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One of the key mechanisms used by Australian governments is the listing of threatened species in various categories - and we can find this information in the ALA.\n\nOne of the first issues we discover is that the classification systems used by Federal, State and Territory governments are all different.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":465,"value":"{\nvar columns = Array.from(colourMap.keys());\nreturn html`\n \n ${columns.map(c => html.fragment``)}\n\n ${summary.map(s => html.fragment` \n \n ${columns.map(c => html.fragment``)} \n `)}\n

	${keyNames.get(c)}
${s.state}	${ s[c] ? html.fragment` ${s[c] ? c: \"\"} ` : \"\"}

	${keyNames.get(c)}
${s.state}	set(viewof select,{state:s.state,code:c})}> ${ s[c] ? html.fragment` ${s[c]} ` : \"\"}

Click on a cell in the table to see a list of species in that category

${filterSpecies.length} species coded ${keyNames.get(select.code)} in ${select.state}

${pickListSpecies.commonName}

${pickListSpecies.name}

\n ${focusSpecies.imageIdentifier ? html.fragment`

` : html.fragment`

No Image

` }\n

`\n} else return html`

No species selected

`\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1069,"value":"__Prompts__\n* What categories and numbers in the classification system seem most important to you?\n* Do categories tend to have different kinds of living things?\n* Does this matrix show something different to other lists of species?\n\nPlease enter thoughts here: https://forms.gle/iPifAQ4xFqHL63p27","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1111,"value":"## Threatened Species by Region","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1245,"value":"html`We can also explore spatial distribution. This map shows the number of threatened species observation by IBRA region. set(viewof mapMode,\"Relative\")}>Relative mode shows threatened species as a proportion of the observations in that region.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1173,"value":"viewof mapMode = Inputs.select([\"Absolute\",\"Relative\"],{label:\"Map mode\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1198,"value":"Legend(d3.scaleSequential(viewof regionDomain, d3.interpolateYlGnBu), {\n title: `${mapMode == \"Relative\" ? \"Threatened species observations (% of all obs)\" : \"Threatened species observation count\" }`,\n tickFormat: `${mapMode == \"Relative\" ? \"%\" : \",.0f\" }`\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":233,"value":"$45","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1365,"value":"html`

Select a region for a list of threatened species

\n ${rollProfile.imageIdentifier ? html.fragment`

` : html.fragment`

No Image

` }\n

${rollSpecies.commonName ? rollSpecies.commonName : rollSpecies.name }

${rollSpecies.commonName ? rollSpecies.name : \"\" }

\n ${states.map(s => html.fragment`${rollSpecies[s]? \n html.fragment`

${s}: ${keyNames.get(rollSpecies[s])}` : \"\"}

`)}\n

","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":889,"value":"## De-Extinction?\nALA data also shows traces of recent interventions to support threatened species. This graph shows a timeline of observations since 1980. We can see big gains in Endangered and Critically Endangered species, but also a boom in Extinct species since 2019. Are we seeing de-extinction? Not quite, but we can see traces of increasing attention and new forms of intervention.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":877,"value":"viewof listCat = Inputs.select([\"Extinct\",\"Critically Endangered\",\"Endangered\"],{label:\"Conservation status\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":883,"value":"Plot.plot({\n marginLeft:60,\n marginBottom:40,\n width:900,\n color:{type:\"linear\",scheme:\"OrRd\"},\n x: {type:\"time\",label:\"year\"},\n marks: [\n Plot.ruleX(extinctYears.facets, {x:\"label\", y: \"count\",sort:\"label\",strokeWidth: 15,stroke:\"count\"}),\n Plot.ruleY([0])\n ]})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1462,"value":"Digging in a bit further, we find that almost all these occurrences are from one state:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1429,"value":"Inputs.table(extinctStates.facets,{columns:[\"label\",\"count\"],width:300})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1464,"value":"...and almost all are mammals","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1455,"value":"Inputs.table(extinctClasses.facets,{columns:[\"label\",\"count\"],\n header:{label:\"Class\"}, \n format: {label: c => new Map([[\"Aves\",\"Birds\"],[\"Equisetopsida\",\"Horsetail ferns\"],[\"Gastropoda\",\"Snails\"],[\"Mammalia\",\"Mammals\"],[\"Reptilia\",\"Reptiles\"]]).get(c)},\n width:300})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":197,"value":"## Tracing interventions","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":745,"value":"html`Increasingly fenced reserves are being used to exclude introduced predators like foxes and cats, and enable vulnerable species to be reintroduced. These maps focus on three sites, loading the 2000 most recent observations:\n

Scotia Sanctuary, in western NSW, is a 650 sq km reserve managed by the Australian Wildlife Conservancy. It was established in 1994.\n
Mallee Cliffs National Park in south-western NSW includes a 9,570 hectare predator-free fenced area. It is managed under a partnership between NSW National Parks and the Austalian Wildlife Conservancy\n
The Pilliga, in northern NSW a 35,000 hectare reserve co-managed by NSW National Parks and the AWC.\n

Select sites from the menu above - zoom and pan the map to explore, and click observations for more info.

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1517,"value":"viewof showConsStatus = Inputs.select([\"NSW\",\"Aus\",\"ACT\",\"QLD\",\"TAS\",\"VIC\",\"WA\"],{value:\"NSW\",label:\"Show conservation status:\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":190,"value":"Plot.plot({\n marginLeft:320,\n color:{legend:true},\n y:{domain:speciesFacetsStatus.map(s => s.commonName ? s.commonName : s.scientificName)},\n x:{type:\"sqrt\"},\n marks: [\n Plot.barX(speciesFacetsStatus,{\n x:\"count\",y: s=> s.commonName ? s.commonName : s.scientificName,\n fill: d => d.status !=\"none\" && d.status[showConsStatus] ? colourMap.get(d.status[showConsStatus]) : \"#ccc\",\n sort: {y: \"x\", reverse: true}\n }),\n Plot.text(speciesFacetsStatus,{\n x: 1, y: s=> s.commonName ? s.commonName : s.scientificName, \n text: d => d.status[showConsStatus], fill: d => d.status[showConsStatus] == \"EX\" ? \"white\" : \"black\"\n }),\n //Plot.cellX(speciesGroupsStatus,{x:0,y:\"vernacularName\",sort: {y: \"x\", reverse: true}} ),\n Plot.ruleX([0])\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1579,"value":"## Prompts\n* How do fenced reserves affect observation of species?\n* Are there other ways or places in which interventions could become visible?\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":126,"value":"## Appendix","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1342,"value":"### Threatened Species Summary","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":406,"value":"colourMap = new Map([\n [\"NT\",\"#E0FFA7\"],\n [\"RA\",\"#E0FFA7\"],\n [\"P\",\"#F2FF5C\"],\n [\"VU\",\"#F2FF5C\"],\n [\"EN\",\"#FFE897\"],\n [\"TH\",\"#FFE897\"],\n [\"CR\",\"#FFC6A5\"],\n [\"CD\",\"#FF9D93\"],\n [\"EW\",\"#FF4E53\"],\n [\"EX\",\"#000000\"]\n])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":416,"value":"formatCell = function(code){\n return html`

\n ${code}

`\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":299,"value":"listKeys = new Map([[\"dr649\",\"ACT\"],[\"dr656\",\"Aus\"],[\"dr650\",\"NSW\"],[\"dr655\",\"VIC\"],[\"dr653\",\"SA\"],[\"dr651\",\"NT\"],[\"dr2201\",\"WA\"],[\"dr652\",\"QLD\"],[\"dr654\",\"TAS\"]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1467,"value":"statusMap = new Map([[\"Critically Endangered\",\"CR\"],[\"Vulnerable\",\"VU\"],[\"Endangered\",\"EN\"],[\"Extinct in the wild\",\"EW\"],[\"Extinct\",\"EX\"],[\"Conservation Dependent\",\"CD\"],[\"Near threatened\",\"NT\"],[\"Threatened\",\"TH\"],[\"Rare\",\"RA\"]]);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":352,"value":"buildAllSpecies = async function(){\n let allCodes = Array.from(listKeys.keys());\n let results = await Promise.all(allCodes.map(c => getSpeciesList(c,5000,0))).then(\n (values) => { return values }\n )\n let merged = d3.merge(results);\n let folded = new Set(merged.map(s=>s.lsid)); // unique values\n let compiled = [];\n\n folded.forEach(s => {\n var c = {}; // new entry\n const matches = merged.filter(m => m.lsid == s); // get entries with this lsid\n matches.forEach(a => {\n const status = a.kvpValues[0].value;\n var ss = statusMap.get(status) ? statusMap.get(status) : status\n // WA priority species - group together\n if (ss.includes(\"P1\") || ss.includes(\"P2\") || ss.includes(\"P3\") || ss.includes(\"P4\")){\n ss = \"P\"\n }\n c[listKeys.get(a.dataResourceUid)] = ss;\n })\n c.name = matches[0].name;\n c.commonName = matches[0].commonName;\n c.lsid = s;\n compiled.push(c);\n })\n return compiled;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1486,"value":"allSpecies = FileAttachment(\"allSpecies.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":443,"value":"summary = {\n var t = []\n for (const s of listKeys.values()){\n const g = d3.group(allSpecies, d => d[s])\n var r = {state:s}\n Array.from(colourMap.keys()).forEach(k => {if (g.get(k)) r[k] = g.get(k).length})\n if (s == \"Aus\") t.unshift(r); else t.push(r)\n }\n return t\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":507,"value":"viewof select = Inputs.input()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":526,"value":"filterSpecies = allSpecies.filter(s => s[select.state] == select.code)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":549,"value":"keyNames = new Map([[\"NT\",\"Near threatened\"], [\"RA\",\"Rare\"], [\"VU\",\"Vulnerable\"], [\"EN\",\"Endangered\"],[\"P\",\"Priority\"], [\"TH\",\"Threatened\"], [\"CR\",\"Critically Endangered\"], [\"CD\",\"Conservation Dependent\"], [\"EW\",\"Extinct in the Wild\"], [\"EX\",\"Extinct\"]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":285,"value":"getSpeciesList = async function(listID,count,offset){\n if (!offset) offset = 0;\n let baseQuery =`https://api.ala.org.au/specieslist/ws/speciesListItems/${listID}?includeKVP=true&max=${count}&offset=${offset}&nonulls=true`\n const response = await fetch(encodeURI(baseQuery))\n const data = await response.json()\n return data;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1305,"value":"listFocusMapPane = buildRegionMap(listSpeciesRegionMap,\"#listFocusMapContainer\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":611,"value":"listFocusSpeciesRegions = {\n if (focusSpecies) return getFacets(focusSpecies.classification.scientificName,500,\"cl1048\")\n return null\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":620,"value":"listSpeciesRegionMap = { return listFocusSpeciesRegions ? new Map(listFocusSpeciesRegions.facets.map(r => [r.label,r.count])) : null } ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":573,"value":"focusSpecies = { return pickListSpecies ? getSpeciesProfile(pickListSpecies.lsid) : null }","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1375,"value":"### Threatened Species By Region","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":246,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":60,"value":"baselineFacets = getFacets(\"*\", 1000, \"cl1048\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":63,"value":"relativeFacets = baselineFacets.facets.map(f => {\n let endangeredFacet = ibra_endangered.facets.find(i => i.label == f.label);\n if (endangeredFacet) return {...f, endangeredCount:endangeredFacet.count}\n return f\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":39,"value":"ibra_endangered = getFacets(consStatusAll,1000,\"cl1048\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":96,"value":"ibraMap = new Map(ibra_endangered.facets.map(({label,count}) => [label,count])) //lgaMap = new Map(LGAfacets.facets.map(({label, count}) => [label.replace(regex,''), count]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":44,"value":"ibraRelativeMap = new Map(relativeFacets.map(({label,count,endangeredCount}) => [label,endangeredCount/count])) //lgaMap = new Map(LGAfacets.facets.map(({label, count}) => [label.replace(regex,''), count]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":255,"value":"regionObs = getRegionFacets(focusIbraRegion,consStatusAll,100,focusIbraRegion)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1587,"value":"matchedRegionObs = {\n var matched = [];\n regionObs.forEach(r => {\n const m = allSpecies.find(a => a.lsid == r.lsid);\n if (m){\n m.count = r.count\n matched.push(m);\n } \n })\n return matched;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1202,"value":"viewof regionDomain = {\n var dom = [];\n if (mapMode == \"Relative\") dom = [0,0.1]\n if (mapMode == \"Absolute\") dom = [0, d3.max(Array.from(ibraMap.values()))] \n return dom;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":680,"value":"buildRegionMap = function(regionMap,container){\n if (!regionMap) return\n document.querySelector(container)\n .appendChild(\n Plot.plot({\n width: 400,\n height: 300,\n color: {\n legend:true,\n scheme:\"OrRd\",\n // domain:[0,0.045],\n type:\"sqrt\",\n //label: `Caladenias: week ${caladeniaWeek} of year`,\n },\n projection: {\n type: \"mercator\",\n rotate: [-133, 27],\n domain: {type: \"MultiPoint\", coordinates: [[129, -9], [145, -26], [148, -1820.5], [148, -44]]}\n },\n marks:[\n Plot.geo(ibra_regions,{stroke:\"#ddd\",fill:\"#f0f0f0\",strokeWidth:0.5}),\n Plot.geo(ibra_regions,\n {stroke:\"#888\",strokeWidth:0.5,\n fill: d => regionMap.get(d.properties.REG_NAME_7), \n title: d => `${d.properties.REG_NAME_7}: ${regionMap.get(d.properties.REG_NAME_7)}`\n }),\n ]\n })\n )}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1316,"value":"regionFocusMapPane = buildRegionMap(regionSpeciesRegionMap,\"#regionFocusMapContainer\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1337,"value":"regionFocusSpeciesRegions = {\n if (focusRegionSpecies) return getFacets(focusRegionSpecies.classification.scientificName,500,\"cl1048\")\n return null\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1332,"value":"regionSpeciesRegionMap = { return regionFocusSpeciesRegions ? new Map(regionFocusSpeciesRegions.facets.map(r => [r.label,r.count])) : null } ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1258,"value":"focusRegionSpecies = { return pickRegionSpecies ? getSpeciesProfile(pickRegionSpecies.lsid) : null }","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1247,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1189,"value":"consStatusAll = `((countryConservation:*) OR (stateConservation:*)) AND -(countryConservation:\"Not Listed\") AND -(stateConservation:\"Not Listed\")`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":30,"value":"aus_ibra = FileAttachment(\"IBRA7_verysimple_topo.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":33,"value":"ibra_regions = topojson.feature(aus_ibra, aus_ibra.objects.IBRA7_subregions_states)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1404,"value":"### Roll Call","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":803,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":765,"value":"rollSpecies = allSpecies[ticker]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1633,"value":"rollProfile = getSpeciesProfile(rollSpecies.lsid)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":761,"value":"ticker = {\n let i = 0;\n yield i;\n while (true && tickerButton > 0) {\n if (i == allSpecies.length-1) i = 0; \n yield Promises.delay(3000, ++i);\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1412,"value":"### De-extinction?\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":868,"value":"extinctYears=getFacets(`(countryConservation:${listCat}) OR (stateConservation:${listCat}) AND year:[1980 TO 2022]`,1000,\"year\",\"index\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1434,"value":"extinctStates= getFacets(`(countryConservation:Extinct) OR (stateConservation:Extinct) AND year:[1980 TO 2022]`,1000,\"state\",\"index\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1438,"value":"extinctClasses=getFacets(`(countryConservation:Extinct) OR (stateConservation:Extinct) AND year:[1980 TO 2022]`,1000,\"class\",\"index\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1540,"value":"### Interventions","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":128,"value":"$46","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":173,"value":"speciesFacets = facetObs(obs,\"scientificName\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":182,"value":"speciesFacetsStatus = findSpeciesStatus(speciesFacets,obs).slice(0,20)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1484,"value":"findSpeciesStatus = function(speciesFacets,sourceObs){\n let statusFacets = speciesFacets.map(f => {\n let sf = {};\n sf.scientificName = f.field;\n sf.count = f.count;\n const cn = sourceObs.find(o => o.scientificName == sf.scientificName)\n if (cn) sf.commonName = cn.vernacularName;\n const listed = allSpecies.find(s => s.name == f.field);\n if (listed) { sf.status = listed } else sf.status = \"none\";\n return sf;\n })\n return statusFacets.sort((a,b) => b.count - a.count);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":133,"value":"vernacularMap = [{key: \"kingdom\" , value: \"Plantae\" , label: \"Plants\" },\n {key: \"kingdom\" , value: \"Fungi\" , label: \"Fungi\" },\n {key: \"classs\", value: \"Aves\", label: \"Birds\"},\n {key: \"classs\", value: \"Arachnida\", label: \"Spiders\"},\n {key: \"classs\", value: \"Insecta\", label: \"Insects\"},\n {key: \"classs\", value: \"Reptilia\", label: \"Reptiles\"},\n {key: \"classs\", value: \"Gastropoda\", label: \"Snails\"},\n {key: \"classs\", value: \"Mammalia\", label: \"Mammals\"},\n {key: \"classs\",value: \"Actinopterygii\",label:\"Fishes\"},\n {key: \"classs\",value: \"Amphibia\",label:\"Frogs\"},\n {key: \"classs\",value: \"Malacostraca\",label:\"Crustaceans\"},\n {key: \"classs\",value: \"Bivalvia\",label:\"Bivalves\"}\n // Bivalvia\n // {key: \"classs\",value: \"Magnoliopsida\",label:\"Plant\"},\n ]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":143,"value":"groupVernacular = function(o){\n for (var k of vernacularMap){\n if (o[k.key] && o[k.key] == k.value) return k.label;\n }\n return \"unClass\";\n }","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":135,"value":"obs = getGeoObs(\"*\",location.value.lat,location.value.lon,location.value.radius,2000)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":145,"value":"classObs = await obs.map(o => {o.vernacularClass = groupVernacular(o); return o })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":149,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1344,"value":"### Helper functions","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":18,"value":"async function getFacets(query,count,facet,facetSort){\n let baseQuery = 'https://biocache-ws.ala.org.au/ws/occurrence/facets?q='+query+'&fq=taxonRank:\"species\"&fq=spatiallyValid:\"true\"&facets='+facet+'&flimit='+count+\"&fsort=\"+facetSort+\"&dir=desc\";\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":"$undefined"},{"id":137,"value":"getGeoObs = async function(_q,_lat,_lon,_radius,_count){\n var base = 'https://api.ala.org.au/occurrences/occurrences/search?'\n const queryparams ={q:_q,lat:_lat,lon:_lon,radius:_radius,im:true,pageSize:_count,sort:\"eventDate\",dir:\"desc\"}\n const paramString = Object.keys(queryparams).map(function(k){ return '&' + k + '=' + queryparams[k]}).join(\"\"); //\n\tvar url = encodeURI(base + paramString);\n \n const res = await fetch(url);\n const info = await res.json();\n return info.occurrences;\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":839,"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, im: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 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":"$undefined"},{"id":258,"value":"async function getRegionFacets(regionName,taxaQuery,count,label){\n let baseQuery = 'https://biocache-ws.ala.org.au/ws/occurrence/facets?q=cl1048:\"'\n +regionName+\n'\"&fq=taxonRank:\"species\"&fq=spatiallyValid:\"true\"&facets=common_name_and_lsid&flimit='\n +count+\n '&fq='\n +taxaQuery;\n //console.log(encodeURI(baseQuery));\n const facets = await fetch(encodeURI(baseQuery))\n const payload = await facets.json();\n if (payload.length == 0) return []; // no facets\n const labelled = await payload[0].fieldResult.map(f => {f.name=label; return f})\n const unpacked = await unpackFacets(labelled)\n return unpacked;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":579,"value":" getSpeciesProfile = async function(lsid){\n let baseQuery =`https://api.ala.org.au/species/species/${lsid}`\n const response = await fetch(encodeURI(baseQuery))\n const data = await response.json()\n return data;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":260,"value":"unpackFacets = function(facets){\n return facets.map(r => { \n var o={}; \n var v=r.label.split(\"|\"); \n [\"commonName\",\"scientificName\",\"lsid\"].forEach((k,i) => o[k] = v[i]);\n o.count = r.count;\n return o;\n})\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":171,"value":"facetObs = function(obs,field){\n const groups = d3.flatGroup(obs, d => d[field]).map(g => {return {field: g[0],count:g[1].length}})\n return groups\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":237,"value":"function set(input, value) {\n input.value = value;\n input.dispatchEvent(new Event(\"input\", {bubbles: true}));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":862,"value":"oz = FileAttachment(\"australia (1).json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":864,"value":"states = topojson.feature(oz, oz.objects.states)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1194,"value":"import {Legend, Swatches} from \"@d3/color-legend\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":484,"value":"html = htl.html","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W47","stdlib":"1"}} 44:"$43:body"