2b:null 2c:["$","title",null,{"children":"LaMer biota data - identify elevated levels | maanchu | Observable"}] 31:T7a1,histogram = Plot.plot({ round: true, color: { legend: true, type: "categorical", scheme: "tableau10" }, marks: [ // Plot.rectY(dataBiogroup, Plot.binX({y: "count"}, {x: "ln_activity", fill: "displaytext", mixBlendMode: "multiply"})), Plot.rectY( dataWithout, Plot.binX( { y: "count" }, { x: "ln_activity", fill: datasets ? "displaytext" : "steelblue", stroke: "black", thresholds: d3.thresholdSturges, tip: true } ) ), Plot.ruleY([0]), Plot.lineY(normalData, { x: "x", y: "y", stroke: "orange", strokeWidth: 2 }), Plot.text( [ "GM: " + d3.format(".3")( Math.exp(d3.mean(dataWithout, (d) => d.ln_activity)) ) + ", GSD: " + d3.format(".3")( Math.exp(d3.deviation(dataWithout, (d) => d.ln_activity)) ) ], { frameAnchor: "top-right", dy: 5, fontSize: 12 } ), Plot.text( [ "Median: " + d3.format(".3")( Math.exp(d3.median(dataWithout, (d) => d.ln_activity)) ) ], { frameAnchor: "top-right", dy: 22, fontSize: 12 } ), Plot.text( [ "AM: " + d3.format(".3")(d3.mean(dataWithout, (d) => d.activity)) + ", SD: " + d3.format(".3")(d3.deviation(dataWithout, (d) => d.activity)) ], { frameAnchor: "top-right", dy: 37, fontSize: 12 } ), Plot.text( [ "Min: " + d3.format(".3")( Math.exp(d3.min(dataWithout, (d) => d.ln_activity)) ) + ", Max: " + d3.format(".3")(Math.exp(d3.max(dataWithout, (d) => d.ln_activity))) ], { frameAnchor: "top-right", dy: 52, fontSize: 12 } ), Plot.text(["N: " + dataWithout.length], { frameAnchor: "top-right", dy: 67, fontSize: 12 }) ] })32:T562,map = Plot.plot( (() => { return { width: 600, marginBottom: 5, axis: null, y: { insetTop: 10 }, fx: { padding: 0.03 }, color: { type: "threshold", scheme: "YlGnBu", domain: activityBins }, projection: { type: "azimuthal-equidistant", rotate: center.map((d) => -d), domain: circle, inset: 10 }, marks: [ Plot.geo(land, { fill: "#fafafa", stroke: "black", strokeWidth: 0.5 }), Plot.graticule(), Plot.dot( dataSelected, Plot.hexbin( { fill: (g) => d3["max"](g, (d) => d.activity), title: (elems) => `Max: ${parseInt(d3["max"](elems, (d) => d.activity))}` }, { x: "lon", y: "lat", fillOpacity: 0.8, symbol: "hexagon", stroke: "black", strokeWidth: 0.2, binWidth: hexBinSize, fx: (d) => minYear, fy: (d) => maxYear } ) ), Plot.geo(circle, { stroke: "#bbb", strokeWidth: 1, strokeDasharray: "5,3" }), Plot.sphere({ strokeWidth: 0.5 }) ], //caption: `${nuclide} activity concentration in Bq/kg .f.w.` }; })() )33:[{"id":"e168a6f02218c79c0a540a2cc14dc3f846d717cf48026948c14e0b7658d46a019c38addb48633c295c7a570c13a7dedf1ce2f2f9016e8aed0b9f70292f1a4ae9","href":"https://static.observableusercontent.com/files/e168a6f02218c79c0a540a2cc14dc3f846d717cf48026948c14e0b7658d46a019c38addb48633c295c7a570c13a7dedf1ce2f2f9016e8aed0b9f70292f1a4ae9","name":"2024-05-01 extract all LaMer rads no restriction by location v4.csv","type":"text/csv","lastModified":1714525761278.873,"size":30490087},{"id":"1dd786733d2c60213b1c4b048a979e9fc0ac8e7a605ab25d67d6d774721014ca36571a4dce0e743f7272cb984acb941ecfd37346bfd3cbaa56fd7766922f799e","href":"https://static.observableusercontent.com/files/1dd786733d2c60213b1c4b048a979e9fc0ac8e7a605ab25d67d6d774721014ca36571a4dce0e743f7272cb984acb941ecfd37346bfd3cbaa56fd7766922f799e","name":"Current db - all LaMer rads, no aggregation, no restriction by FDNPS, Sellafield etc (14 Apr).csv","type":"text/csv","lastModified":1713299223039.075,"size":29608650},{"id":"8c96f21bb0ea7902a3c1c5ecd94e50a2a07649647606d79d144b62325f4e197d2774e4ed3ad2945388e5c2f342a0b6d1d240e8f83aded3a70c38fae16457bc92","href":"https://static.observableusercontent.com/files/8c96f21bb0ea7902a3c1c5ecd94e50a2a07649647606d79d144b62325f4e197d2774e4ed3ad2945388e5c2f342a0b6d1d240e8f83aded3a70c38fae16457bc92","name":"2024-05-01 extract all LaMer rads no restriction by location v4 - recombined - duplicates removed.csv","type":"text/csv","lastModified":1715119390914.908,"size":28307016}] 2f:{"id":"5926d619aff6136f","slug":null,"title":"LaMer biota data - identify elevated levels","thumbnail":"dd758b53d22ff211f9e9e75f9f2f62ac84779d50881d0f9e34b1d71dc422a235","access_level":"public","create_time":"$D2024-04-16T20:20:12.889Z","update_time":"$D2024-05-09T20:44:37.938Z","view_time":null,"first_public_time":"$D2024-04-19T07:00:09.773Z","has_unpublished_edits":null,"fork":{"id":"1892bb13c87e1a30","slug":"maris-report-seawater","title":"MARIS report [Seawater]","owner":{"id":"5d646434b0cbc3e4","login":"francobollo","name":"francobollo"}},"stars":0,"starred":false,"owner":{"type":"team","id":"b28b6e68c664f664","login":"maanchu","name":"","avatar_url":null,"tier":"starter_2024"},"version":3725,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"f9fa119bd727c22e","login":"maanchu","name":"","avatar_url":null,"tier":null}],"members":[{"type":"team","id":"b28b6e68c664f664","login":"maanchu","name":"","avatar_url":null,"tier":"starter_2024","role":"editor"},{"type":"individual","id":"f9fa119bd727c22e","login":"maanchu","name":"","avatar_url":null,"tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"LaMer biota data - identify elevated levels","cells":[{"id":0,"value":"# LaMer biota data - identify elevated levels\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3630,"value":"After choosing radionuclide and biogroup of interest, choose a location to focus on. Exclude data from the histogram and qqplot by varying the radius of the circle and the start and end date of the time window for excluding data. Beware of Cs-137 in 🐟 - too much data! ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3523,"value":"viewof nuclide = Inputs.select(new Set(data.map((d) => d.nuclide)), {\n label: \"Nuclide: \",\n sort: true, \n unique: true\n})\n// https://observablehq.com/@observablehq/input-select","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3265,"value":"viewof biogroup = Inputs.select(new Set(data.map((d) => d.biogroup)), {\n label: \"Biogroup: \",\n sort: true, \n unique: true\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3670,"value":"viewof startDate = Inputs.date({label: \"Start of LaMer assessment period:\", value: \"2010-01-01\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3014,"value":"viewof centerLabel = Inputs.select(Object.keys(centers), {\n value: \"FNDPP\",\n label: \"Focus on: \"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3340,"value":"viewof windowStartDate = Inputs.date({label: \"Start of period to exclude\", value: (centerLabel == \"FDNPP\") ? \"2011-03-11\" :d3.min(dataSelected.map((d) => d.begperiod))})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3344,"value":"viewof windowEndDate = Inputs.date({label: \"End of period to exclude\", value: d3.max(dataSelected.map((d) => d.begperiod))})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3461,"value":"viewof kms = Inputs.range([0, 3000], {\n value: 800,\n step: 5,\n label: \"Radius around selected center point(in km): \"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3570,"value":"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3611,"value":"\n \n \n \n

\n ${histogram}\n ${viewof datasets}\n

\n {map}\n ${legend}\n${viewof hexBinSize}\n

\n${qqplot}\n

\n {timeseries}\n ${viewof logscale}\n

\n \n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3685,"value":"viewof datasets = Inputs.toggle({ label: \"Show data sources?\" })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3626,"value":"viewof hexBinSize = Inputs.range([4, 30], {\n value: 8,\n step: 1,\n label: \"Hegagons size: \"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3488,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3535,"value":"qqplot = Plot.plot({\n round: true,\n color: {legend: true},\n marks: [\n Plot.dot(dataQQ, {x: \"zscore\", y: \"ln_activity\", stroke: \"steelblue\"}),\n Plot.linearRegressionY(dataQQ, {x: \"zscore\", y: \"ln_activity\", stroke: \"orange\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3440,"value":"timeseries = Plot.plot({\n inset: 8,\n y:{\n type: logscale ? \"log\": \"linear\"\n },\n grid: true,\n color: {\n legend: true},\n marks: [\n Plot.dot(dataWithout, {x: \"begperiod\", y: \"activity\", tip: true, fill: \"steelblue\"}),\n Plot.dot(dataWithin, {x: \"begperiod\", y: \"activity\", tip: true, fill:\"orange\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2900,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3467,"value":"legend = map.legend(\"color\", {\n label: `Max ${nuclide} activity concentration in Bq/kg .f.w.`,\n width: 320,\n tickFormat: \"~s\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":965,"value":"## Utils","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3453,"value":"// Adjust it manually based on histogram\n// activityBins = [1, 10, 100, 1000, 10000] // FNDPP\nactivityBins = [1, 20, 1000, 10000] // FNDPP","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3437,"value":"// Feel free to add your point of interest\ncenters = ({\n FDNPP: [141.042132, 37.423152],\n LaHague: [-1.874036, 49.677189],\n Sellafield: [-3.5123504711704308, 54.41517679941927],\n Sellafield2: [-3.5623504711704308, 54.41517679941927],\n \"Baltic Sea\": [21.443082725926867, 58.67250942256951],\n \"Irish Sea\": [-4.6, 54.3],\n \"Rhone delta\": [ 165.37580568407597, 11.60768921413143],\n \"Marshall islands\": [165.830103, 8.225226],\n \"Aleutian islands\": [-164.430045, 54.192722]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3617,"value":"viewof logscale = Inputs.toggle({ label: \"Log y-axis?\" })","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":714,"value":"sphere = ({ type: \"Sphere\" })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":699,"value":"// width = 800","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":701,"value":"// height = 610","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":581,"value":"## Data loading","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3268,"value":"dataRaw = FileAttachment(\"2024-05-01 extract all LaMer rads no restriction by location v4 - recombined - duplicates removed.csv\").csv()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2430,"value":"data = dataRaw.map((d) => ({\n lon: d[\"longitude\"],\n lat: d[\"latitude\"],\n biogroup: d[\"biogroup\"],\n nuclide: d[\"nusymbol\"],\n begperiod: d3.utcParse(\"%Y-%m-%d\")(d[\"begperiod\"]),\n activity: +d[\"corr_activity\"],\n ln_activity: log(d[\"corr_activity\"]),\n displaytext: d[\"displaytext\"],\n }))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2481,"value":"dataSelected = data.filter(\n (d) => d.nuclide == nuclide && d.biogroup == biogroup && d.begperiod > startDate\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2867,"value":"center = centers[centerLabel]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2503,"value":"minYear = d3.min(dataSelected.map((d) => d.begperiod))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2513,"value":"maxYear = d3.max(dataSelected.map((d) => d.begperiod))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":651,"value":"world = (\n await fetch(\"https://cdn.jsdelivr.net/npm/world-atlas@2/land-50m.json\")\n).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":740,"value":"land = topojson.feature(world, world.objects.land)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2865,"value":"circle = d3\n .geoCircle()\n .center(center)\n .radius((kms / (6371 * Math.PI * 2)) * 360)\n .precision(10)()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3178,"value":"dataWithin = dataSelected.filter(\n (d) => (d3.geoDistance([d.lon, d.lat], center) < kms / 6371) && (d.begperiod >= windowStartDate) && (d.begperiod <= windowEndDate )\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3324,"value":"dataWithout = dataSelected.filter(\n (d) => (d3.geoDistance([d.lon, d.lat], center) > kms / 6371) && (d.begperiod >= windowStartDate) && (d.begperiod <= windowEndDate ) ||\n (d.begperiod < windowStartDate) || (d.begperiod > windowEndDate)\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":104,"value":"## Imports","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":609,"value":"// source: https://observablehq.com/@mkfreeman/plot-tooltip\nimport { Plot } from \"@mkfreeman/plot-tooltip\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":648,"value":"topojson = require(\"topojson-client@3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3290,"value":"import {log, pow, round, abs} from \"@fil/math\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3490,"value":"## Histogram","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3497,"value":"bin1 = d3.bin().thresholds(d3.thresholdSturges)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3495,"value":"bin1(dataWithout.map((d) => d.ln_activity))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3499,"value":"defaultBinInterval = abs(bin1(dataWithout.map((d) => d.ln_activity))[0].x0-bin1(dataWithout.map((d) => d.ln_activity))[0].x1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3501,"value":"dataRange = bin1(dataWithout.map((d) => d.ln_activity))[bin1(dataWithout.map((d) => d.ln_activity)).length-1].x1-bin1(dataWithout.map((d) => d.ln_activity))[0].x0","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3503,"value":"function normal_pdf (input_value, mean, sd) {\n return 1/(sd*(Math.sqrt(2*Math.PI)))* Math.exp(-(((input_value-mean)/sd)**2)/2)\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3493,"value":"normalData = {\n var d = []\n for (let i = bin1(dataWithout.map((d) => d.ln_activity))[0].x0; i < bin1(dataWithout.map((d) => d.ln_activity))[bin1(dataWithout.map((d) => d.ln_activity)).length-1].x1; i=i+dataRange/1000) {\n d.push({'x':i, 'y': normal_pdf(i,d3.mean(dataWithout, d => d.ln_activity),d3.deviation(dataWithout, d => d.ln_activity))*dataWithout.length*defaultBinInterval})\n }\nreturn d;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3537,"value":"## QQ plot","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3564,"value":"dataWithout.sort((a,b) => a.ln_activity - b.ln_activity)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3545,"value":"n = dataWithout.length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3547,"value":"a = n <= 10 ? 5 / 8 : 0.5","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3543,"value":"percentile = i => (i + a) / (n + 1 - 2 * a)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3551,"value":"erfinv = {\n const a = 8 * (Math.PI - 3) / (3 * Math.PI * (4 - Math.PI));\n return x => {\n const b = Math.log(1 - x * x);\n const c = b / 2 + (2 / (Math.PI * a));\n return Math.sign(x) * Math.sqrt(Math.sqrt((c * c) - b / a) - c);\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3549,"value":"qnorm = p => Math.SQRT2 * erfinv(2 * p - 1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3541,"value":"z = i => qnorm(percentile(i))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3539,"value":"dataQQ = {\nvar x = []\nfor (let i = 0; i < dataWithout.length; i++) {\nx.push({'ln_activity': dataWithout.map((d) => d.ln_activity)[i], \n 'percentile': percentile(i),\n 'zscore': z(i) \n })\n}\nreturn x;\n}\n//dataBiogroup.map((d) => d.ln_activity)[1]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 30:"$2f:body"