31:T224b,plot = { // make the svg const svg = d3.create("svg").attr("width", width).attr("height", height); // add the title const title = svg.append("g"); title.append("g").call(addTitle, "DToL Plant Sampling Group Summary", 0.035); // add the introductory sentences const para1 = svg.append("g"); para1 .append("g") .call( addText, `This document charts the progress made so far in collecting plant samples for the Darwin Tree of Life project. Overall, ${ noSpecimensCollected.Bryophytes + noSpecimensCollected.Vascular } specimens have been collected up until ${DATE}. A full and updated list of the DToL plant species, priorities, and collections can be found here for bryophytes, and here for vascular plants.`, 0.04, 0.5 ); // add figure 1, the horizontal bar chart const bars1 = svg .append("g") .selectAll("rect") .data(familyBarPlotData.filter((d) => d.type !== "All ")) .join("rect") .style("mix-blend-mode", "multiply") .attr("fill", (d) => (d.type === "Bryophyte " ? "#e5f5e0" : "#a1d99b")) .attr("x", (d) => x0(0)) .attr("y", (d) => y0(d.type)) .attr("width", (d) => x0(d.value) - x0(0)) .attr("height", y0.bandwidth()) .append("title") .text( (d) => `${d.type}: ${d.value} families Target: ${ d.type === "Vascular " ? familyBarPlotData.vascularLine : familyBarPlotData.bryophyteLine }` ); // add target lines const vascularTargetLine = svg .append("g") .append("line") .attr("x1", x0(totalBItargetFamNeo.Vascular)) .attr("x2", x0(totalBItargetFamNeo.Vascular)) .attr("y1", y0("Vascular ") + y0.bandwidth()) .attr("y2", y0("Vascular ")) .attr("stroke", "red") .attr("stroke-dasharray", 3); // add target lines const bryophyteTargetLine = svg .append("g") .append("line") .attr("x1", x0(totalBItargetFamNeo.Bryophytes)) .attr("x2", x0(totalBItargetFamNeo.Bryophytes)) .attr("y1", y0("Bryophyte ") + y0.bandwidth()) .attr("y2", y0("Bryophyte ")) .attr("stroke", "red") .attr("stroke-dasharray", 3); // add the axes for figure 1 const bars1x = svg.append("g").call(xAxis0); const bars1y = svg.append("g").call(yAxis0); // add the description for figure 1 const para2 = svg.append("g"); para2 .append("g") .call( addText, `Fig. 1 - the bar shows the current number of plant families collected, split by vascular plants and bryophytes. The target is ${totalBItargetFamNeo.Vascular} for vascular plants, and ${totalBItargetFamNeo.Bryophytes} for bryophytes (red dashes).`, 0.17, 1.5 ); // add the three bar charts which split by family, genus, species (for vascular, bryophyte & total) const bars2 = svg .append("g") .selectAll("rect") .data(familyBarPlotData) .join("rect") .style("mix-blend-mode", "multiply") .attr("fill", "#a1d99b") .attr("x", (d) => x1(d.type)) .attr("y", (d) => y1(d.value)) .attr("height", (d) => y1(0) - y1(d.value)) .attr("width", x1.bandwidth()) .append("title") .text((d) => `${d.type.trim()}: ${d.value} families`); // add the axes for figure 2 const bars2x = svg.append("g").call(xAxis1); const bars2y = svg.append("g").call(yAxis1); const bars3 = svg .append("g") .selectAll("rect") .data(genusBarPlotData) .join("rect") .style("mix-blend-mode", "multiply") .attr("fill", "#a1d99b") .attr("x", (d) => x2(d.type)) .attr("y", (d) => y2(d.value)) .attr("height", (d) => y2(0) - y2(d.value)) .attr("width", x2.bandwidth()) .append("title") .text((d) => `${d.type.trim()}: ${d.value} genera`); // add the axes for figure 2 const bars3x = svg.append("g").call(xAxis2); const bars3y = svg.append("g").call(yAxis2); const bars4 = svg .append("g") .selectAll("rect") .data(speciesBarPlotData) .join("rect") .style("mix-blend-mode", "multiply") .attr("fill", "#a1d99b") .attr("x", (d) => x3(d.type)) .attr("y", (d) => y3(d.value)) .attr("height", (d) => y3(0) - y3(d.value)) .attr("width", x3.bandwidth()) .append("title") .text((d) => `${d.type.trim()}: ${d.value} species`); // add the axes for figure 2 // future Max, please sort out the axes positioning behind the scenes const bars4x = svg.append("g").call(xAxis3); const bars4y = svg.append("g").call(yAxis3); // add the description for figure 2 const para3 = svg.append("g"); para3 .append("g") .call( addText, `Fig. 2 - bar charts split by family, genus, and species which show the number of taxa collected at each taxonomic level.`, 0.42, 1.5 ); // the c-value distribution would be here, but no data yet... const cvals_hist = svg .append("g") .selectAll("rect") .data(bins) .join("rect") .attr("fill", "#a1d99b") .attr("x", (d) => gsx(d.x0) + 1) .attr("width", (d) => Math.max(0, gsx(d.x1) - gsx(d.x0) - 1)) .attr("y", (d) => gsy(d.length)) .attr("height", (d) => gsy(0) - gsy(d.length)) .append("title") .text( (d) => `${d.x0} - ${d.x1} Gb ${d.length} species` ); const cvals_histx = svg.append("g").call(gsAxis); const cvals_histy = svg.append("g").call(gsyAxis); const para4 = svg.append("g"); para4 .append("g") .call( addText, `Fig. 3 - the distribution of genome size variation in collected plants. Genomes greater than 25Gb excluded (${ excludedBins.length }). There is currently a ${Math.round( GBRange.max / GBRange.min )}-fold variation in genome sizes collected.`, 0.64, 1.5 ); // go on to the map const path = d3.geoPath(projection); // move the map const transX = 0, transY = height * 0.31; const ukCounties = svg .append("g") .selectAll("path") .data(ukLand.features) .join("path") .attr("class", "provinceShape") .attr("stroke", "white") .attr("fill", "#e0e0e0") .attr("transform", (d) => `translate(${transX},${transY})`) .attr("d", path); const irelandCounties = svg .append("g") .selectAll("path") .data(irelandLand.features) .join("path") .attr("class", "provinceShape") .attr("stroke", "white") .attr("fill", "#e0e0e0") .attr("transform", (d) => `translate(${transX},${transY})`) .attr("d", path); // add the lat long for individual points countyData.forEach(function (d) { var coords = projection([d.county_lon, d.county_lat]); d.position = [coords[0], coords[1]]; }); const spikes = svg .append("g") .attr("fill", "green") .attr("fill-opacity", 0.3) .attr("stroke", "green") .attr("class", "spikes") .selectAll("path") .data(countyData) .join("path") .attr("transform", (d) => `translate(${d.position})`) .attr("d", (d) => plant_spike(length(d.n))); spikes.append("title").text((d) => `${d.county}`); svg .selectAll(".spikes") .attr("transform", (d) => `translate(${transX},${transY})`); const legend = svg .append("g") .attr("fill", "#777") .attr("text-anchor", "middle") .attr("font-family", "sans-serif") .attr("font-size", 10) .attr("class", "legend") .selectAll("g") .data(length.ticks(6).slice(1).reverse()) .join("g") .attr("transform", (d, i) => `translate(${1 - (i + 1) * 18},0)`); legend .append("path") .attr("fill", "green") .attr("fill-opacity", 0.3) .attr("stroke", "green") .attr("d", (d) => plant_spike(length(d))); legend.append("text").attr("dy", "1.3em").text(length.tickFormat(4, "s")); // move the legend around svg .selectAll(".legend") .attr( "transform", (d) => `translate(${width - margin.right},${height * 0.9})` ); // add the description for figure 3(4) const para5 = svg.append("g"); para5 .append("g") .call( addText, `Fig. 4 - spike map of Great Britain and Ireland, showing areas where samples have been collected so far. Data drawn from COPO.`, 0.92, 1.5 ); const footer = svg.append("g"); footer .append("g") .call( footNote, `Summary charts by Max Brown, Lucia Campos-Dominguez, and Alex Twyford. Plant collections were made by Maarten Christenhusz at the Royal Botanic Garden Kew, David Bell and Markus Ruhsam at the Royal Botanic Garden Edinburgh, and by Darwin Tree of Life collaborators around Britain and Ireland. Genome size estimates were generated by Sahr Mian and Ilia Leitch at the Royal Botanical Gardens, Kew.`, 0.955, 1.5 ); return svg.node(); }32:[] 2f:{"title":"DToL Plant Sampling Summary","cells":[{"id":2568,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":1102,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":328,"value":"md`### Global parameters & functions`","pinned":false,"hidden":false,"mode":"ojs"},{"id":694,"value":"addTitle = (g, title, scale, type = 'title') =>\n g\n .attr(\n 'transform',\n `translate(${margin.left * 0.5}, ${height * scale +\n (type == 'subtitle' ? 25 : 0)})`\n )\n .attr(\"font-family\", \"sans-serif\")\n .attr(\"font-weight\", 700)\n .attr(\"font-size\", \"28px\")\n .append('text')\n .attr('class', type)\n .text(title)","pinned":false,"hidden":false,"mode":"ojs"},{"id":746,"value":"addText = (g, text, hscale, wscale) =>\n g\n .append(\"foreignObject\")\n .attr(\"width\", width - 100)\n .attr(\"height\", height / 6)\n .attr('transform', `translate(${margin.left * wscale}, ${height * hscale})`)\n .attr(\"font-family\", \"sans-serif\")\n .attr(\"font-weight\", 200)\n .attr(\"font-size\", \"14px\")\n .append('xhtml:div')\n .style(\"color\", \"black\")\n .attr('class', 'paragraph')\n .html(`

${text}

`)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1730,"value":"footNote = (g, text, hscale, wscale) =>\n g\n .append(\"foreignObject\")\n .attr(\"width\", width - 100)\n .attr(\"height\", height / 6)\n .attr('transform', `translate(${margin.left * wscale}, ${height * hscale})`)\n .attr(\"font-family\", \"sans-serif\")\n .attr(\"font-weight\", 100)\n .attr(\"font-size\", \"12px\")\n .append('xhtml:div')\n .style(\"color\", \"grey\")\n .attr('class', 'paragraph')\n .html(`

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`)","pinned":false,"hidden":false,"mode":"ojs"},{"id":559,"value":"width = 700","pinned":false,"hidden":false,"mode":"ojs"},{"id":81,"value":"height = 2000","pinned":false,"hidden":false,"mode":"ojs"},{"id":588,"value":"margin = ({ left: 30, right: 30, top: 20, bottom: 50 })","pinned":false,"hidden":false,"mode":"ojs"},{"id":318,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":627,"value":"md`#### Barplots`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2008,"value":"x0consts = ({\n low: 0.115,\n high: 0.17\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2016,"value":"x1consts = ({\n low: 0.21,\n high: 0.40\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2058,"value":"gsconsts = ({\n low: 0.48,\n high: 0.62\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1026,"value":"// family targets\n// Vascular: 132\n// Bryophytes: 128\n\nfamilyBarPlotData = Object.assign(\n [\n {\n type: \"Vascular \",\n value: noFamiliesCollected.Vascular,\n group: \"family\",\n yMax: noFamiliesCollected.Vascular + 10\n },\n {\n type: \"Bryophyte \",\n value: noFamiliesCollected.Bryophytes,\n group: \"family\",\n yMax: noFamiliesCollected.Bryophytes + 10\n },\n {\n type: \"All \",\n value: noFamiliesCollected.Vascular + noFamiliesCollected.Bryophytes,\n group: \"family\",\n yMax: noFamiliesCollected.Vascular + noFamiliesCollected.Bryophytes + 10\n }\n ],\n { vascularLine: 132 },\n { bryophyteLine: 128 },\n { xLab: \"Family\" }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1121,"value":"genusBarPlotData = Object.assign(\n [\n {\n type: \"Vascular\",\n value: noGeneraCollected.Vascular,\n group: \"genus\",\n yMax: noGeneraCollected.Vascular + 20\n },\n {\n type: \"Bryophyte\",\n value: noGeneraCollected.Bryophytes,\n group: \"genus\",\n yMax: noGeneraCollected.Bryophytes + 20\n },\n {\n type: \"All\",\n value: noGeneraCollected.Vascular + noGeneraCollected.Bryophytes,\n group: \"genus\",\n yMax: noGeneraCollected.Vascular + noGeneraCollected.Bryophytes + 20\n }\n ],\n { xLab: \"Genus\" }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1030,"value":"speciesBarPlotData = Object.assign(\n [\n {\n type: \"Vascular\",\n value: noSpeciesCollected.Vascular,\n group: \"species\",\n yMax: noSpeciesCollected.Vascular + 20\n },\n {\n type: \"Bryophyte\",\n value: noSpeciesCollected.Bryophytes,\n group: \"species\",\n yMax: noSpeciesCollected.Bryophytes + 20\n },\n {\n type: \"All\",\n value: noSpeciesCollected.Vascular + noSpeciesCollected.Bryophytes,\n group: \"species\",\n yMax: noSpeciesCollected.Vascular + noSpeciesCollected.Bryophytes + 20\n }\n ],\n { xLab: \"Species\" }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1143,"value":"x0 = d3\n .scaleLinear()\n .domain([0, totalBItargetFamNeo.Vascular + 10])\n .range([margin.left + 25, width - margin.right])","pinned":false,"hidden":false,"mode":"ojs"},{"id":640,"value":"x1 = d3\n .scaleBand()\n .domain(familyBarPlotData.map(d => d.type))\n .range([margin.left, (width - margin.left - margin.right) / 3]) // might need to change this\n .padding(0.1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1314,"value":"x2 = d3\n .scaleBand()\n .domain(genusBarPlotData.map(d => d.type))\n .range([\n (width - margin.left - margin.right) / 3 + 50,\n ((width - margin.left - margin.right) / 3) * 2 + 20\n ]) // might need to change this\n .padding(0.1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1021,"value":"x3 = d3\n .scaleBand()\n .domain(speciesBarPlotData.map(d => d.type))\n .range([453.3333333333333 + 50, 453.3333333333333 + 187 + 50]) // might need to change this\n .padding(0.1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1907,"value":"gsx = d3\n .scaleLinear()\n .domain([bins[0].x0, bins[bins.length - 1].x1])\n .range([margin.left, width - margin.right])","pinned":false,"hidden":false,"mode":"ojs"},{"id":1172,"value":"xAxis0 = g =>\n g\n .attr(\"transform\", `translate(0,${height * x0consts.low})`)\n .call(d3.axisTop(x0))\n// .call(g => g.select(\".tick:last-of-type text\").attr(\"fill\", \"red\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":649,"value":"xAxis1 = g =>\n g\n .attr(\"transform\", `translate(0,${height * x1consts.high})`)\n .call(d3.axisBottom(x1).tickSizeOuter(0))\n .call(g =>\n g\n .select(\".tick text\")\n .clone()\n .attr(\"x\", x1.bandwidth())\n .attr(\"y\", 25)\n .attr(\"text-anchor\", \"middle\")\n .attr(\"font-weight\", \"bold\")\n .text(familyBarPlotData.xLab)\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":1321,"value":"xAxis2 = g =>\n g\n .attr(\"transform\", `translate(0,${height * x1consts.high})`)\n .call(d3.axisBottom(x2).tickSizeOuter(0))\n .call(g =>\n g\n .select(\".tick text\")\n .clone()\n .attr(\"x\", x2.bandwidth())\n .attr(\"y\", 25)\n .attr(\"text-anchor\", \"middle\")\n .attr(\"font-weight\", \"bold\")\n .text(genusBarPlotData.xLab)\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":1024,"value":"xAxis3 = g =>\n g\n .attr(\"transform\", `translate(0,${height * x1consts.high})`)\n .call(d3.axisBottom(x3).tickSizeOuter(0))\n .call(g =>\n g\n .select(\".tick text\")\n .clone()\n .attr(\"x\", x3.bandwidth())\n .attr(\"y\", 25)\n .attr(\"text-anchor\", \"middle\")\n .attr(\"font-weight\", \"bold\")\n .text(speciesBarPlotData.xLab)\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":2065,"value":"gsAxis = g =>\n g\n .attr(\"transform\", `translate(0,${height * gsconsts.high})`)\n .call(d3.axisBottom(gsx).tickSizeOuter(0))\n .call(g =>\n g.call(g =>\n g\n .append(\"text\")\n .attr(\"x\", width / 2 + margin.left)\n .attr(\"y\", 30)\n .attr(\"fill\", \"currentColor\")\n .attr(\"font-weight\", \"bold\")\n .attr(\"text-anchor\", \"end\")\n .text(bins.x)\n )\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":1157,"value":"y0 = d3\n .scaleBand()\n .domain(familyBarPlotData.filter(d => d.type !== \"All \").map(d => d.type))\n .range([height * x0consts.high, height * x0consts.low])\n .padding(0.1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":653,"value":"y1 = d3\n .scaleLinear()\n .domain([0, familyBarPlotData[2].yMax])\n .range([height * x1consts.high, height * x1consts.low])","pinned":false,"hidden":false,"mode":"ojs"},{"id":1324,"value":"y2 = d3\n .scaleLinear()\n .domain([0, genusBarPlotData[2].yMax])\n .range([height * x1consts.high, height * x1consts.low])","pinned":false,"hidden":false,"mode":"ojs"},{"id":1041,"value":"y3 = d3\n .scaleLinear()\n .domain([0, speciesBarPlotData[2].yMax])\n .range([height * x1consts.high, height * x1consts.low])","pinned":false,"hidden":false,"mode":"ojs"},{"id":1937,"value":"gsy = d3\n .scaleLinear()\n .domain([0, d3.max(bins, (d) => d.length) + 5])\n .nice()\n .range([height * gsconsts.high, height * gsconsts.low])","pinned":false,"hidden":false,"mode":"ojs"},{"id":1163,"value":"yAxis0 = g =>\n g\n .attr(\"class\", \"yAxis\")\n .attr(\"transform\", `translate(${margin.left + 25},0)`)\n .call(d3.axisLeft(y0))\n//.call(g => g.select(\".tick\").remove())","pinned":false,"hidden":false,"mode":"ojs"},{"id":655,"value":"yAxis1 = g =>\n g\n .attr(\"class\", \"yAxis\")\n .attr(\"transform\", `translate(${margin.left},0)`)\n .call(d3.axisLeft(y1))\n //.call(g => g.select(\".domain\").remove())\n .call(g =>\n g\n .select(\".tick:last-of-type text\")\n .clone()\n .attr(\"x\", 3)\n .attr(\"text-anchor\", \"start\")\n .attr(\"font-weight\", \"bold\")\n .attr(\"class\", \"show-phase1_1\")\n .html(\" \")\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":1045,"value":"yAxis2 = g =>\n g\n .attr(\"class\", \"yAxis\")\n .attr(\n \"transform\",\n `translate(${(width - margin.left - margin.right) / 3 + 50},0)`\n )\n .call(d3.axisLeft(y2))\n //.call(g => g.select(\".domain\").remove())\n .call(g =>\n g\n .select(\".tick:last-of-type text\")\n .clone()\n .attr(\"x\", 3)\n .attr(\"text-anchor\", \"start\")\n .attr(\"font-weight\", \"bold\")\n .attr(\"class\", \"show-phase1_2\")\n .html(\" \")\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":1349,"value":"yAxis3 = g =>\n g\n .attr(\"class\", \"yAxis\")\n .attr(\"transform\", `translate(${453.3333333333333 + 50},0)`)\n .call(d3.axisLeft(y3))\n //.call(g => g.select(\".domain\").remove())\n .call(g =>\n g\n .select(\".tick:last-of-type text\")\n .clone()\n .attr(\"x\", 3)\n .attr(\"text-anchor\", \"start\")\n .attr(\"font-weight\", \"bold\")\n .attr(\"class\", \"show-phase1_3\")\n .html(\" \")\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":2080,"value":"gsyAxis = (g) =>\n g\n .attr(\"transform\", `translate(${margin.left},0)`)\n .call(d3.axisLeft(gsy))\n .call((g) =>\n g\n .select(\".tick:last-of-type text\")\n .clone()\n .attr(\"x\", 4)\n .attr(\"text-anchor\", \"start\")\n .attr(\"font-weight\", \"bold\")\n .text(\"Counts\")\n )","pinned":false,"hidden":false,"mode":"ojs"},{"id":1896,"value":"md`#### Genome size data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1904,"value":"bins = Object.assign(\n d3.bin().thresholds(70)(\n gs_data.filter(d => d.GB > 0 && d.GB < 25).map(d => d.GB)\n ),\n { x: \"Genome size (Gbp)\" }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":2354,"value":"GENOME_SIZE_DATA = fetch(\n \"https://raw.githubusercontent.com/DToL-Plant-Working-Group/collections/main/data/DTOL_genome_sizes_final.csv\"\n).then((response) => {\n return response.text();\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1901,"value":"gs_data = d3.csvParse(GENOME_SIZE_DATA).map((d) => {\n return {\n species: d.taxon_name,\n GB: +d.GB\n };\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2117,"value":"GBRange = ({\n min: d3.min(gs_data.filter(d => d.GB > 0).map(d => d.GB)),\n max: d3.max(gs_data.filter(d => d.GB > 0).map(d => d.GB))\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1990,"value":"excludedBins = gs_data.filter(d => d.GB >= 25)","pinned":false,"hidden":false,"mode":"ojs"},{"id":630,"value":"md`#### Targets & specimens`","pinned":false,"hidden":false,"mode":"ojs"},{"id":350,"value":"totalBItargetSpNeo = ({\n type: \"totalBItargetSpNeo\",\n Vascular: 1648,\n Bryophytes: 1098\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":353,"value":"totalBItargetFamNeo = ({\n type: \"totalBItargetFamNeo\",\n Vascular: 132,\n Bryophytes: 128\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":357,"value":"phase1SpTarget = ({ type: \"phase1SpTarget\", Vascular: 275, Bryophytes: 450 })","pinned":false,"hidden":false,"mode":"ojs"},{"id":359,"value":"phase1FamTarget = ({ type: \"phase1FamTarget\", Vascular: 132, Bryophytes: 128 }) // same as totals","pinned":false,"hidden":false,"mode":"ojs"},{"id":2553,"value":"data_.filter((d) => d.group === \"bryophyte\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":499,"value":"noFamiliesCollected = ({\n type: \"noSpeciesCollected\",\n Vascular: new Set(\n data_\n .filter(\n (d) =>\n d.group === \"Flowering plants\" || // was Angiosperms\n d.group === \"Conifers\" || // Gymnosperms\n d.group === \"Ferns & ferns allies\" // was Pteridophytes\n )\n .map((d) => d.family)\n ).size,\n Bryophytes: new Set(\n data_.filter((d) => d.group === \"bryophyte\").map((d) => d.family)\n ).size\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2545,"value":"data_.filter((d) => d.group === \"bryophyte\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1123,"value":"noGeneraCollected = ({\n type: \"noSpeciesCollected\",\n Vascular: new Set(\n data_\n .filter(\n (d) =>\n d.group === \"Flowering plants\" || // was Angiosperms\n d.group === \"Conifers\" || // Gymnosperms\n d.group === \"Ferns & ferns allies\" // was Pteridophytes\n )\n .map((d) => d.genus)\n ).size,\n Bryophytes: new Set(\n data_.filter((d) => d.group === \"bryophyte\").map((d) => d.genus)\n ).size\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":488,"value":"noSpeciesCollected = ({\n type: \"noSpeciesCollected\",\n Vascular: new Set(\n data_\n .filter(\n (d) =>\n d.group === \"Flowering plants\" || // was Angiosperms\n d.group === \"Conifers\" || // Gymnosperms\n d.group === \"Ferns & ferns allies\" // was Pteridophytes\n )\n .map((d) => d.species)\n ).size,\n Bryophytes: new Set(\n data_.filter((d) => d.group === \"bryophyte\").map((d) => d.species)\n ).size\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":379,"value":"// no duplicates so this is redundant?\nnoSpecimensCollected = ({\n type: \"noSpecimensCollected\",\n Vascular: data_.filter(\n (d) =>\n d.group === \"Flowering plants\" || // was Angiosperms\n d.group === \"Conifers\" || // Gymnosperms\n d.group === \"Ferns & ferns allies\" // was Pteridophytes\n ).length,\n Bryophytes: data_.filter((d) => d.group === \"bryophyte\").length // was Bryophytes\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":362,"value":"// duplicate collections - how do we calculate this now??\nnoDupCollections = ({\n type: \"noDupCollections\",\n Vascular:\n COPOdata.filter(\n (d) =>\n d.group === \"Angiosperms\" ||\n d.group === \"Gymnosperms\" ||\n d.group === \"Pteridophytes\"\n ).length -\n new Set(\n COPOdata.filter(\n (d) =>\n d.group === \"Angiosperms\" ||\n d.group === \"Gymnosperms\" ||\n d.group === \"Pteridophytes\"\n ).map((d) => d.taxon_name)\n ).size,\n Bryophytes:\n COPOdata.filter((d) => d.group === \"Bryophytes\").length -\n new Set(\n COPOdata.filter((d) => d.group === \"Bryophytes\").map((d) => d.taxon_name)\n ).size\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":633,"value":"md`#### Map data & functions`","pinned":false,"hidden":false,"mode":"ojs"},{"id":19,"value":"plant_spike = (length, width = 7) =>\n `M${-width / 2},0L0,${-length}L${width / 2},0`","pinned":true,"hidden":false,"mode":"ojs"},{"id":296,"value":"length = d3.scaleLinear([0, d3.max(countyData, d => d.n)], [0, 100])","pinned":true,"hidden":false,"mode":"ojs"},{"id":79,"value":"projection = d3CompositeProjections\n .geoAlbersUk()\n .translate([width / 2, height / 2])","pinned":false,"hidden":false,"mode":"ojs"},{"id":71,"value":"ukLand = topojson.feature(ukCounties, ukCounties.objects.UK)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1620,"value":"irelandLand = topojson.feature(ireland, ireland.objects.IRL_adm1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":262,"value":"countyData = {\n const countyArr = d3.rollups(\n COPOdata,\n (v) => v.length,\n (d) => d.county\n );\n let res = [];\n for (let i = 0; i < countyArr.length; i++) {\n for (let j = 0; j < COPOdata.length; j++) {\n if (countyArr[i][0] === COPOdata[j].county) {\n res.push({\n county: countyArr[i][0],\n n: countyArr[i][1],\n county_lat: COPOdata[j].county_lat,\n county_lon: COPOdata[j].county_lon\n });\n }\n }\n }\n\n return res\n .filter(\n (v, i, a) =>\n a.findIndex((t) => JSON.stringify(t) === JSON.stringify(v)) === i\n )\n .filter((d) => d.county !== \"\")\n .filter((d) => d.county_lat !== \"\");\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":637,"value":"md`#### Master data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2304,"value":"DATE = parseDate(new Date(data_[0].date))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2346,"value":"GOOGLE_SHEET_DATA = fetch(\n \"https://raw.githubusercontent.com/DToL-Plant-Working-Group/collections/main/data/all_collected_final.csv\"\n).then((response) => {\n return response.text();\n})","pinned":true,"hidden":false,"mode":"ojs"},{"id":2267,"value":"data_ = d3.csvParse(GOOGLE_SHEET_DATA)","pinned":true,"hidden":false,"mode":"ojs"},{"id":2328,"value":"COPOdtolPlantCollections = fetch(\n \"https://raw.githubusercontent.com/DToL-Plant-Working-Group/collections/main/data/COPO_parsed_DToL_plant_collections.csv\"\n).then((response) => {\n return response.text();\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2,"value":"COPOdata = d3.csvParse(COPOdtolPlantCollections)","pinned":false,"hidden":false,"mode":"ojs"},{"id":908,"value":"function parseDate(date) {\n const dtf = new Intl.DateTimeFormat('en', {\n year: 'numeric',\n month: 'short',\n day: '2-digit'\n });\n const [{ value: mo }, , { value: da }, , { value: ye }] = dtf.formatToParts(\n date\n );\n return `${da}-${mo}-${ye}`;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":711,"value":"dateData = COPOdata.map((d) => {\n // let splits = d.collection_date_verbatim.split(\"/\");\n // let date = new Date(splits[2], splits[1] - 1, splits[0]);\n let date = new Date(d.collection_date_verbatim);\n return date;\n})\n .filter(\n (date, i, self) =>\n self.findIndex((d) => d.getTime() === date.getTime()) === i\n )\n .sort(function (a, b) {\n // Turn your strings into dates, and then subtract them\n // to get a value that is either negative, positive, or zero.\n return new Date(b) - new Date(a);\n })\n .map((d) => parseDate(d))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2361,"value":"ireland = fetch(\n \"https://raw.githubusercontent.com/DToL-Plant-Working-Group/collections/main/data/ireland.json\"\n).then((response) => {\n return response.json();\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2367,"value":"ukCounties = fetch(\n \"https://raw.githubusercontent.com/DToL-Plant-Working-Group/collections/main/data/uk.json\"\n).then((response) => {\n return response.json();\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":315,"value":"md`### Module imports`","pinned":false,"hidden":false,"mode":"ojs"},{"id":42,"value":"topojson = require(\"topojson-client@3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":77,"value":"d3CompositeProjections = require(\"d3-composite-projections@1.3.1\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"d3 = require(\"d3@6\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":2404,"value":"md`### Pipeline information`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2401,"value":"The data is drawn from several sources, including google sheets (see links on the chart) and the COPO API. The entire pipeline can be run from a single shell script. Node & R are required. For full details please see the GitHub repository. I expect things shall break, especially as more locality data from COPO is drawn in.","pinned":false,"hidden":false,"mode":"md"}],"files":"$W32","stdlib":"1","titling":"auto"}