3e:null 3f:["$","title",null,{"children":"Seeking locally distinctive species | Mitchell Whitelaw | Observable"}] 45:T49c,rankedList = function(localData, nationalData){ return svg``}46:[{"id":"a47b1b1f5b8059084924eab9641cebb017e2c3659c38b725edbd6f4008362a1b206ccc06b505d98b07a5fc167cb9be8966c33c4be5941641d4b94c1ab5b2e17a","href":"https://static.observableusercontent.com/files/a47b1b1f5b8059084924eab9641cebb017e2c3659c38b725edbd6f4008362a1b206ccc06b505d98b07a5fc167cb9be8966c33c4be5941641d4b94c1ab5b2e17a","name":"murrumbateman-facets500.json","type":"application/json","lastModified":1665629730249.524,"size":245723},{"id":"9407545612833617fe143e30c3dabc8c79423292f6ec5dd6ef3f0a8d0850ca0f48076e99e754f374830a5064b5e057ae42bf7da182897cf1634c93cd42560a5f","href":"https://static.observableusercontent.com/files/9407545612833617fe143e30c3dabc8c79423292f6ec5dd6ef3f0a8d0850ca0f48076e99e754f374830a5064b5e057ae42bf7da182897cf1634c93cd42560a5f","name":"aus-facets500.json","type":"application/json","lastModified":1665629730252.212,"size":261685},{"id":"a7a8c0f1e4eda25e845571ea9657abc4f0322cdd0fed4c6ae63fb99c307cb2985e83e8173c7d987f29dbde63d29f887b64ac8e9defc0723db3c9349735ac47a6","href":"https://static.observableusercontent.com/files/a7a8c0f1e4eda25e845571ea9657abc4f0322cdd0fed4c6ae63fb99c307cb2985e83e8173c7d987f29dbde63d29f887b64ac8e9defc0723db3c9349735ac47a6","name":"aus-facets-10k-species.json","type":"application/json","lastModified":1665973457245.462,"size":4580386}] 43:{"id":"6ff715e7f0057635","slug":null,"title":"Seeking locally distinctive species","thumbnail":"6d370be8668de94c7d6a62a8c6fdec356283b7eaa357ec5565c2870b65248371","access_level":"public","create_time":"$D2022-10-13T02:54:25.607Z","update_time":"$D2025-07-15T07:14:32.083Z","view_time":null,"first_public_time":"$D2022-10-16T23:53:38.127Z","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":332,"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"}],"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":"Seeking locally distinctive species","cells":[{"id":0,"value":"# Seeking locally distinctive species\n## Comparing regional and national occurrence frequencies ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":6,"value":"We can easily get data for the 500 most frequently occurring species in a single IBRA 7 Subregion (for this test, Murrumbateman). We can also run the same query for the whole ALA. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":228,"value":"localFacetCall = 'https://biocache-ws.ala.org.au/ws/occurrence/facets?q=cl1048:\"Tasmanian Northern Midlands\"&fq=taxonRank:\"species\"&fq=spatiallyValid:\"true\"&facets=common_name_and_lsid&flimit=1000'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":240,"value":"nationalFacetCall = 'https://biocache-ws.ala.org.au/ws/occurrence/facets?q=*&fq=taxonRank:\"species\"&facets=common_name_and_lsid&flimit=1000'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":230,"value":"murrumbatemanFacets = (await fetch(localFacetCall)).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":35,"value":"nationalFacets = (await fetch(nationalFacetCall)).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":18,"value":"labelKeys = [\"commonName\",\"scientificName\",\"lsid\"]\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"unpackFacets = function(facets){\n return facets.map(r => { \n var o={}; \n var v=r.label.split(\"|\"); \n labelKeys.forEach((k,i) => o[k] = v[i]);\n o.count = r.count;\n return o;\n})\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"murrumbatemanData = unpackFacets(murrumbatemanFacets[0].fieldResult)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":33,"value":"nationalData = unpackFacets(nationalFacets[0].fieldResult)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":67,"value":"matchedData = murrumbatemanData.map((s,i) => {\n var matchIndex = nationalData.findIndex(n => n.lsid == s.lsid);\n s.nationalMatch = matchIndex;\n s.deltaMatch = matchIndex - i; // delta between the two indices\n return s;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":118,"value":"overlapCount = matchedData.filter(m => m.nationalMatch > -1).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":116,"value":"We have two lists showing the 500 most frequently occurring species for both the local region (Murrumbateman) and the whole country. 43 of the top 500 local species occur in the national top 500; so there are 257 (500-243) species that don't co-occur.\n\nThis visualisation shows both lists ranked by frequency. Connecting lines are drawn between matching species, and coloured according to the difference between the two rankings. Higher ranked locally = blue; higher ranked nationally = red.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":45,"value":"$45","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":137,"value":"rankedList(matchedData,nationalData)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":89,"value":"sortedMatched = [...matchedData].sort((a,b) => b.deltaMatch - a.deltaMatch) // NB copy the array to avoid sorting the original!","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":132,"value":"To focus on the species with the biggest difference in rankings, we can sort the local list by the *difference* between the local and national rankings. This gives us some likely-seeming candidates for \"most distinctive\" local species.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":92,"value":"rankedList(sortedMatched,nationalData)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":145,"value":"But what about the local species that do not appear in the national top 500? These might be *even more distinctive*, because they are presumably less frequent nationally. It includes some notable locals like the Golden Sun Moth, and note the substantial occurrence numbers (so these aren't ultra-rare species with only a handful of occurrences).\n\nSo this is a problem with this naive method. It would be better to have a much bigger national list - maybe to set a threshhold for occurrences, eg 1000, and list every species above that count. That way we'd get a much more comprehensive account of which local species occur more frequently than in the national data.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":147,"value":"unmatchedLocals = murrumbatemanData.filter(s => s.nationalMatch == -1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":150,"value":"html`

${l.commonName ? l.commonName : l.scientificName} - ${l.count}

${l.commonName ? l.commonName : l.scientificName} - ${l.count}

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":201,"value":"If we use a national list of 10,000 species, we get quite different results","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":186,"value":"aus10k = FileAttachment(\"aus-facets-10k-species.json\").json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":193,"value":"ausBigger = unpackFacets(aus10k[0].fieldResult)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":188,"value":"matchedDataBig = murrumbatemanData.map((s,i) => {\n var matchIndex = ausBigger.findIndex(n => n.lsid == s.lsid);\n s.nationalMatch = matchIndex;\n s.deltaMatch = matchIndex - i; // delta between the two indices\n if (matchIndex == -1) s.deltaMatch = ausBigger.length - i; // it's going to be at least rank 10000...\n return s;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":206,"value":"Only ${unmatched10k.length} of the top 500 Murrumbateman species are now unmatched from the national top 10,000","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":199,"value":"unmatched10k = matchedDataBig.filter(m => m.nationalMatch == -1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":197,"value":"matchedBiggerSorted = [...matchedDataBig].sort((a,b) => b.deltaMatch - a.deltaMatch)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":212,"value":"Now the top 10 are much less common species. Note that for the unmatched species, we give them an estimated differential rank - they will be ranked *at least* 10000 in the national list, so the difference will be at least 10000 minus their local rank.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":210,"value":"html`

Top 10 most distinctive Murrumbateman species ranked against national top 10000

${l.commonName ? l.commonName : l.scientificName} - ${l.count}

Top 10 most distinctive Murrumbateman species (> ${mbThresh} occurrences) ranked against national top 10000

${l.commonName ? l.commonName : l.scientificName} - ${l.count}

`\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":226,"value":"[...matchedBiggerSorted].filter(m => m.count > 1000)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":256,"value":"Let's compare with another IBRA 7 subregion! How about Scenic Rim, in the Byron Bay hinterland, including Nimbin, Lismore and the Border Ranges National Park","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":258,"value":"scenicrimFacetCall = 'https://biocache-ws.ala.org.au/ws/occurrence/facets?q=cl1049:\"Scenic Rim\"&fq=taxonRank:\"species\"&facets=common_name_and_lsid&flimit=500'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":261,"value":"scenicRimFacets = (await fetch(scenicrimFacetCall)).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":266,"value":"srFacets = unpackFacets(scenicRimFacets[0].fieldResult)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":272,"value":"srMatched = srFacets.map((s,i) => {\n var matchIndex = ausBigger.findIndex(n => n.lsid == s.lsid);\n s.nationalMatch = matchIndex;\n s.deltaMatch = matchIndex - i; // delta between the two indices\n if (matchIndex == -1) s.deltaMatch = ausBigger.length - i; // it's going to be at least rank 10000...\n return s;\n})\n.sort((a,b) => b.deltaMatch - a.deltaMatch)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":291,"value":"NB In this case there are still 23 unmatched local species, even in the national top 10,000!","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":287,"value":"srUnMatched = srMatched.filter(s => s.nationalMatch == -1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":320,"value":"viewof srThresh = Inputs.range([10,1000],{step:10})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":280,"value":"html`

Top 10 most distinctive Scenic Rim species > ${srThresh} occurrences, ranked against national top 10000

${l.commonName ? l.commonName : l.scientificName} - ${l.count}