45:["$","title",null,{"children":"Covid-19 Test Accuracy Simulator | Eli Holder | Observable"}] 4d:T404,md`# Covid-19 Test Accuracy Simulator A few weeks ago I was talking with my dad. He had heard someone on CNN hyperventilating about the accuracy of covid-10 tests. "What's the point?" he said, "the tests are basically like flipping a coin." That didn't sound quite right, but I didn't know how to explain it. So what can we expect from common Covid-19 tests? This is a somewhat naive look at test accuracy statistics. We're ignoring things like the timing of the disease, viral load, etc. So this can apply to any test, but I've included some relavent defaults / notes for common Covid tests. Writeup for this is here, with more detail on the test types and a slightly more cogent explanation of testing accuracy in general: # [Writeup: Visualizing Covid-19 Test Accuracy](https://towardsdatascience.com/interactive-visualizing-covid-19-test-accuracy-4a24b4e1ffbf) (Thank you to Propublica's [Wee People Project](https://github.com/propublica/weepeople)) (Thanks [@fil](https://observablehq.com/@fil) for the proof-read) `4e:T518,md`Test Sensitivity measures how accurate a test is for people who are actually infected. * For "gold standard" RT-PCR tests, sensitivity can range from 66% - 97% ([src](https://en.wikipedia.org/wiki/COVID-19_testing#Sensitivity_and_specificity), [src](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350782/)), depending on how it's collected. For example, a PCR test based on a Nasopharyngeal (icky deep nasal) swab is shown to have 73% sensitivity, while sputum ([coughing up phlegm](https://youtu.be/92dT_1kbbek?t=117)) is as high as 97.2%. * The White House uses an Abbot ID NOW test, which has the benefit of returning results in 13 minutes, but it's sensitivity can be much lower, between 50% and 75% ([src](https://www.nbcnews.com/health/health-news/abbott-covid-19-test-used-white-house-could-be-inaccurate-n1207466), [src](https://jcm.asm.org/content/58/8/e00798-20), [src](https://pubmed.ncbi.nlm.nih.gov/32425657/)) * Then there are antibody tests, which detect the disease after you've already had it. Some studies suggest sensitivities for these are between 87% and 93% ([src](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287442/)). In our population, these are the ${ exposedPeople.filter(p => p.infected).length } people that are infected (from the original ${exposedPeople.length}):`4f:T621,{ let people = infectedTestedPeople; const cellWidth = defaultCellDims.width; const cellHeight = defaultCellDims.height; const colCount = Math.ceil(width / cellWidth) - 4; const height = cellHeight * (Math.ceil(people.length / colCount) + 7) + 8; const gridParams = { colCount, cellWidth }; const truePosPeople = infectedTestedPeople.filter(p => p.testResult == true); const falseNegPeople = infectedTestedPeople.filter( p => p.testResult == false ); const truePosLabel = renderLabel( `~${truePosPeople.length}/${truePosPeople.length + falseNegPeople.length} infected people correctly test positive (true positive):` ); const falseNegLabel = renderLabel( `~${falseNegPeople.length}/${truePosPeople.length + falseNegPeople.length} infected people incorrectly test negative (false negative):` ); //✔️👍⚠️❌✅ const truePosGrid = svg` ✔️ ${renderPersonGrid(truePosPeople, gridParams)} `; const falseNegGrid = svg` ❌ ${renderPersonGrid(falseNegPeople, gridParams)} `; return html` `; }50:T5ad,{ let people = healthyTestedPeople; const cellWidth = defaultCellDims.width; const cellHeight = defaultCellDims.height; const colCount = Math.ceil(width / cellWidth) - 4; const height = cellHeight * (Math.ceil(people.length / colCount) + 6) + 8; const gridParams = { colCount, cellWidth }; const trueNegPeople = people.filter(p => p.testResult == false); const falsePosPeople = people.filter(p => p.testResult); const trueNegLabel = renderLabel( `~${trueNegPeople.length}/${trueNegPeople.length + falsePosPeople.length} healthy people would test negative for covid (true negative):` ); const falsePosLabel = renderLabel( `~${falsePosPeople.length}/${trueNegPeople.length + falsePosPeople.length} healthy people will test positive (false positive):` ); //✔️👍⚠️❌✅ const trueNegGrid = svg` ✔️ ${renderPersonGrid(trueNegPeople, gridParams)} `; const falsePosGrid = svg` ❌ ${renderPersonGrid(falsePosPeople, gridParams)} `; return html` `; }51:Tb77,{ regenerate; let people = exposedPeople; const cellWidth = defaultCellDims.width; const cellHeight = defaultCellDims.height; const colCount = Math.ceil(width / cellWidth) - 2; const height = cellHeight * (Math.ceil(people.length / colCount) + 2) + 272; // infect people & test people people = people // .map(p => ({ // ...p, // infected: Math.random() <= prevalence // })) .map(p => ({ ...p, testResults: simulateTestResult(p) })); const peopleByTestResult = _.groupBy(people, p => p.testResults); let testStats = { negCount: peopleByTestResult[false].length, posCount: peopleByTestResult[true].length, trueNegCount: peopleByTestResult[false].filter(p => !p.infected).length, falseNegCount: peopleByTestResult[false].filter(p => p.infected).length, truePosCount: peopleByTestResult[true].filter(p => p.infected).length, falsePosCount: peopleByTestResult[true].filter(p => !p.infected).length, positivityRate: peopleByTestResult[true].length / people.length }; testStats.posPredictiveValue = testStats.truePosCount / testStats.posCount; testStats.negPredictiveValue = testStats.trueNegCount / testStats.negCount; const gridParams = { colCount }; const negativePersonGrid = renderPersonGrid( peopleByTestResult[false], gridParams ); const positivePersonGrid = renderPersonGrid( peopleByTestResult[true], gridParams ); const accuracyTable = svg` TN: ${testStats.trueNegCount} FN: ${testStats.falsePosCount} TP: ${testStats.truePosCount} FP: ${testStats.falsePosCount} Test Positivity: ${testStats.positivityRate} `; // return peopleByTestResult // return getPrerenderedBBox(negativeGridLabel).height const titleText = svg`Covid-19 Test Simulation Results`; return html` `; }52:T1832,//https://stackoverflow.com/questions/1655769/fastest-md5-implementation-in-javascript md5 = { function md5cycle(x, k) { var a = x[0], b = x[1], c = x[2], d = x[3]; a = ff(a, b, c, d, k[0], 7, -680876936); d = ff(d, a, b, c, k[1], 12, -389564586); c = ff(c, d, a, b, k[2], 17, 606105819); b = ff(b, c, d, a, k[3], 22, -1044525330); a = ff(a, b, c, d, k[4], 7, -176418897); d = ff(d, a, b, c, k[5], 12, 1200080426); c = ff(c, d, a, b, k[6], 17, -1473231341); b = ff(b, c, d, a, k[7], 22, -45705983); a = ff(a, b, c, d, k[8], 7, 1770035416); d = ff(d, a, b, c, k[9], 12, -1958414417); c = ff(c, d, a, b, k[10], 17, -42063); b = ff(b, c, d, a, k[11], 22, -1990404162); a = ff(a, b, c, d, k[12], 7, 1804603682); d = ff(d, a, b, c, k[13], 12, -40341101); c = ff(c, d, a, b, k[14], 17, -1502002290); b = ff(b, c, d, a, k[15], 22, 1236535329); a = gg(a, b, c, d, k[1], 5, -165796510); d = gg(d, a, b, c, k[6], 9, -1069501632); c = gg(c, d, a, b, k[11], 14, 643717713); b = gg(b, c, d, a, k[0], 20, -373897302); a = gg(a, b, c, d, k[5], 5, -701558691); d = gg(d, a, b, c, k[10], 9, 38016083); c = gg(c, d, a, b, k[15], 14, -660478335); b = gg(b, c, d, a, k[4], 20, -405537848); a = gg(a, b, c, d, k[9], 5, 568446438); d = gg(d, a, b, c, k[14], 9, -1019803690); c = gg(c, d, a, b, k[3], 14, -187363961); b = gg(b, c, d, a, k[8], 20, 1163531501); a = gg(a, b, c, d, k[13], 5, -1444681467); d = gg(d, a, b, c, k[2], 9, -51403784); c = gg(c, d, a, b, k[7], 14, 1735328473); b = gg(b, c, d, a, k[12], 20, -1926607734); a = hh(a, b, c, d, k[5], 4, -378558); d = hh(d, a, b, c, k[8], 11, -2022574463); c = hh(c, d, a, b, k[11], 16, 1839030562); b = hh(b, c, d, a, k[14], 23, -35309556); a = hh(a, b, c, d, k[1], 4, -1530992060); d = hh(d, a, b, c, k[4], 11, 1272893353); c = hh(c, d, a, b, k[7], 16, -155497632); b = hh(b, c, d, a, k[10], 23, -1094730640); a = hh(a, b, c, d, k[13], 4, 681279174); d = hh(d, a, b, c, k[0], 11, -358537222); c = hh(c, d, a, b, k[3], 16, -722521979); b = hh(b, c, d, a, k[6], 23, 76029189); a = hh(a, b, c, d, k[9], 4, -640364487); d = hh(d, a, b, c, k[12], 11, -421815835); c = hh(c, d, a, b, k[15], 16, 530742520); b = hh(b, c, d, a, k[2], 23, -995338651); a = ii(a, b, c, d, k[0], 6, -198630844); d = ii(d, a, b, c, k[7], 10, 1126891415); c = ii(c, d, a, b, k[14], 15, -1416354905); b = ii(b, c, d, a, k[5], 21, -57434055); a = ii(a, b, c, d, k[12], 6, 1700485571); d = ii(d, a, b, c, k[3], 10, -1894986606); c = ii(c, d, a, b, k[10], 15, -1051523); b = ii(b, c, d, a, k[1], 21, -2054922799); a = ii(a, b, c, d, k[8], 6, 1873313359); d = ii(d, a, b, c, k[15], 10, -30611744); c = ii(c, d, a, b, k[6], 15, -1560198380); b = ii(b, c, d, a, k[13], 21, 1309151649); a = ii(a, b, c, d, k[4], 6, -145523070); d = ii(d, a, b, c, k[11], 10, -1120210379); c = ii(c, d, a, b, k[2], 15, 718787259); b = ii(b, c, d, a, k[9], 21, -343485551); x[0] = add32(a, x[0]); x[1] = add32(b, x[1]); x[2] = add32(c, x[2]); x[3] = add32(d, x[3]); } function cmn(q, a, b, x, s, t) { a = add32(add32(a, q), add32(x, t)); return add32((a << s) | (a >>> (32 - s)), b); } function ff(a, b, c, d, x, s, t) { return cmn((b & c) | ((~b) & d), a, b, x, s, t); } function gg(a, b, c, d, x, s, t) { return cmn((b & d) | (c & (~d)), a, b, x, s, t); } function hh(a, b, c, d, x, s, t) { return cmn(b ^ c ^ d, a, b, x, s, t); } function ii(a, b, c, d, x, s, t) { return cmn(c ^ (b | (~d)), a, b, x, s, t); } function md51(s) { let txt = ''; var n = s.length, state = [1732584193, -271733879, -1732584194, 271733878], i; for (i=64; i<=s.length; i+=64) { md5cycle(state, md5blk(s.substring(i-64, i))); } s = s.substring(i-64); var tail = [0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0]; for (i=0; i>2] |= s.charCodeAt(i) << ((i%4) << 3); tail[i>>2] |= 0x80 << ((i%4) << 3); if (i > 55) { md5cycle(state, tail); for (i=0; i<16; i++) tail[i] = 0; } tail[14] = n*8; md5cycle(state, tail); return state; } /* there needs to be support for Unicode here, * unless we pretend that we can redefine the MD-5 * algorithm for multi-byte characters (perhaps * by adding every four 16-bit characters and * shortening the sum to 32 bits). Otherwise * I suggest performing MD-5 as if every character * was two bytes--e.g., 0040 0025 = @%--but then * how will an ordinary MD-5 sum be matched? * There is no way to standardize text to something * like UTF-8 before transformation; speed cost is * utterly prohibitive. The JavaScript standard * itself needs to look at this: it should start * providing access to strings as preformed UTF-8 * 8-bit unsigned value arrays. */ function md5blk(s) { /* I figured global was faster. */ var md5blks = [], i; /* Andy King said do it this way. */ for (i=0; i<64; i+=4) { md5blks[i>>2] = s.charCodeAt(i) + (s.charCodeAt(i+1) << 8) + (s.charCodeAt(i+2) << 16) + (s.charCodeAt(i+3) << 24); } return md5blks; } var hex_chr = '0123456789abcdef'.split(''); function rhex(n) { var s='', j=0; for(; j<4; j++) s += hex_chr[(n >> (j * 8 + 4)) & 0x0F] + hex_chr[(n >> (j * 8)) & 0x0F]; return s; } function hex(x) { for (var i=0; i> 16) + (y >> 16) + (lsw >> 16); return (msw << 16) | (lsw & 0xFFFF); } } return md5 }53:[{"id":"3a8238e5575c36b2102343cd30f8f16327c77d732f3d4fb46902d95d790078186ec8c25620097b546294ad68b88f753ab53d52cd2966770123ae78fdb5d10c68","href":"https://static.observableusercontent.com/files/3a8238e5575c36b2102343cd30f8f16327c77d732f3d4fb46902d95d790078186ec8c25620097b546294ad68b88f753ab53d52cd2966770123ae78fdb5d10c68","name":"weepeople.css","type":"text/css","lastModified":1601067063125.088,"size":77947}] 49:{"id":"379a4373f855d61f","slug":"covid-19-test-accuracy-simulator","title":"Covid-19 Test Accuracy Simulator","thumbnail":"a1485e412e24198d1fdfe513b1343c24e6b3c7cfcd652916fc8bdd30accb1e5b","access_level":"public","create_time":"$D2020-09-25T20:22:15.308Z","update_time":"$D2021-07-23T15:39:38.742Z","view_time":null,"first_public_time":"$D2020-10-07T07:10:06.735Z","has_unpublished_edits":null,"fork":false,"stars":19,"starred":false,"owner":{"type":"team","id":"58eacf8e202aa99c","login":"elibryan","name":"Eli Holder","avatar_url":"https://avatars-next.observableusercontent.com/f42ede38e59d5fab5318c3a05de38dc47c2f88ee4bd796d32ced88733e2b8d50","tier":"starter_2024","bio":"","followed_by_you":false,"follows_you":false},"version":1209,"publish_version":1209,"role":null,"authored":false,"authors":[{"type":"individual","id":"d17a47a44abf3446","login":"elibryan","name":"Eli Holder","avatar_url":"https://avatars-next.observableusercontent.com/f42ede38e59d5fab5318c3a05de38dc47c2f88ee4bd796d32ced88733e2b8d50","tier":null,"bio":"","followed_by_you":false,"follows_you":false}],"members":[{"type":"individual","id":"d17a47a44abf3446","login":"elibryan","name":"Eli Holder","avatar_url":"https://avatars-next.observableusercontent.com/f42ede38e59d5fab5318c3a05de38dc47c2f88ee4bd796d32ced88733e2b8d50","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":true,"trashed":false,"lapsed":null,"subscribed":null,"forks":5,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Covid-19 Test Accuracy Simulator","cells":[{"id":0,"value":"$4d","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":861,"value":"md`\n---\n# The People\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":539,"value":"md`First we need some people as test subjects...`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":624,"value":"viewof populationSize = {\n const output = slider({\n title: \"Population Size\",\n min: 10,\n max: 300,\n step: 10,\n value: 300,\n description: \"\"\n });\n // output.addEventListener(\"mouseup\", ()=>{\n // // Update state for sharing\n // mutable state = {...state, caffeineHalfLifeHrs: parseFloat(output.value)}\n // })\n return output;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":573,"value":"{\n return simplePersonGrid(allPeople);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":219,"value":"allPeople = d3.range(populationSize).map(generatePerson)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":660,"value":"md`\n---\n# The Plague\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":640,"value":"md`Unfortunately, some of our people have become infected. We'll set the Prevalence rate to determine how many people have the virus. (Note: In real life, we don't / can't know the actual prevalence.)`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":642,"value":"viewof prevalence = {\n const output = slider({\n title: \"Prevalence\",\n min: 0,\n max: 1,\n step: 0.01,\n format: \".0%\",\n value: 0.05,\n description:\n \"Prevalence is the percent of the population that's actually infected.\"\n })\n // output.addEventListener(\"mouseup\", ()=>{\n // // Update state for sharing\n // mutable state = {...state, caffeineHalfLifeHrs: parseFloat(output.value)}\n // })\n return output\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":656,"value":"{\n return simplePersonGrid(exposedPeople);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":985,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":664,"value":"md`A ${formatPercent(prevalence)} prevalence rate means ~${\n exposedPeople.filter(p => p.infected).length\n} of our original ${\n exposedPeople.length\n} people are infected. They're randomly selected and indicated above in orange.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":666,"value":"exposedPeople = {\n// return allPeople\n// .map(p => ({\n// ...p,\n// infected: Math.random() <= prevalence\n// }));\n const infectedCount = Math.round(populationSize * prevalence)\n const infectedPersonIds = new Set(choose(allPeople, infectedCount, false).map(p=>p.id))\n return allPeople.map(p=>({...p, infected: infectedPersonIds.has(p.id)}))\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":693,"value":"md`\n---\n# The Test\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":695,"value":"md`Now let's setup our test. There are 2 parameters that we need to consider: Sensitivity & Specificity. These cover 2 different dimensions of \"accuracy\":\n* **Sensitivity** - If you have Covid, will the test result be positive?\n* **Specificity** - If you don't have Covid, will the test result be negative?`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":869,"value":"md`## Test Sensitivity`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":299,"value":"//sensitivity = results.tp / (results.tp + results.fn)\n//https://www.ncbi.nlm.nih.gov/books/NBK557491/\nviewof sensitivity = {\n const output = slider({\n title: \"Sensitivity\",\n min: 0,\n max: 1,\n precision: 3,\n step: 0.01,\n value: .73,\n format: \".0%\",\n description: \"What % of infected people correctly test positive?\"\n });\n return output;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":829,"value":"$4e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":833,"value":"{\n return simplePersonGrid(infectedTestedPeople);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":837,"value":"md`Given a ${formatPercent(\n sensitivity\n)} sensitive test, we'd expect ${formatPercent(sensitivity)} of our ${\n exposedPeople.filter(p => p.infected).length\n} infected people to test positive, which looks like...`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":734,"value":"$4f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":807,"value":"md`When ${infectedTestedPeople.length} infected people take a ${formatPercent(\n sensitivity\n)} sensitive test, ${\n infectedTestedPeople.filter(p => p.testResult == true).length\n} will be correctly diagnosed as positive (these are \"true positives\"), ${\n infectedTestedPeople.filter(p => p.testResult == false).length\n} will be incorrectly diagnosed as negative (these are \"false negatives\"). \n\nThese \"false negatives\" are concerning because they're likely to go out and potentially infect others.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":730,"value":"infectedTestedPeople = {\n const infectedPeople = exposedPeople.filter(p=>p.infected)\n const truePosCount = Math.round(infectedPeople.length * sensitivity)\n const truePosPersonIds = new Set(choose(infectedPeople, truePosCount, false).map(p=>p.id))\n\n return infectedPeople.map(p=>({...p, testResult: truePosPersonIds.has(p.id)}))\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":848,"value":"md`## Test Specificity`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":290,"value":"// specificity = results.tn / (results.tn + results.fp)\n//specificity = results.tn / (results.tn + results.fp)\n//https://www.ncbi.nlm.nih.gov/books/NBK557491/\n\nviewof specificity = {\n const output = slider({\n title: \"Test Specificity\",\n min: 0,\n max: 1,\n precision: 3,\n step: 0.01,\n value: .98,\n format: \".0%\",\n description:\n \"Specificity measures what % of healthy people correctly test negative.\"\n });\n return output;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":854,"value":"md`Test Specificity measures accuracy for people who are not infected. \n* For RT-PCR tests, specificity has been measured at 98.6% ([src](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350782/)). \n* For Abbot ID Now tests, specificity has been measured at 99-100% ([src](https://jcm.asm.org/content/58/8/e00798-20), [src](https://pubmed.ncbi.nlm.nih.gov/32425657/)).\n\nIn our population, these are the ${\n exposedPeople.filter(p => !p.infected).length\n} healthy people:`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":858,"value":"{\n return simplePersonGrid(healthyTestedPeople);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":874,"value":"md`Given a ${formatPercent(specificity)} specific test...`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":877,"value":"$50","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":882,"value":"md`When ${healthyTestedPeople.length} healthy people take a ${formatPercent(\n specificity\n)} specific test, ${\n healthyTestedPeople.filter(p => p.testResult == false).length\n} will be correctly diagnosed as negative (these are \"true negatives\"), ${\n healthyTestedPeople.filter(p => p.testResult == true).length\n} will be incorrectly diagnosed as positive (these are \"false positive\"). \n\nThese \"false positives\" are concerning because they're likely to use healthcare resources that they don't need, since they're not actually infected.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":851,"value":"healthyTestedPeople = {\n const people = exposedPeople.filter(p=>!p.infected)\n const trueNegCount = Math.round(people.length * specificity)\n const trueNegPersonIds = new Set(choose(people, trueNegCount, false).map(p=>p.id))\n\n return people.map(p=>({...p, testResult: !trueNegPersonIds.has(p.id)}))\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":887,"value":"md`---\n# The Simulator\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":961,"value":"md`Above we were showing test results that perfectly match the parameters. In the real world there's more left to chance. Use the simulator below to see different scenarios that might unfold given the paramters we've selected above.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"$51","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":955,"value":"viewof regenerate = button({\n value: \"Re-Run\",\n description: \"Click here to re-run the simulator with the same parameters.\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1094,"value":"md`## Data Generation`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":302,"value":"/**\n * Roll the dice to see how a test goes for a given person\n */\nsimulateTestResult = p => {\n if (p.infected) {\n return Math.random() <= sensitivity;\n } else {\n return specificity < Math.random();\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":4,"value":"/**\n * Generate a random-ish person based on the seed\n */\ngeneratePerson = seed => {\n const avatarChoices = \"abcdefghijklmnopqrstuABCDEEFGHIJKLMNOPQRSTUVWXYZ\";\n const id = \"person_\" + d3.format(\"0>4\")(seed);\n // Choose a letter for the avatar based on a hash of the ID\n const avatar =\n avatarChoices[parseInt(md5(id).slice(0, 2), 16) % avatarChoices.length];\n return {\n id,\n avatar,\n infected: false\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":296,"value":"md`## Graphs, etc`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":810,"value":"/**\n * Render some text, split new lines into tspans\n */\nrenderLabel = text => {\n const padding = svg``;\n return svg`\n\n\n${text.split(\"\\n\").map(t => {\n return svg`${t}`;\n})}\n\n\n`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1104,"value":"/**\n * Return a person grid with defaults / correct size\n */\nsimplePersonGrid = people => {\n const cellWidth = defaultCellDims.width;\n const cellHeight = defaultCellDims.height;\n const colCount = Math.ceil(width / cellWidth) - 2;\n const height = cellHeight * (Math.ceil(people.length / colCount) + 1) + 8;\n const gridParams = { colCount, cellWidth };\n const personGrid = renderPersonGrid(people, gridParams);\n\n return html`\n\n`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":281,"value":"/**\n * Render a person grid inside a \n */\nrenderPersonGrid = (people, params = {}) => {\n const {\n colCount = 10,\n cellWidth = defaultCellDims.width,\n cellHeight = defaultCellDims.height\n } = params;\n return svg`\n\n\n${people.map((p, i) => {\n const col = i % colCount;\n const row = Math.floor(i / colCount);\n return svg`\n\n${renderPerson(p)}\n`;\n})}\n`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":249,"value":"/**\n * Render a person as a weepeople character\n * Uses a different color if p.infected == true\n */\nrenderPerson = (p, params = {}) => {\n const { personDims = defaultPersonDims } = params;\n // \n // const fillColor = p.infected ? \"#84B844\" : \"#000000\";\n // const fillColor = p.infected ? \"#84B844\" : \"#05090D\";\n const fillColor = p.infected ? \"#F58141\" : \"#000000\";\n\n const strokeColor = \"#ffffffaa\";\n\n // Render the stroke and body separately for cleaner outline\n return svg`\n\n\n\n${p.avatar}\n\n\n\n${p.avatar}\n\n\n`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":264,"value":"defaultPersonDims = ({ width: 24, height: 48 })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1126,"value":"defaultCellDims = ({ width: 12, height: 24 })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":577,"value":"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1080,"value":"md`## Utils`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":673,"value":"/**\n * Choose with/without replacement\n **/\nchoose = (arr, n = 1, replace = true) => {\n // Simple random choice\n const chooseOne = arr => {\n if (arr.length == 0) throw \"Can't choose from an empty array\";\n return arr[Math.floor(Math.random() * arr.length)];\n };\n\n if (replace == false && arr.length < n) {\n throw \"Can't choose more than arr.length items\";\n }\n\n //Get a set of indices to choose from [0, ..., array.length -1]\n let indicesRemaining = new Set(arr.map((_, i) => i));\n\n let output = [];\n\n // For each selection we need to make...\n for (let i = 0; i < n; i++) {\n // Choose the next index / item from the array\n const nextIndex = chooseOne(Array.from(indicesRemaining));\n output.push(arr[nextIndex]);\n\n // If we're not replacing, remove the index so we don't choose it again\n if (replace === false) {\n indicesRemaining.delete(nextIndex);\n }\n }\n return output;\n}\n//choose([1, 2, 3, 4, 5], 3, false)\n//choose([1, 2, 3, 4, 5], 10, true)\n//choose([], 3)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":506,"value":"formatPercent = n => d3.format(\".0%\")(n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":175,"value":"$52","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":384,"value":"/**\n * Get an element's bounding box by adding it to the dom\n * calculating the bbox, then removing it from the dom\n * Should probably be used with caution...\n * https://talk.observablehq.com/t/getbbox/1222/3\n */\ngetPrerenderedBBox = svgElement => {\n // Defensive copy in case element is already used\n svgElement = svgElement.cloneNode(true);\n\n const renderedSVG = html`\n`;\n\n // Add the SVG element to the DOM so we can determine its size.\n document.body.appendChild(renderedSVG);\n\n // Computing the bounding box of the content.\n const box = renderedSVG.querySelector(\"[name=content]\").getBBox();\n\n // Remove the SVG element from the DOM.\n renderedSVG.remove();\n\n return box;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":383,"value":"/**\n * Given an array of elements, wrap each with a\n * tag positioned to be below the bounding boxes\n * of the previous elements\n */\npositionRelatively = (elements, params) => {\n params = params || {};\n const spacing = params[\"spacing\"] || 0;\n\n // Wrap the elements in the positioned groups\n let wrappedElements = [];\n let accumulatedHeight = 0;\n elements.forEach(el => {\n // Position element relative to previous elements\n const wrappedElement = svg`\n\n${el}\n`;\n wrappedElements.push(wrappedElement);\n\n // Update the accumulated height based on this element\n const elementBBox = getPrerenderedBBox(el);\n accumulatedHeight += elementBBox.y + elementBBox.height + spacing;\n });\n\n return svg`\n\n${wrappedElements.map(el => svg`${el}`)}\n\"`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1075,"value":"md`## Imports`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"\nd3 = require(\"d3@6\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"jstat = require(\"https://cdn.jsdelivr.net/npm/jstat@latest/dist/jstat.min.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":18,"value":"import { slider, radio, button } from '@jashkenas/inputs'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1173,"value":"gtag = {\n await require(\"https://www.googletagmanager.com/gtag/js?id=UA-19745547-3\").catch(\n () => {}\n );\n const dataLayer = (window.dataLayer = window.dataLayer || []);\n function gtag() {\n dataLayer.push(arguments);\n }\n await gtag('js', new Date());\n await gtag('config', 'UA-19745547-3', {\n page_path: \"/@elibryan/covid-19-test-accuracy-simulator\"\n });\n return function() {\n dataLayer.push(arguments);\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":222,"value":"_ = require(\"https://cdn.jsdelivr.net/npm/lodash@4.17.20/lodash.min.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W53","stdlib":"1"}} 44:null