2f:[{"id":"f9375d17ab6f245005b50d4eaf44d7f5e6a9eab1ac5f5dc563663654ee38df406192096edbc660f7553189470c24c4607039b2f67088f2390dbf6c3be8c349e0","href":"https://static.observableusercontent.com/files/f9375d17ab6f245005b50d4eaf44d7f5e6a9eab1ac5f5dc563663654ee38df406192096edbc660f7553189470c24c4607039b2f67088f2390dbf6c3be8c349e0","name":"parsed_sentences@1.json","type":"application/json","lastModified":1676573663330.19,"size":447342},{"id":"cda7fd58de74b13d5f653da882dec1d05c46996d6546e72cb9c848b47e75bf92f002c98c9f30874050b100debc7d32926505eafb4afa1f0aa310da4e394fba1d","href":"https://static.observableusercontent.com/files/cda7fd58de74b13d5f653da882dec1d05c46996d6546e72cb9c848b47e75bf92f002c98c9f30874050b100debc7d32926505eafb4afa1f0aa310da4e394fba1d","name":"parsed_sentences@2.json","type":"application/json","lastModified":1677616648269.615,"size":232121},{"id":"2d84ed3cff9756f95885a357269e60d0e4c5bb6b380b3dc6194eb7b8e59394f5645a2406796a6842d16d445e6c8ab334697de542efbbbcefc8c98e507cb386b4","href":"https://static.observableusercontent.com/files/2d84ed3cff9756f95885a357269e60d0e4c5bb6b380b3dc6194eb7b8e59394f5645a2406796a6842d16d445e6c8ab334697de542efbbbcefc8c98e507cb386b4","name":"links_scraped_complete.tsv","type":"text/tab-separated-values","lastModified":1676563846916.184,"size":40842},{"id":"bffcd25397e27616e6be759b8224cfb5e90df02d45fca3f2b85fb47c9e318004a3c09fdca6cf8d1a33dec973d1798aa4fec93671fdee0d7ed6537bb84413a2a8","href":"https://static.observableusercontent.com/files/bffcd25397e27616e6be759b8224cfb5e90df02d45fca3f2b85fb47c9e318004a3c09fdca6cf8d1a33dec973d1798aa4fec93671fdee0d7ed6537bb84413a2a8","name":"parsed_sentences.json","type":"application/json","lastModified":1676569514345.895,"size":381834}] 2d:{"title":"epiVerseTracker [Code] [Platform] [YouTube]","cells":[{"id":0,"value":"

epiVerseTracker ^{[Code] [Platform] [YouTube]}

\n\nDevelopment notes for the epiVerseTracker platform with Adalberto Filho. See his initial notes for motivation and original plan.","pinned":false,"hidden":false,"mode":"md"},{"id":42,"value":"//tracker = import('http://localhost:8000/tracker/export.js')\ntracker = import('https://epiverse.github.io/tracker/export.js')","pinned":false,"hidden":false,"mode":"ojs"},{"id":75,"value":"The modern ES6 module import mechanism is preferred here (see *tracker* above), but note the older CommonJS require would work as well as *tracker = require('https://epiverse.github.io/tracker/tracker.js')*. Should we bother?","pinned":false,"hidden":false,"mode":"md"},{"id":21,"value":"# Data Sources","pinned":false,"hidden":false,"mode":"md"},{"id":24,"value":"## CDC\n...","pinned":false,"hidden":false,"mode":"md"},{"id":26,"value":"## SEER\n...","pinned":false,"hidden":false,"mode":"md"},{"id":28,"value":"## IARC\nData is organized along three axes: Location, cancer types, and risk factors. The corresponding data resources are managed at IARC's Global Cancer Observatory.","pinned":false,"hidden":false,"mode":"md"},{"id":38,"value":"### Causes","pinned":false,"hidden":false,"mode":"md"},{"id":82,"value":"iarcCauseData=tracker.iarc.causesGetAll(false)","pinned":true,"hidden":false,"mode":"ojs"},{"id":108,"value":"### Fetching data about carcinogenic agents","pinned":false,"hidden":false,"mode":"md"},{"id":160,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":110,"value":"/*async function getTable(){\n var a = await fetch('https://raw.githubusercontent.com/filhoalm/monoapp1/main/data_10012021.csv')\n var table = await a.text()\n table=table.replaceAll('\\r','').split('\\n').map( x => x.split(';'))\n var header=table[0]\n table=table.slice(1).filter(x => x.length==header.length )\n var rows = []\n table.forEach( x => {\n var dat={}\n var i=0\n var h=''\n for (h of header){\n dat[h]=x[i]\n i+=1\n }\n rows.push(dat)\n })\n return rows\n}\n*/\nasync function getTable(){\n var rows = d3.csv('https://raw.githubusercontent.com/filhoalm/monoapp1/main/data2102023c.csv')\n return rows\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":115,"value":"table = await getTable()","pinned":true,"hidden":false,"mode":"ojs"},{"id":124,"value":"function getColumnUniqueValues(key){\n var values = ['All']\n table.forEach( x => {\n var keys = Object.keys(x)\n if(keys.includes(key)){\n if( ! values.includes(x[key]) ){\n values.push(x[key])\n }\n }\n })\n return values\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":163,"value":"#### Filtering agents and their categories according to evidence level and cancer sites and subtypes","pinned":false,"hidden":false,"mode":"md"},{"id":131,"value":"evidences = getColumnUniqueValues('evidence')","pinned":true,"hidden":false,"mode":"ojs"},{"id":138,"value":"sites = getColumnUniqueValues('cancer_site')","pinned":true,"hidden":false,"mode":"ojs"},{"id":148,"value":"subtypes = getColumnUniqueValues('cancer_subtype')","pinned":true,"hidden":false,"mode":"ojs"},{"id":217,"value":"organs = getColumnUniqueValues('organ')","pinned":true,"hidden":false,"mode":"ojs"},{"id":246,"value":"","pinned":false,"hidden":false,"mode":"html"},{"id":234,"value":"viewof filters = Inputs.form({\n selEvidence: Inputs.select(evidences, {label: \"Evidence Level\", id:\"field\"}),\n selType: Inputs.select(subtypes, {label: \"Cancer subtypes\", id:\"field\"}),\n selOrgan: Inputs.select(organs, {label: \"Organs\", id:\"field\"})\n})\n/* ************** Apparently there is no way to overwrite css to put the fields next to each other, to save vertical space ******************** */","pinned":true,"hidden":false,"mode":"ojs"},{"id":257,"value":"viewof selEvidence= Inputs.select(evidences, {label: \"Evidence Level\", id:\"field\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":142,"value":"viewof selSite = Inputs.select(sites, {label: \"Cancer sites\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":150,"value":"viewof selType = Inputs.select(subtypes, {label: \"Cancer subtypes\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":221,"value":"viewof selOrgan = Inputs.select(organs, {label: \"Organs\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":155,"value":"\n function getTableFiltered(){\n var filtered = table\n if(selEvidence!='All'){\n filtered=filtered.filter( x => x['evidence']==selEvidence )\n }\n if(selSite!='All'){\n filtered=filtered.filter( x => x['cancer_site']==selSite )\n }\n if(selType!='All'){\n filtered=filtered.filter( x => x['cancer_subtype']==selType )\n }\n if(selOrgan!='All'){\n filtered=filtered.filter( x => x['organ']==selOrgan )\n }\n return filtered\n }\n \n \n","pinned":true,"hidden":false,"mode":"ojs"},{"id":174,"value":"#### Getting Agents participation according to the filters","pinned":false,"hidden":false,"mode":"md"},{"id":172,"value":"function getOrderedFilteredAgentsData(){\n var filtered = getTableFiltered()\n \n var agents={}\n filtered.forEach(x => {\n var keys = Object.keys(agents)\n if( ! keys.includes(x['agent']) ){\n agents[x['agent']] = 0\n }\n agents[x['agent']] += 1\n })\n var agentsDat={'x': Object.keys(agents), 'y': Object.values(agents)}\n return agentsDat\n }","pinned":true,"hidden":false,"mode":"ojs"},{"id":166,"value":"filtered = getOrderedFilteredAgentsData()","pinned":true,"hidden":false,"mode":"ojs"},{"id":261,"value":"/* ******************** Ordering barplot data from higher to low ***************** */\nfunction orderDict(x,y){\n var tuples = [];\n \n for (var i=0; i b ? -1 : 0);\n });\n var objr={'x': [], 'y': []}\n for (var i = 0; i < tuples.length; i++) {\n var key = tuples[i][0];\n var value = tuples[i][1];\n objr['x'].push(key)\n objr['y'].push(value)\n // do something with key and value\n }\n return objr\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":157,"value":"{\n var ordered=orderDict( filtered['x'], filtered['y'])\n var trace = {\n x: ordered['x'],\n y: ordered['y'],\n name: 'Agents',\n marker: {color: 'rgb(26, 118, 255)'},\n type: 'bar'\n };\n \n var data = [trace];\n \n var layout = {\n title: 'Agents filtered with constraints',\n xaxis: {\n title: 'Agents',\n tickfont: {\n size: 14,\n color: 'rgb(107, 107, 107)'\n }},\n yaxis: {\n title: 'Occurrences',\n },\n legend: {\n x: 0,\n y: 1.0,\n bgcolor: 'rgba(255, 255, 255, 0)',\n bordercolor: 'rgba(255, 255, 255, 0)'\n },\n barmode: 'group',\n bargap: 0.15,\n bargroupgap: 0.1,\n width: width\n };\n \n const div = DOM.element('div');\n Plotly.newPlot(div, data, layout);\n return div;\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":176,"value":"#### Getting classes of agents according to filters","pinned":false,"hidden":false,"mode":"md"},{"id":178,"value":"function getOrderedFilteredAgentClassesData(){\n var filtered = getTableFiltered()\n \n var agents={}\n filtered.forEach(x => {\n var keys = Object.keys(agents)\n if( ! keys.includes(x['class']) ){\n agents[x['class']] = 0\n }\n agents[x['class']] += 1\n })\n var agentsDat={'x': Object.keys(agents), 'y': Object.values(agents)}\n return agentsDat\n }","pinned":true,"hidden":false,"mode":"ojs"},{"id":180,"value":"filteredClass = getOrderedFilteredAgentClassesData()","pinned":true,"hidden":false,"mode":"ojs"},{"id":182,"value":"{\n var trace = {\n values: filteredClass['y'],\n labels: filteredClass['x'],\n type: 'pie'\n };\n \n var data = [trace];\n \n var layout = {\n width: width,\n title: 'Classes of Agents filtered with constraints'\n };\n \n const div = DOM.element('div');\n Plotly.newPlot(div, data, layout);\n return div;\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":358,"value":"#### Summary of agents by cancer site","pinned":false,"hidden":false,"mode":"md"},{"id":369,"value":"\nevs=evidences.filter(x => x!='All')","pinned":true,"hidden":false,"mode":"ojs"},{"id":360,"value":"viewof selEvidenceTree= Inputs.select(evs, {label: \"Evidence Level\", id:\"field\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":363,"value":"function getTableFilteredTree(){\n var filtered = table\n filtered=filtered.filter( x => x['evidence']==selEvidenceTree )\n \n var tree={}\n filtered.forEach( x => {\n var agent = x['agent_subtype']\n var site = x['cancer_site']\n \n var keys=Object.keys(tree)\n keys=Object.keys(tree)\n if(!keys.includes(site)){\n tree[site]={}\n }\n keys=Object.keys(tree[site])\n if(!keys.includes(agent)){\n tree[site][agent]=0\n }\n tree[site][agent]+=1\n })\n \n var leaves=['Agents by Cancer sites']\n var parents=['']\n var z = [0]\n var all=0\n for (var site of Object.keys(tree)){\n for (var agent of Object.keys(tree[site])){\n parents.push(site)\n leaves.push(agent)\n z.push(tree[site][agent])\n }\n var total = d3.sum(Object.values(tree[site]))\n parents.push('Agents by Cancer sites')\n leaves.push(site)\n z.push(total)\n all+=1\n }\n z[0]=all\n return [leaves, parents, z]\n }","pinned":true,"hidden":false,"mode":"ojs"},{"id":365,"value":"infomap=getTableFilteredTree()","pinned":true,"hidden":false,"mode":"ojs"},{"id":367,"value":"{\n \n var data = [{\n type: \"treemap\",\n labels: infomap[0],\n parents: infomap[1],\n values: infomap[2],\n //textinfo: \"label+value+percent parent+percent entry\",\n textinfo: \"label+value+percent entry\",\n domain: {\"x\": [0, 0.48]},\n outsidetextfont: {\"size\": 20, \"color\": \"#377eb8\"},\n marker: {\"line\": {\"width\": 2}},\n pathbar: {\"visible\": false}\n }];\nvar layout = {\n width: 2000,\n annotations: [{\n showarrow: false,\n text: \"Distribution of agents according to cancer site - \"+selEvidenceTree,\n x: 0.25,\n xanchor: \"center\",\n y: 1.1,\n yanchor: \"bottom\"\n }]}\n \n const div = DOM.element('div');\n Plotly.newPlot(div, data, layout);\n return div;\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":186,"value":"#### Filtering data according to agents and their classes","pinned":false,"hidden":false,"mode":"md"},{"id":188,"value":"agents = getColumnUniqueValues('agent_subtype')","pinned":true,"hidden":false,"mode":"ojs"},{"id":190,"value":"agentClasses = getColumnUniqueValues('class')","pinned":true,"hidden":false,"mode":"ojs"},{"id":192,"value":"viewof selAgent = Inputs.select(agents, {label: \"Agents\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":194,"value":"viewof selAgentClass = Inputs.select(agentClasses, {label: \"Classes of Agents\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":198,"value":"function getTableFilteredByClassAgent(){\n var filtered = table\n if(selEvidence!='All'){\n filtered=filtered.filter( x => x['evidence']==selEvidence )\n }\n if(selSite!='All'){\n filtered=filtered.filter( x => x['cancer_site']==selSite )\n }\n if(selType!='All'){\n filtered=filtered.filter( x => x['cancer_subtype']==selType )\n }\n if(selAgent!='All'){\n filtered=filtered.filter( x => x['agent_subtype']==selAgent )\n }\n if(selAgentClass!='All'){\n filtered=filtered.filter( x => x['class']==selAgentClass )\n }\n if(selOrgan!='All'){\n filtered=filtered.filter( x => x['organ']==selOrgan )\n }\n return filtered\n }","pinned":true,"hidden":false,"mode":"ojs"},{"id":213,"value":"#### Checking the full data table according to the filters","pinned":false,"hidden":false,"mode":"md"},{"id":202,"value":"tableShow = getTableFilteredByClassAgent()","pinned":true,"hidden":false,"mode":"ojs"},{"id":205,"value":"Inputs.table(tableShow)","pinned":true,"hidden":false,"mode":"ojs"},{"id":279,"value":"### Checking the monographs available","pinned":false,"hidden":false,"mode":"md"},{"id":352,"value":"links_scraped_complete = FileAttachment(\"links_scraped_complete.tsv\").tsv({typed: false})","pinned":true,"hidden":false,"mode":"ojs"},{"id":282,"value":"function getLinksVolumeYear(){\nvar options_ = {'All': []}\nlinks_scraped_complete.forEach( el => {\n options_[ el['volume']+'/'+el['year']] = [el['link'], el['download_link']]\n})\n return options_ \n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":297,"value":"options = getLinksVolumeYear()","pinned":true,"hidden":false,"mode":"ojs"},{"id":291,"value":"keys = Object.keys(options)\n ","pinned":true,"hidden":false,"mode":"ojs"},{"id":329,"value":"viewof selvolyear = Inputs.select(Object.keys(options), {label: 'Monographs by volume/year'})","pinned":true,"hidden":false,"mode":"ojs"},{"id":344,"value":"selAgent\n","pinned":true,"hidden":false,"mode":"ojs"},{"id":306,"value":"document.getElementById('info').innerHTML= selvolyear=='All' ? 'Select the volume and year!' : `Go to this page or download this book to see more information about this volume ${selvolyear.split('/')[0]} and year ${selvolyear.split('/')[1]}`","pinned":true,"hidden":false,"mode":"ojs"},{"id":304,"value":"

","pinned":false,"hidden":false,"mode":"html"},{"id":275,"value":"// links_scraped_complete = FileAttachment(\"links_scraped_complete.tsv\").tsv()\nlinks_scraped_complete","pinned":true,"hidden":false,"mode":"ojs"},{"id":309,"value":"parsed_sentences = FileAttachment(\"parsed_sentences@2.json\").json()","pinned":true,"hidden":false,"mode":"ojs"},{"id":315,"value":"function filterSentencesDb(){\n var txt=\"\"\n for(var k of Object.keys(parsed_sentences)){\n for (var s of parsed_sentences[k]){\n var page = s['page']\n s=s['sentence']\n if( k.replace('_','/')==selvolyear || ( selAgent!='All' && s.toLowerCase().indexOf(selAgent.toLowerCase())!=-1) ){\n txt+=`

${k.replace('_','/')}, page ${page} ${s}

`\n }\n }\n }\n document.getElementById('sentences').innerHTML = txt=='' ? 'No sentences found' : txt\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":339,"value":"filterSentencesDb()","pinned":true,"hidden":false,"mode":"ojs"},{"id":336,"value":"### Sentences filtered by volume/year or agent name","pinned":false,"hidden":false,"mode":"md"},{"id":313,"value":"

","pinned":false,"hidden":false,"mode":"html"}],"files":"$W2f","stdlib":"1","titling":"auto"}