2a:null 2b:["$","title",null,{"children":"Risk visualization survey | Natalia Ciria | Observable"}] 30:T68e,function riskAnalysis(pathogen, cattle_n = 1, test = false, quarantine = false, quarantine_equipment = true, quarantine_cleaning = false) { // Parameters by pathogen a/b const h_prev = (pathogen === "a") ? 0.15 : 0.17; // Herd prevalence const w_prev = (pathogen === "a") ? 0.5 : 0.025; // Within herd prevalence const sensi = (pathogen === "a") ? 0.9 : 0.99; // Test sensitivity const infectious_inf = (pathogen === "a") ? 0.15 : 1; // Probability infected animal is infectious const inf_ic = (pathogen === "a") ? 0.1 : 0.05; // Probability effective indirect contact const disinfection_eff = (pathogen === "a") ? 0.8 : 0.6; // Probability disinfection eliminates pathogen // Probability one animal is infected with a const a_inf = h_prev * w_prev; // Sensitivity b Test const test_sensitivity = test ? sensi : 0; // Probability an infected animal enters the farm let a_entry; if (quarantine) { a_entry = a_inf * (1 - test_sensitivity) ; } else { a_entry = a_inf; } // Probability a fomite infects an animal in the herd let a_indir_contact; if (quarantine_equipment && test) { if (quarantine_cleaning) { a_indir_contact = a_inf * infectious_inf * inf_ic * (1 - disinfection_eff); } else { a_indir_contact = a_inf * infectious_inf * inf_ic; } } else { a_indir_contact = 0; } // Probability one animal introduces the pathogen into the farm const a_total = 1 - ((1 - a_entry) * (1 - a_indir_contact)); // Probability at least one animal in the new batch introduces the pathogen into the farm const b_total = 1 - Math.pow((1 - a_total), cattle_n); return b_total; }31:[] 2e:{"id":"6a9c92e9d92a080b","slug":"risk-visualization-survey","title":"Risk visualization survey","thumbnail":"56a78993a9cb41930006163c8e5666ed0cef3297444af54af561efa40cf1243d","access_level":"public","create_time":"$D2024-01-09T10:14:03.208Z","update_time":"$D2024-01-11T12:03:30.386Z","view_time":null,"first_public_time":"$D2024-01-09T10:14:03.208Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"7876ba8fb6584570","login":"nataliaciria","name":"Natalia Ciria","avatar_url":"https://avatars-next.observableusercontent.com/5557e8ad7cd12cb4e3b8fc95de0f3b9d43d0ef70b78ca954928c0f174a52b579","tier":"starter_2024"},"version":165,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"cb6285295e6cfa25","login":"nataliaciria","name":"Natalia Ciria","avatar_url":"https://avatars-next.observableusercontent.com/5557e8ad7cd12cb4e3b8fc95de0f3b9d43d0ef70b78ca954928c0f174a52b579","tier":null}],"members":[{"type":"individual","id":"cb6285295e6cfa25","login":"nataliaciria","name":"Natalia Ciria","avatar_url":"https://avatars-next.observableusercontent.com/5557e8ad7cd12cb4e3b8fc95de0f3b9d43d0ef70b78ca954928c0f174a52b579","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Risk visualization survey","cells":[{"id":0,"value":"# Risk visualization survey","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":9,"value":" text1 = md`Number of cows purchased`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"viewof cattle_n = Inputs.range([0, 255], {step: 1, value:10})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":159,"value":" text0 = md`Region of origin`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":153,"value":"viewof region = Inputs.select([\"Cowland\"], {disabled: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":12,"value":" text2 = md`When new cattle enter the farm, are they isolated from the herd (quarantine)?`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"viewof quarantine = Inputs.radio(new Map([[\"Yes\", true], [\"No\", false]]), {value: false})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":" text3 = md`What tests are done during quarantine?`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"viewof test_type = {\n if(quarantine){\n return Inputs.checkbox(new Map([[\"Test for Pathogen A\", \"a\"], [\"Test for Pathogen B\", \"b\"]]), {value: \"0\"})\n }else{\n {\n const element = htl.html`

No (no quarantine)

`;\n element.value = \"0\";\n return element;\n }\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":30,"value":" text4 = md`Is quarantine equipment shared with the rest of the herd?`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":35,"value":"viewof quarantine_equipment = {\n if(quarantine){\n return Inputs.radio(new Map([[\"Yes\", true], [\"No\", false]]), {value: true})\n }else{\n {\n const element = htl.html`

No (no quarantine)

`;\n element.value = true;\n return element;\n }\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":38,"value":" text5 = md`Is equipment cleaned after each use?`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":40,"value":"viewof quarantine_cleaning = {\n if(quarantine){\n if(quarantine_equipment){\n return Inputs.radio(new Map([[\"Yes\", true], [\"No\", false]]), {value: false})\n }else{\n {\n const element = htl.html`

No (no shared material)

`;\n element.value = false;\n return element;\n }\n }\n }else{\n {\n const element = htl.html`

No (no quarantine)

`;\n element.value = false;\n return element;\n }\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":97,"value":" text6 = md`### Risk of pathogens entering the farm`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":80,"value":"plot_current = Plot.plot({\n marginLeft: 80,\n marginRight: 50,\n marginTop: 50,\n x: {\n domain: [0,100],\n axis: \"top\",\n label: \"Risk of pathogen entry (%)\",\n labelAnchor: \"center\",\n labelOffset: 35,\n percent: true\n },\n y: {label: \"\"},\n color: {\n legend: false,\n scheme: \"paired\" \n },\n marks: [\n Plot.barX(current_risk, {y: \"name\", x: \"abs_risk\", sort: {y: \"-x\"}}),\n Plot.ruleX([0]),\n Plot.text(current_risk, {x: \"abs_risk\", y: \"name\", text: d => d.abs_risk>0.01 ? format0(d.abs_risk):\"<1%\" , textAnchor: \"end\", dx: 30, fill: \"currentColor\"})\n ],\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":91,"value":" text7 = md`### Impact of biosecurity measures`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":89,"value":"viewof pathogen = Inputs.radio(new Map([[\"Pathogen A\", \"a\"], [\"Pathogen B\", \"b\"]]), {value: \"b\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":99,"value":"plot_wif = Plot.plot({\n axis: null,\n marginRight: 320,\n marginLeft: 60,\n marginTop: 70,\n x: {\n axis: \"top\",\n label: \"Risk reduction of biosecurity measures (baseline = current)\",\n labelAnchor: \"center\",\n labelOffset: 35,\n ticks: 5,\n percent: true,\n tickFormat: (d) => `${d}%`,\n domain: [-100,0],\n labelArrow :\"left\"\n },\n y: {axis: null,\n label: \"\",\n domain: ordered_wif,\n \n },\n color: {\n legend: false,\n scheme: \"ylgn\",\n reverse: false,\n range: [0.3,1],\n },\n marks: [\n Plot.barX(wif_risk, {y: \"measure\", x: (d) => -d.red_risk, sort: { y: \"x\" }, fill: \"red_risk\", anchor: \"right\"}),\n Plot.ruleX([0]),\n Plot.text(wif_risk, Plot.pointerY({x: (d) => -d.red_risk, y: \"measure\", text: d => d.red_risk>0.01 ? format0(d.red_risk):\"<1%\", textAnchor: \"end\", dx: -10, fill:\"Black\"})),\n Plot.text(wif_risk, {x: 0, y: \"measure\", text: d => d.measure, textAnchor: \"start\" , dx: 10, fill:\"Black\"})\n ],\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"test_a = test_type.includes(\"a\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"test_b = test_type.includes(\"b\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":46,"value":"risk_a = riskAnalysis(\"a\", cattle_n, quarantine,test_a,quarantine_equipment,quarantine_cleaning)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":49,"value":"risk_b = riskAnalysis(\"b\", cattle_n, quarantine,test_b,quarantine_equipment,quarantine_cleaning)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"test = {\n if(test_type==pathogen){\n test_a\n }else{\n test_b\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":54,"value":"wif_test = riskAnalysis(pathogen, cattle_n, true,true,quarantine_equipment,quarantine_cleaning)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":57,"value":"wif_cleaning = riskAnalysis(pathogen, cattle_n, true,true,quarantine_equipment,true)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":59,"value":"wif_equipment = riskAnalysis(pathogen, cattle_n, true,true,false,quarantine_cleaning)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":61,"value":"// Create absolute risk by pathogen object\ncurrent_risk = {\n const makePatogen = function(pathogen, name, abs_risk){\n return {\n pathogen: pathogen,\n name: name,\n abs_risk: abs_risk,\n }\n }\n \n return [makePatogen('a',\"Pathogen A\", risk_a),\n makePatogen('b',\"Pathogen B\", risk_b)]\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":63,"value":"format0 = d3.format(\".0%\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":65,"value":"format1 = d3.format(\".1%\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":75,"value":"style = html`