups = dateFilter.group(d3.time.week),
_group = dateFilter.group().reduceSum(function (d) {
return 1;
}),
cumulativeGroups = {
all: function () {
var cumulate = 0;
var g = [];
_group.all().forEach(function (d, i) {
cumulate += d.value;
g.push({key: d.key, value: cumulate})
});
return g;
}
},
countryFilter = crossFilter.dimension(function (d) {
return d.country.name;
}),
countryGroups = countryFilter.group(function (d) {
return d;
}),
countryFilter2 = crossFilter.dimension(function (d) {
return d.country.name;
}),
countryGroups2 = countryFilter.group(function (d) {
return d;
}),
countryCumulativeGroup = {
all: function () {
var cumulate = 0;
var g = [];
countryCountGroup.all().forEach(function (d, i) {
cumulate += d.value;
g.push({key: d.key, value: cumulate})
});
return g;
}
},
deathFilter = crossFilter.dimension(function (d) {
return d.isDead;
}),
deathGroups = deathFilter.group(function (d) {
return d;
}),
confirmedFilter = crossFilter.dimension(function (d) {
return d.isConfirmed;
}),
confirmedGroups = confirmedFilter.group(function (d) {
return d;
});
var width = 800,
height = 320;
var projection = d3.geo.robinson()
.scale(1000)
.translate([width * 0.5, height * 1.0])
.precision(.1);
var scheme = colorbrewer.YlOrRd[9];
var colors = [ '#CCC' ].concat(scheme);
var color2 = d3.scale.linear()
.domain([0, 1000])
.range(scheme);
map.width(width)
.height(height)
.transitionDuration(100)
.dimension(countryFilter2)
.group(countryGroups2)
.colors(colors)
.colorDomain([-100, 1000])
// .colorAccessor(function (d) {
// if (d === 0) {
// return 0;
// }
// return d;
// })
.overlayGeoJson(countryData.features, "country", function (d) {
return d.properties.admin;
})
.projection(projection)
// .on("filtered", function () {
// dc.redrawAll();
// });
.title(function (d) {
if (d.value === undefined) {
return "Country: " + d.key + "\rno cases";
} else {
return "Country: " + d.key + "\rcases: " + d.value;
}
});
timeChart.width(900)
.height(240)
.transitionDuration(100)
.margins({top: 10, right: 20, bottom: 20, left: 40})
.dimension(dateFilter)
.group(dateGroups)
.centerBar(true)
.gap(1)
.elasticY(true)
.x(d3.time.scale().domain([new Date(2014, 2, 1), new Date()]))
.round(d3.time.week.round)
.xUnits(d3.time.weeks);
cumulativeChart
.width(900)
.height(320)
.renderArea(true)
.transitionDuration(100)
.rangeChart(timeChart)
.margins({top: 10, right: 20, bottom: 20, left: 40})
.dimension(dateFilter)
.group(cumulativeGroups)
// .stack(countryGroups, "Country", function (d) {
// return d.value;
// })
.elasticY(true)
.renderHorizontalGridLines(true)
.x(d3.time.scale().domain([new Date(2014, 2, 1), new Date()]))
.round(d3.time.day.round)
.xUnits(d3.time.days);
locationChart.width(280)
.height(140)
.transitionDuration(100)
.margins({top: 0, right: 20, bottom: 38, left: 20})
.dimension(countryFilter)
.group(countryGroups)
.elasticX(false)
.colors(d3.scale.category20c())
.label(function (d) {
return d.value + " " + d.key;
})
.title(function (d) {
return d.value;
})
.xAxis().ticks(5);
console.log(deathGroups.all());
deathChart
.transitionDuration(100)
.width(180)
.height(80)
.margins({top: 0, right: 0, bottom: 20, left: 20})
.dimension(deathFilter)
.group(deathGroups)
.colors(['#CD9B1D', '#FFC125'])
.label(function (d) {
var k = d.value;
var n = deathGroups.all()[0].value + deathGroups.all()[1].value;
return k + (n > 0 ? " " + (d.key ? "dead" : "unknown") + " (" + formatPercent(k / n) + ")" : "");
})
.title(function (d) {
return d.value;
})
.elasticX(false)
.xAxis().ticks(5);
// Render the initial lists.
// var list = d3.selectAll(".list")
// .data([caseList]);
// Render the total.
dc.dataCount("#data-count")
.dimension(crossFilter)
.group(filteredCases);
// var markerLayers = L.layerGroup();
// markerLayers.addTo(map);
// function updateMap() {
// markerLayers.clearLayers();
//
// // Create a layer for all the cities with circles scaled by the number of cases
// provinces.all().forEach(function (province) {
// var markers = L.markerClusterGroup({
// maxClusterRadius: 80,
// spiderfyOnMaxZoom: true,
// showCoverageOnHover: false,
// zoomToBoundsOnClick: true,
// singleMarkerMode: true
// });
//
// var markerList = [];
// allCases.top(Infinity).forEach(function (individual) {
// if (individual.province.name == province.key) {
// var city = individual.city;
// if (city != null) {
// var title = city.name;
// var marker = L.marker(L.latLng(city.coordinates[1], city.coordinates[0]), { title: title });
// marker.bindPopup(title);
// markers.addLayer(marker);
// markerList.push(marker);
// } else {
// var title = individual.province.name + " Province";
// var marker = L.marker(L.latLng(individual.province.coordinates[1], individual.province.coordinates[0]), { title: title });
// marker.bindPopup(title);
// markers.addLayer(marker);
// markerList.push(marker);
// }
// }
// });
//
// markerLayers.addLayer(markers);
// });
// }
dc.renderAll();
// // Renders the specified chart or list.
// function render(method) {
// d3.select(this).call(method);
// }
//
// // Whenever the brush moves, re-rendering everything.
// function renderAll() {
//// list.each(render);
// dc.renderAll();
//// updateMap();
// }
// Like d3.time.format, but faster.
function parseDate(d) {
return new Date(2001,
d.substring(0, 2) - 1,
d.substring(2, 4),
d.substring(4, 6),
d.substring(6, 8));
}
// window.filter = function (filters) {
// renderAll();
// };
//
// window.reset = function (i) {
// renderAll();
// };
var args = getUrlVars();
if ('country' in args) {
console.log(args.country);
countryFilter.filter(args.country);
}
// function caseList(div) {
// var casesByDate = nestByDate.entries(onsetDate.top(Infinity));
//
// div.each(function () {
// var month = d3.select(this).selectAll(".month")
// .data(casesByDate, function (d) {
// return d.key;
// });
//
// month.enter().append("div")
// .attr("class", "month title")
// .text(function (d) {
// return formatMonth(d.values[0].date);
// });
//
// month.exit().remove();
//
// var individual = month.order().selectAll(".individual")
// .data(function (d) {
// return d.values;
// }, function (d) {
// return d.index;
// });
//
// var individualEnter = individual.enter().append("div")
// .attr("class", "individual");
//
// individualEnter.append("div")
// .attr("class", "onset")
// .text(function (d) {
// return formatPrettyDate(d.date);
// });
//
// individualEnter.append("div")
// .attr("class", "death")
// .text(function (d) {
// return (d.death != null ? formatPrettyDate(d.death) : "");
// });
//
// individualEnter.append("div")
// .attr("class", "age")
// .text(function (d) {
// return d.age;
// });
//
// individualEnter.append("div")
// .attr("class", "gender")
// .text(function (d) {
// return d.gender;
// });
//
// individualEnter.append("div")
// .attr("class", "province")
// .text(function (d) {
// return d.province.name;
// });
//
// individualEnter.append("div")
// .attr("class", "city")
// .text(function (d) {
// return d.city ? d.city.name : "-";
// });
//
// individualEnter.append("div")
// .attr("class", "notes")
// .text(function (d) {
// return d.notes;
// });
//
// individualEnter.append("div")
// .attr("class", "ref")
// .append("a")
// .attr("href", function (d) {
// return d.citation;
// })
// .attr("target", "_blank")
// .text(function (d) {
// return d.citation != null && d.citation.length > 0 ? "Ref" : "";
// });
//
// individual.exit().remove();
//
// individual.order();
// });
// } //function caseList(div)
} // function ready(error, cityData, caseData)
</script>