31:Ta9d,viewof map = { let container = DOM.element('div', { style: `width:${width/1.1}px;height:${width/1.5}px;margin-left: auto;margin-right: auto;` , id: 'map'}); yield container; // Centre var centreLonLat = [7.9488428,9.0566997]; var centreWebMercator = ol.proj.fromLonLat(centreLonLat); // Tile layer var tileLayer = new ol.layer.Tile({ source: new ol.source.OSM() }); var rasterLayer = new ol.layer.Tile({ //source: new ol.source.Stamen({layer:"terrain"}) source: new ol.source.XYZ({ //url: 'https://server.arcgisonline.com/ArcGIS/rest/services/World_Terrain_Base/MapServer/tile/{z}/{y}/{x}', //attributions: '© ESRI' url: 'https://{1-4}.basemaps.cartocdn.com/light_all/{z}/{x}/{y}{r}.png', attributions: '© OpenStreetMap © CARTO' }) }); // Study sites var sitelabels = Object.keys(locations); var sites = []; for(var i=0;i"+susByState[feature.get('name_1')]+" suspected"; } }; map.on('pointermove', displayTooltip); return container; }32:T4ec,function randomPointsOnPolygon(number, polygon, properties, fc) { if (typeof properties === 'boolean') { fc = properties; properties = {}; } if (number < 1) { return []; } if(polygon.type !== 'Feature') { return new Error('Polygon parameter must be a Feature<(Polygon|MultiPolygon)>'); if (polygon.geometry.type !== 'Polygon' || polygon.geometry.type !== 'MultiPolygon') { return new Error('Polygon parameter must be a Feature<(Polygon|MultiPolygon)>') } } if (this instanceof randomPointsOnPolygon) { return new randomPointsOnPolygon(number, polygon, properties); } properties = properties || {}; fc = fc || false; var points = []; var bbox = turf.bbox(polygon); var count = Math.round(parseFloat(number)); for (var i = 0; i <= count; i++) { if (i === count) { if (fc) { return turf.featurecollection(points); } return points; } var point = turf.randomPoint(1, { bbox: bbox }); if (turf.booleanPointInPolygon(point.features[0], polygon) === false) { i = --i; } if (turf.booleanPointInPolygon(point.features[0], polygon) === true) { point.features[0].properties = properties; points.push(point.features[0]); } } }33:[] 2f:{"title":"Lassa fever in Nigeria, updated","cells":[{"id":0,"value":"md`# Lassa fever in Nigeria, updated`","pinned":false,"hidden":false,"mode":"ojs"},{"id":269,"value":"md`## Suspected cases by state, 3/2017-present`","pinned":false,"hidden":false,"mode":"ojs"},{"id":6,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":274,"value":"md`## Notifications by week and status`","pinned":false,"hidden":false,"mode":"ojs"},{"id":155,"value":"{\n var postrace = {\n type: \"bar\",\n name: 'Positive',\n x: Object.keys(posByDate),\n y: Object.values(posByDate)\n };\n \n var negtrace = {\n type: \"bar\",\n name: 'Negative',\n x: Object.keys(negByDate),\n y: Object.values(negByDate)\n };\n \n var unttrace = {\n type: \"bar\",\n name: 'Untested',\n x: Object.keys(untByDate),\n y: Object.values(untByDate)\n };\n \n var data = [postrace,negtrace,unttrace];\n \n var layout = {\n width: width,\n height: width/1.5,\n barmode: 'stack'\n };\n \n const div = DOM.element('div');\n Plotly.newPlot(div, data, layout);\n return div;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":277,"value":"md`## Notifications by state and status`","pinned":false,"hidden":false,"mode":"ojs"},{"id":215,"value":"{\n var postrace = {\n type: \"bar\",\n name: 'Positive',\n x: Object.keys(posByState),\n y: Object.values(posByState)\n };\n \n var negtrace = {\n type: \"bar\",\n name: 'Negative',\n x: Object.keys(negByState),\n y: Object.values(negByState)\n };\n \n var unttrace = {\n type: \"bar\",\n name: 'Untested',\n x: Object.keys(untByState),\n y: Object.values(untByState)\n };\n \n var data = [postrace,negtrace,unttrace];\n \n var layout = {\n width: width,\n height: width/1.5,\n barmode: 'stack'\n };\n \n const div = DOM.element('div');\n Plotly.newPlot(div, data, layout);\n return div;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":260,"value":"md`## Background`","pinned":false,"hidden":false,"mode":"ojs"},{"id":262,"value":"md`This is a visualisation of data on notifications of Lassa fever from Nigeria published by [the Nigerian CDC](? http://ncdc.gov.ng/reports/), extracted by [myself](https://www.vet.cam.ac.uk/directory/sdf22@cam.ac.uk) and [Chinedu Ugwu](https://www.vet.cam.ac.uk/directory/acu21).`","pinned":false,"hidden":false,"mode":"ojs"},{"id":42,"value":"md`## Data sources`","pinned":false,"hidden":false,"mode":"ojs"},{"id":96,"value":"md`### Maps`","pinned":false,"hidden":false,"mode":"ojs"},{"id":45,"value":"statesURL = \"https://raw.githubusercontent.com/sdwfrost/nigeria-lassa-data/master/nigeria_states.geojson\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":59,"value":"states = fetchJSON(statesURL)","pinned":false,"hidden":false,"mode":"ojs"},{"id":310,"value":"sstates = turf.simplify(states)","pinned":true,"hidden":false,"mode":"ojs"},{"id":51,"value":"statesLayer = {\n var statesLayer = new ol.layer.Vector({\n source: new ol.source.Vector({\n features: (new ol.format.GeoJSON()).readFeatures(states, {\n dataProjection: 'EPSG:4326',\n featureProjection: 'EPSG:3857'\n })\n })\n });\n \n statesLayer.getSource().forEachFeature(function(feature){\n //console.log(feature.getProperties());\n var style = new ol.style.Style({\n stroke: new ol.style.Stroke({\n color: 'rgba(0,0,0,1)',\n width: 2\n }),\n fill: new ol.style.Fill({ color: statecolors[feature.get('name_1')]})\n });\n feature.setStyle(style);\n });\n\n return statesLayer;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":467,"value":"pointsLayer = {\n var pointsLayer = new ol.layer.Vector({\n source: new ol.source.Vector({\n features: (new ol.format.GeoJSON()).readFeatures(countryPoints, {\n dataProjection: 'EPSG:4326',\n featureProjection: 'EPSG:3857'\n })\n })\n });\n \n //pointsLayer.getSource().forEachFeature(function(feature){\n // //console.log(feature.getProperties());\n // });\n\n return pointsLayer;\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":63,"value":"locations = ({})","pinned":false,"hidden":false,"mode":"ojs"},{"id":112,"value":"md`### Population sizes`","pinned":false,"hidden":false,"mode":"ojs"},{"id":114,"value":"population = d3.csv(\"https://raw.githubusercontent.com/sdwfrost/nigeria-lassa-data/master/nigeria_population.csv\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":98,"value":"md`### Notifications`","pinned":false,"hidden":false,"mode":"ojs"},{"id":100,"value":"notifications = d3.csv(\"https://raw.githubusercontent.com/sdwfrost/nigeria-lassa-data/master/notifications_state.csv\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":137,"value":"dates = unpack(notifications, \"date\").unique().map((x)=>{\n var parts = x.split(\"/\");\n var dt = new Date(parseInt(parts[2], 10),\n parseInt(parts[1], 10) - 1,\n parseInt(parts[0], 10));\n return dt;\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":150,"value":"posByDate = notifications.reduce(function(posByDate, datum){\n var parts = datum.date.split(\"/\");\n var dt = new Date(parseInt(parts[2], 10),\n parseInt(parts[1], 10) - 1,\n parseInt(parts[0], 10));\n var value = parseInt(datum.labpositive,10);\n posByDate[dt] = (posByDate[dt] || 0) + value;\n\n return posByDate;\n}, {})\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":179,"value":"negByDate = notifications.reduce(function(negByDate, datum){\n var parts = datum.date.split(\"/\");\n var dt = new Date(parseInt(parts[2], 10),\n parseInt(parts[1], 10) - 1,\n parseInt(parts[0], 10));\n var value = parseInt(datum.labnegative,10);\n negByDate[dt] = (negByDate[dt] || 0) + value;\n\n return negByDate;\n}, {})","pinned":false,"hidden":false,"mode":"ojs"},{"id":182,"value":"untByDate = notifications.reduce(function(untByDate, datum){\n var parts = datum.date.split(\"/\");\n var dt = new Date(parseInt(parts[2], 10),\n parseInt(parts[1], 10) - 1,\n parseInt(parts[0], 10));\n var value = parseInt(datum.untested,10);\n untByDate[dt] = (untByDate[dt] || 0) + value;\n\n return untByDate;\n}, {})","pinned":false,"hidden":false,"mode":"ojs"},{"id":190,"value":"posByState = aggregate(notifications,\"state\",\"labpositive\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":200,"value":"negByState = aggregate(notifications,\"state\",\"labnegative\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":208,"value":"untByState = aggregate(notifications,\"state\",\"untested\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":213,"value":"susByState = aggregate(notifications,\"state\",\"suspected\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":193,"value":"statecolors = {\n var color = d3.scaleThreshold()\n .domain([0, 1, 10, 100, 500])\n .range([\"#f2f0f7\", \"#dadaeb\", \"#bcbddc\", \"#9e9ac8\", \"#756bb1\", \"#54278f\"]);\n var keys = Object.keys(susByState);\n var values = Object.values(susByState);\n var result = {};\n for(var i=0;i fetch(url).then(r => r.json())","pinned":false,"hidden":false,"mode":"ojs"},{"id":119,"value":"function unpack(rows, key) {\n return rows.map(function(row) { return row[key]; });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":130,"value":"Array.prototype.contains = function(v) {\n for(var i = 0; i < this.length; i++) {\n if(this[i] === v) return true;\n }\n return false;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":133,"value":"Array.prototype.unique = function() {\n var arr = [];\n for(var i = 0; i < this.length; i++) {\n if(!arr.includes(this[i])) {\n arr.push(this[i]);\n }\n }\n return arr; \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":198,"value":"function aggregate(data,key,value){\n var result = data.reduce(function(result, datum){\n var group = datum[key];\n var val = parseInt(datum[value],10);\n result[group] = (result[group] || 0) + val;\n\n return result;\n }, {});\n return result;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":347,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":49,"value":"md`## Dependencies`","pinned":false,"hidden":false,"mode":"ojs"},{"id":106,"value":"d3 = require('d3')","pinned":false,"hidden":false,"mode":"ojs"},{"id":2,"value":"ol = require(\"openlayers\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":305,"value":"turf = require(\"@turf/turf\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":4,"value":"stylesheet = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":91,"value":"tooltipstyle = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":121,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W33","stdlib":"1","titling":"auto"}