3e:null 3f:["$","title",null,{"children":"Gang-gangs and other cockatoos by IBRA subregion | Riia Järvenpää | Observable"}] 45:T595,function getCoOccurs(species, regions, target_species, threshhold){ // https://biodiversity.org.au/afd/taxa/6c646af8-06fb-40ae-83aa-3dd001cc4ea6 -- gang-gang // https://biodiversity.org.au/afd/taxa/34b31e86-7ade-4cba-960f-82a6ae586206 -- little corella threshhold = threshhold || 0; // zero if not set let co = species.map(s => { let totals = {target:0, pair:0, both:0, neither:0}; let reco = []; for (let rg=0; rg threshhold && tr.count > threshhold) totals.both ++; if (r.count > threshhold && tr.count <= threshhold) totals.pair ++; if (r.count < threshhold && tr.count <= threshhold) totals.neither ++; if (r.count <= threshhold && tr.count > threshhold) totals.target ++; if (r.count > threshhold && tr.count > threshhold) reco[rg] = 1; if (r.count <= threshhold && tr.count <= threshhold) reco[rg] = 1; if (r.count <= threshhold && tr.count > threshhold) reco[rg] = -1; if (r.count > threshhold && tr.count <= threshhold) reco[rg] = -1; if (r.count <= threshhold && tr.count <= threshhold) reco[rg] = 0; } return {species: s, cooc: reco, sum: reco.reduce((a, b) => a + b, 0) / reco.length, totals: totals}; }) return co.sort((a,b) => b.sum - a.sum); }46:[{"id":"3936d9d09f0b44a0608f60b500fac9f31fbb59e83a6a7100e01da3d1f59d05f9f50a7bc7256247bf843feab155d60ac743c96840a74fc47a3be403ef05e2eebe","href":"https://static.observableusercontent.com/files/3936d9d09f0b44a0608f60b500fac9f31fbb59e83a6a7100e01da3d1f59d05f9f50a7bc7256247bf843feab155d60ac743c96840a74fc47a3be403ef05e2eebe","name":"cockatoos-regions.json","type":"application/json","lastModified":1682830863779.935,"size":1043602},{"id":"23f9e4a71da85fbeeba8957f8d509aeb44bdc7bb8eb91c609aa1c836a836de8b4abd4732acaae0c063458ff07fcedad3ccf07386c9e1b82226567577de11b59d","href":"https://static.observableusercontent.com/files/23f9e4a71da85fbeeba8957f8d509aeb44bdc7bb8eb91c609aa1c836a836de8b4abd4732acaae0c063458ff07fcedad3ccf07386c9e1b82226567577de11b59d","name":"mammals-regions-100.json","type":"application/json","lastModified":1682830863779.935,"size":6896269}] 43:{"id":"2aea813ca0c852ad","slug":null,"title":"Gang-gangs and other cockatoos by IBRA subregion","thumbnail":"8691f182d923f33a2ff817e6fea5ebb7c0e40ad011b985ebed677440f086edef","access_level":"public","create_time":"$D2023-04-30T05:01:03.779Z","update_time":"$D2023-04-30T05:01:03.779Z","view_time":null,"first_public_time":"$D2023-04-30T05:01:03.779Z","has_unpublished_edits":null,"fork":{"id":"7ea27281ef54d688","slug":null,"title":"Gang-gangs and other cockatoos by IBRA subregion","owner":{"id":"aff35a2a633c89c4","login":"mtchl","name":"Mitchell Whitelaw"}},"stars":0,"starred":false,"owner":{"type":"team","id":"1a7853441e3c211d","login":"rialistic","name":"Riia Järvenpää","avatar_url":"https://avatars-next.observableusercontent.com/b4c8ff27583b2087427edc32f10cb51d0ca63b15edff86fe2bb5e15692bcf867","tier":"starter_2024","bio":"Trying to be a social data researcher. Kallio, Helsinki, Finland. I like to data, but been mostly doing raw communications so far.","following":false},"version":519,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"02643ec94659c257","login":"rialistic","name":"Riia Järvenpää","avatar_url":"https://avatars-next.observableusercontent.com/b4c8ff27583b2087427edc32f10cb51d0ca63b15edff86fe2bb5e15692bcf867","tier":null,"bio":"Trying to be a social data researcher. Kallio, Helsinki, Finland. I like to data, but been mostly doing raw communications so far.","following":false}],"members":[{"type":"individual","id":"02643ec94659c257","login":"rialistic","name":"Riia Järvenpää","avatar_url":"https://avatars-next.observableusercontent.com/b4c8ff27583b2087427edc32f10cb51d0ca63b15edff86fe2bb5e15692bcf867","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Gang-gangs and other cockatoos by IBRA subregion","cells":[{"id":0,"value":"# Gang-gangs and other cockatoos by IBRA subregion\nTrying out ways to link species through their co-occurrence in IBRA regions.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":274,"value":"This source data was generated by harvesting facets for all IBRA 7 subregions (field cl1049), using a query for cockatoos (family:Cacatuidae)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":5,"value":"cockatooRegions = await(FileAttachment(\"cockatoos-regions.json\").json())","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":278,"value":"We derive a list of all the unique species listed in these facets, and reduce to the most frequently occurring 20 species","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":7,"value":"getAllSpecies = function(speciesFacets){\n let sp = [];\n let lsids = [];\n speciesFacets.forEach(r => r.species.forEach(s => {\n if (lsids.indexOf(s.lsid) == -1) {\n lsids.push(s.lsid);\n sp.push(s)\n } else {\n let exs = sp.find(p => p.lsid == s.lsid);\n exs.count += s.count;\n }\n }))\n return sp.sort((a,b) => b.count - a.count).slice(0,20);\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"allSpecies = getAllSpecies(cockatooRegions)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":434,"value":"gg = cockatooSpeciesByRegion[4]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"regionsBySpecies = function(speciesData,regionData){\n // let reg = cockatooRegions.sort((a,b) => b.species.length - a.species.length);\n //let gg = allSpecies.find(s => s.lsid == \"https://biodiversity.org.au/afd/taxa/6c646af8-06fb-40ae-83aa-3dd001cc4ea6\"); //gang-gang\n // let gg_reg = gg.regions.sort((a,b) => b.count - a.count) // sort matrix by gang gang count\n let gg_reg = regionData.sort((a,b) => b.species.length - a.species.length);\n let speciesRegionCounts = speciesData.map(s => {\n let ns = {};\n Object.keys(s).forEach(k => ns[k] = s[k])\n return ns\n });\n speciesRegionCounts.forEach(s => {\n s.regions = gg_reg.map(r => {\n let rcount = 0;\n let reg = regionData.find(cr => cr.region == r.region)\n let match = reg.species.find(sp => sp.lsid == s.lsid);\n if (match) rcount = match.count;\n return {region: r.region, count: rcount};\n })\n })\n return speciesRegionCounts;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":36,"value":"cockatooSpeciesByRegion = regionsBySpecies(allSpecies,cockatooRegions)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":282,"value":"Here's a matrix visualisation of the occurrence of the top 20 cockatoos by IBRA 7 subregions. Regions are sorted by the number of cockatoo species, and species are sorted by overall prevalence across regions.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":43,"value":"svg``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":63,"value":"gridScale = 12\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":48,"value":"scale = d3.scaleSequentialLog(d3.interpolateYlOrRd).domain([1,1000000])\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":105,"value":"$45","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":287,"value":"What would be a sensible way of finding which other cockatoo species most co-occur with Gang-gangs? Here I simply count the regions where each species co-occurs with Gang-gangs, and divide by the total number of regions where either species occur. This gives the **overlap_pc** column in the table below. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":341,"value":"Note that we set a threshhold to eliminate outliers / regions with very low counts. Try different values for this threshhold to see the results change.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":339,"value":"ggThresh = 5; // minimum number of occurrences per region to count as a co-occurrence","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":109,"value":"ggCo = getCoOccurs(cockatooSpeciesByRegion,cockatooRegions,gg,ggThresh) // gang-gang","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":131,"value":"ggCoTable = ggCo.map((c) => {return { species: c.species.commonName ? c.species.commonName :c.species.scientificName, target_only: c.totals.target, pair_only: c.totals.pair, total_regions: c.totals.pair + c.totals.both, overlap: c.totals.both, overlap_pc: c.totals.both / (c.totals.target + c.totals.both + c.totals.pair)}}).sort((a,b) => b.overlap_pc - a.overlap_pc)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":135,"value":"Inputs.table(ggCoTable)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":293,"value":"We can visualise this pretty easily as a kind of Venn diagram bar chart. This is the top 10 cockatoos that co-occur with Gang-gangs. Btw *Zanda* is a Genus, not a species (it includes the YTBC), so I'm not sure it should be here. Notice that despite common species like the Galah co-occurring with the Gang-gang in all the regions where it appears, it's ranked lower due to the proportional overlap.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":398,"value":"coOccurBarchart(ggCoTable,cockatooRegions,120)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":296,"value":"Of course we can use the same data to look at co-occurrences between other cockies too. This is the top 10 cockatoos that co-occur with **Red-tailed Black Cockatoos**.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":439,"value":"rtbc = cockatooSpeciesByRegion[7]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":121,"value":"rtbcCoOccurs = getCoOccurs(cockatooSpeciesByRegion,cockatooRegions,rtbc,5) // RTBC","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":254,"value":"rtbcCoTable = rtbcCoOccurs.map((c) => {return { species: c.species.commonName ? c.species.commonName :c.species.scientificName, target_only: c.totals.target, pair_only: c.totals.pair, total_regions: c.totals.pair + c.totals.both, overlap: c.totals.both, overlap_pc: c.totals.both / (c.totals.target + c.totals.both + c.totals.pair)}}).sort((a,b) => b.overlap_pc - a.overlap_pc)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":252,"value":"coOccurBarchart(rtbcCoTable,cockatooRegions,160)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":349,"value":"Let's try with a different family - here's mammals","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":353,"value":"mammalRegions = FileAttachment(\"mammals-regions-100.json\").json(); // using top 100 mammals instead","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":357,"value":"mammalSpecies = getAllSpecies(mammalRegions)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":419,"value":"mammalsByRegion = regionsBySpecies(mammalSpecies,mammalRegions)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":485,"value":"combinedByRegion = [gg, ...mammalsByRegion]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":488,"value":"ggMammalCoOccur = getCoOccurs(combinedByRegion,mammalRegions,gg,5)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":497,"value":"mammalCoTable = ggMammalCoOccur.map((c) => {return { species: c.species.commonName ? c.species.commonName :c.species.scientificName, target_only: c.totals.target, pair_only: c.totals.pair, total_regions: c.totals.pair + c.totals.both, overlap: c.totals.both, overlap_pc: c.totals.both / (c.totals.target + c.totals.both + c.totals.pair)}}).sort((a,b) => b.overlap_pc - a.overlap_pc)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":508,"value":"Inputs.table(mammalCoTable)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":503,"value":"coOccurBarchart(mammalCoTable,mammalRegions,160)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":395,"value":"coOccurBarchart = function(coTable,regions,leftMargin){\n return svg``}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"html = htl.html","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":45,"value":"svg = htl.svg","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W46","stdlib":"1"}} 44:"$43:body"