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43:{"id":"8c32af03b9b80db8","slug":null,"title":"Seasonal & spatial change","thumbnail":"49e3b8e7b5c25c76853ac31b4ed41e895e2facb91573182f4e68e995d0ccb899","access_level":"public","create_time":"$D2023-01-10T03:38:25.324Z","update_time":"$D2023-08-23T10:48:34.272Z","view_time":null,"first_public_time":"$D2023-02-21T01:51:32.250Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"aff35a2a633c89c4","login":"mtchl","name":"Mitchell Whitelaw","avatar_url":"https://avatars-next.observableusercontent.com/52a1b7e44268ad38323892ecffa497a4389484a1d7521eb07575bb99fcadfc56","tier":"starter_2024","bio":"","following":false},"version":418,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"abea9226ca0112c4","login":"mtchl","name":"Mitchell Whitelaw","avatar_url":"https://avatars-next.observableusercontent.com/52a1b7e44268ad38323892ecffa497a4389484a1d7521eb07575bb99fcadfc56","tier":null,"bio":"","following":false}],"members":[{"type":"individual","id":"abea9226ca0112c4","login":"mtchl","name":"Mitchell Whitelaw","avatar_url":"https://avatars-next.observableusercontent.com/52a1b7e44268ad38323892ecffa497a4389484a1d7521eb07575bb99fcadfc56","tier":null,"role":"editor"},{"type":"individual","id":"ca7537a255944485","login":"rian39","name":"adrian mackenzie","avatar_url":"https://avatars-next.observableusercontent.com/d591db5c2105bfb5a6e1cf19ce3b4485f42c26aa3af6bba82f9c90aa640506a5","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":{"id":"5f7ed58bb7ccc0e9","slug":"ala-data-stories","title":"ALA Data Story Sketches","owner":{"id":"aff35a2a633c89c4","login":"mtchl","name":"Mitchell Whitelaw"}},"type":"notebook","body":{"titling":"auto","title":"Seasonal & spatial change","cells":[{"id":0,"value":"# Seasonal & spatial change","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":5,"value":"banjos = FileAttachment(\"ala-banjo-frogs.json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":39,"value":"banjosRecent = banjos.filter(d => +d.year > 2000)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":63,"value":"banjoBins = makeMonthBins(banjosRecent)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":131,"value":"function makeMonthBins(data){\n let bins = [];\n for (let m=0; m<12; m++){\n bins[m] = data.filter(b => +b.month == m+1)\n}\n return bins\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":57,"value":"## Banjo frogs\nAnimated by month of occurrence","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":50,"value":"Plot.plot({\n width: 800,\n height: 600,\n color: {\n legend:true,\n scheme:\"YlGnBu\",\n domain:[0,1200],\n type:\"sqrt\",\n label: `Banjo frogs: ${monthNames[monthIndex]}`,\n },\n projection: {\n type: \"mercator\",\n rotate: [-133, 27],\n domain: {type: \"MultiPoint\", coordinates: [[143, -27], [154, -28], [141, -1820.5], [146, -44]]}\n },\n marks:[\n Plot.geo(states,{stroke:\"#eee\",fill:\"#fdfdfd\"}),\n Plot.dot(banjoBins[monthIndex], Plot.hexbin(\n {fill:\"count\"},\n { x: \"decimalLongitude\", y: \"decimalLatitude\",binWidth:10 }\n ))\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":84,"value":"monthIndex = {\n let i = 0;\n while (true) {\n if (i == 11) i=0\n yield Promises.tick(500, ++i);\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":127,"value":"swifties = FileAttachment(\"ala-swift-parrot@1.json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":139,"value":"swiftBins = makeMonthBins(swifties)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":260,"value":"## Swift Parrots\nMonthly sequence shows them heading north around March - April","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":74,"value":"viewof selectMonth = Inputs.range([0, 11], {label: \"Month\", step: 1})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":129,"value":"Plot.plot({\n width: 800,\n height: 600,\n color: {\n legend:true,\n scheme:\"YlGnBu\",\n domain:[0,500],\n type:\"sqrt\",\n label: `Swift parrots: ${monthNames[selectMonth]}`,\n },\n projection: {\n type: \"mercator\",\n rotate: [-133, 27],\n domain: {type: \"MultiPoint\", coordinates: [[145, -26], [145, -26], [148, -1820.5], [148, -46]]}\n },\n marks:[\n Plot.geo(states,{stroke:\"#eee\",fill:\"#fdfdfd\"}),\n Plot.dot(swiftBins[selectMonth], Plot.hexbin(\n {fill:\"count\"},\n { x: \"decimalLongitude\", y: \"decimalLatitude\",binWidth:10 }\n ))\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":263,"value":"This animation uses a finer time scale - essentially week of year (1-52)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":189,"value":"Plot.plot({\n width: 800,\n height: 600,\n color: {\n legend:true,\n scheme:\"YlGnBu\",\n domain:[0,100],\n type:\"sqrt\",\n label: `Swift Parrots: week ${dayAnimateIndex} of year`,\n },\n projection: {\n type: \"mercator\",\n rotate: [-133, 27],\n domain: {type: \"MultiPoint\", coordinates: [[145, -26], [145, -26], [148, -1820.5], [148, -46]]}\n },\n marks:[\n Plot.geo(states,{stroke:\"#eee\",fill:\"#fdfdfd\"}),\n Plot.dot(swiftDays.filter(s => s.doy > dayAnimateIndex*7 && s.doy < (dayAnimateIndex+1)*7), Plot.hexbin(\n {fill:\"count\"},\n { x: \"decimalLongitude\", y: \"decimalLatitude\",binWidth:9 }\n ))\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":198,"value":"dayAnimateIndex = {\n let i = 0;\n while (true) {\n if (i == 52) i=0\n yield Promises.tick(100, ++i);\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":175,"value":"swiftDays = swifties.map(s => {\n let d = new Date(s.eventDate)\n s.doy = dayOfYear(d);\n return s;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":45,"value":"humpbacks = FileAttachment(\"ala-humpback.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":211,"value":"humpbackDays = humpbacks.map(s => {\n let d = new Date(s.eventDate)\n s.doy = dayOfYear(d);\n return s;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":273,"value":"## Humpback Whales\nMigration harder to see because it's bi-directional? ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":191,"value":"viewof selectWeek = Inputs.range([0, 52], {label: \"Week of Year\", step: 1})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":214,"value":"Plot.plot({\n width: 800,\n height: 600,\n color: {\n legend:true,\n scheme:\"blues\",\n domain:[0,500],\n type:\"sqrt\",\n label: `Humpbacks: week ${selectWeek} of year`,\n },\n projection: {\n type: \"mercator\",\n rotate: [-133, 27],\n domain: {type: \"MultiPoint\", coordinates: [[120, -8], [145, -26], [148, -1820.5], [148, -46]]}\n },\n marks:[\n Plot.geo(states,{stroke:\"#eee\",fill:\"#fdfdfd\"}),\n Plot.dot(humpbackDays.filter(s => s.doy > selectWeek*7 && s.doy < (selectWeek+1)*7), Plot.hexbin(\n {fill:\"count\"},\n { x: \"decimalLongitude\", y: \"decimalLatitude\",binWidth:9 }\n ))\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":240,"value":"alaCaladenia = FileAttachment(\"ala-caladenia.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":241,"value":"caladeniaDays = alaCaladenia.filter(d => d.eventDate).map(s => {\n let d = new Date(s.eventDate)\n s.doy = dayOfYear(d);\n return s;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":284,"value":"## Caladenia Orchids\nThis is the whole genus - many species. It nicely shows seasonal timing of flowering changing with latitude as well as elevation. Maybe also differences with the WA species - could we show species differences somehow? ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":248,"value":"viewof caladeniaWeek = Inputs.range([0, 52], {label: \"Week of Year\", step: 1})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":244,"value":"Plot.plot({\n width: 800,\n height: 600,\n color: {\n legend:true,\n scheme:\"YlGnBu\",\n domain:[0,800],\n type:\"sqrt\",\n label: `Caladenias: week ${caladeniaWeek} of year`,\n },\n projection: {\n type: \"mercator\",\n rotate: [-133, 27],\n domain: {type: \"MultiPoint\", coordinates: [[120, -8], [145, -26], [148, -1820.5], [148, -46]]}\n },\n marks:[\n Plot.geo(states,{stroke:\"#eee\",fill:\"#fdfdfd\"}),\n Plot.dot(caladeniaDays.filter(s => s.doy > caladeniaWeek*7 && s.doy < (caladeniaWeek+1)*7), \n Plot.hexbin({fill:\"count\"},{ x: \"decimalLongitude\", y: \"decimalLatitude\", binWidth:8 })\n )\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":308,"value":"There's a curious spike around day 1 of the year - suspect this is a default date of some kind? ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":292,"value":"Plot.plot({\n marks: [\n Plot.barY(caladeniaDays, Plot.binX({y: \"count\"}, {x: \"doy\"})),\n Plot.ruleY([0])\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":297,"value":"caladeniaDays.filter(d => d.doy == 1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":310,"value":"getObs = async function(_q,_fq,_count){\n var base = 'https://api.ala.org.au/occurrences/occurrences/search?'\n const queryparams ={q:_q,fq:_fq,image:true,pageSize:_count,sort:\"eventDate\",dir:\"desc\"}\n const paramString = Object.keys(queryparams).map(function(k){ return '&' + k + '=' + queryparams[k]}).join(\"\"); //\n\tvar url = encodeURI(base + paramString);\n \n const res = await fetch(url);\n const info = await res.json();\n return info.occurrences;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":313,"value":"getObs(\"genus:Caladenia\",\"month:1\",100)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":318,"value":"getObsByMonth = async function(query){\n let months = [1,2,3,4,5,6,7,8,9,10,11,12];\n \n let stack = months.map( m => getObs(query,\"month:\"+m,50))\n let results = Promise.all(stack).then((value) => {\n return value.map((r,i) => {return {month:months[i], obs: r.filter( o => o.smallImageUrl)}});\n })\n return results\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":321,"value":"caladeniaObs = getObsByMonth(\"genus:Caladenia\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":328,"value":"html`

Caladenias by month

\n\n ${caladeniaObs.map(m => html.fragment``)}\n \n

${monthNames[m.month-1]}

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":370,"value":"async function getFacets(query,count,facet){\n let baseQuery = 'https://biocache-ws.ala.org.au/ws/occurrence/facets?q='+query+'&fq=taxonRank:\"species\"&fq=spatiallyValid:\"true\"&facets='+facet+'&flimit='+count\n const facets = await fetch(encodeURI(baseQuery))\n const payload = await facets.json();\n if (payload.length == 0) return []; // no facets\n return { query: query, facets: payload[0].fieldResult};\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":374,"value":"topCaladenias = getFacets(\"genus:Caladenia\",10,\"scientificName\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":391,"value":"topCaladeniasMonthly = Promise.all(topCaladenias.facets.map(s => getFacets(s.label,12,\"month\")))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":399,"value":"flatCaladeniasMonthly = {\n var a = [];\n topCaladeniasMonthly.forEach(c => c.facets.forEach(f => a.push({species:c.query,count:f.count,month: +f.i18nCode.split(\".\")[1] })))\n return a;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":405,"value":"Plot.plot({\n padding: 0,\n marginLeft:180,\n // grid: true,\n x: {axis: \"top\", label: \"month\"},\n y: {label: \"species\"},\n color: {type: \"sqrt\", scheme: \"YlGnBu\"},\n marks: [\n Plot.cell(flatCaladeniasMonthly, {x: \"month\",y:\"species\",fill:\"count\"}),\n // Plot.text(simpsons, {x: \"season\", y: \"number_in_season\", text: (d) => d.imdb_rating?.toFixed(1), fill: \"black\", title: \"title\"})\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":267,"value":"## Appendix","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":182,"value":"dayOfYear = date =>\n Math.floor((date - new Date(date.getFullYear(), 0, 0)) / 1000 / 60 / 60 / 24);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":101,"value":"monthNames = [\"January\", \"February\", \"March\", \"April\", \"May\", \"June\", \"July\", \"August\", \"September\", \"October\", \"November\", \"December\"];","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":109,"value":"oz = FileAttachment(\"australia (1).json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":115,"value":"states = topojson.feature(oz, oz.objects.states)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":338,"value":"html = htl.html","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"Plot.plot({\n width: 960,\n height: 800,\n color: {\n legend:true,\n scheme:\"blues\"\n },\n projection: {\n type: \"mercator\",\n rotate: [-133, 27],\n domain: {type: \"MultiPoint\", coordinates: [[133, -24], [154, -28], [141, -1820.5], [146, -44]]}\n },\n marks:[\n Plot.dot(banjosRecent, {\n x: \"decimalLongitude\",\n y: \"decimalLatitude\",\n r: 0.5,\n fill: \"black\"\n }),\n \n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W45","stdlib":"1"}} 44:"$43:body"