2b:null 2c:["$","title",null,{"children":"Occellated lizards | Thomas Sibley | Observable"}] 31:[] 2f:{"id":"f2a73981ce197ac7","slug":null,"title":"Occellated lizards","thumbnail":"eb49ab049d360f1f35b0ff4f3b5de6f9251af114494298b33a240620cfa86041","access_level":"public","create_time":"$D2019-12-01T08:22:16.786Z","update_time":"$D2023-10-15T09:59:37.403Z","view_time":null,"first_public_time":"$D2023-10-15T09:36:48.951Z","has_unpublished_edits":null,"fork":false,"stars":1,"starred":false,"owner":{"type":"team","id":"ac70d42baed38f03","login":"tsibley","name":"Thomas Sibley","avatar_url":"https://avatars-next.observableusercontent.com/c09d4a5f03660eb710f364664acf86c2aea254284aa23ad90fe7fbd3a61aa407","tier":"starter_2024"},"version":671,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"b38bde8911ee799e","login":"tsibley","name":"Thomas Sibley","avatar_url":"https://avatars-next.observableusercontent.com/c09d4a5f03660eb710f364664acf86c2aea254284aa23ad90fe7fbd3a61aa407","tier":null}],"members":[{"type":"individual","id":"b38bde8911ee799e","login":"tsibley","name":"Thomas Sibley","avatar_url":"https://avatars-next.observableusercontent.com/c09d4a5f03660eb710f364664acf86c2aea254284aa23ad90fe7fbd3a61aa407","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Occellated lizards","cells":[{"id":0,"value":"md`\n# Occellated lizards\n\nImplementing the cellular automaton described in _[A living mesoscopic cellular automaton made of skin scales (Nature 2017)](https://doi.org/10.1038/nature22031)_.\n\n## Todo\n\n* Data for an initial condition for the CA\n* Numeric probabilities for the CA\n* Code for the CA?\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":345,"value":"lagBy = (offset = 1) => ((item, index, array) => [item, array[index - offset]])","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":373,"value":"layout = {\n let row = 0,\n col = 0;\n \n return hexgrid\n .centers()\n .map(([x, y], index) => ({x, y, index}))\n .map(lagBy(1))\n .reduce((grid, [scale, prevScale]) => {\n if (prevScale) {\n if (scale.y !== prevScale.y) {\n // Start a new row\n grid.push([]);\n row++;\n col = 0;\n }\n }\n\n // Add to current row\n grid[grid.length - 1].push({...scale, row, col: col++});\n\n return grid;\n }, [[]]);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":279,"value":"neighbors = ([row, col]) => [\n [row, col + 1], // east\n [row + 1, col + (even(row) ? 0 : 1)], // southeast\n [row + 1, col - (even(row) ? 1 : 0)], // southwest\n [row, col - 1], // west\n [row - 1, col - (even(row) ? 1 : 0)], // northwest\n [row - 1, col + (even(row) ? 0 : 1)], // northeast\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":453,"value":"neighborStates = (state, scale) =>\n neighbors([scale.row, scale.col])\n .map(([row, col]) => (layout[row] || [])[col])\n .filter(scale => scale != null)\n .map(scale => state[scale.index])","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":478,"value":"alikeNeighbors = (state, scale) =>\n neighborStates(state, scale)\n .filter(neighbor => neighbor.colorIndex === scale.colorIndex)\n .length","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":418,"value":"even = n => n % 2 == 0","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":199,"value":"paintSvg = {\n const hexagonPath = hexgrid.hexagon();\n return svg`\n \n `;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":603,"value":"mutable colorInversions = 0","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":622,"value":"inversionLimit = 1500","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":540,"value":"viewof simulating = html``;","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":524,"value":"viewof debug = html`\n \n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":609,"value":"viewof black = html`` // yellow","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":611,"value":"viewof green = html`` // lawngreen","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":166,"value":"viewof initialColorSplit = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":332,"value":"initialState = layout.flat().map(scale => ({\n ...scale,\n colorIndex: Math.random() > initialColorSplit ? 0 : 1,\n}))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":148,"value":"colors = [black, green]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":582,"value":"mutable state = initialState","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":564,"value":"{\n while (simulating && mutable colorInversions < inversionLimit)\n yield mutable state = next(mutable state);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"// “The probability of changing colour for a black scale with n first-neighbour black scales”\n// and “the probability of changing colour for a green scale with n first-neighbour green scales”\n//\n// “Colour-change probabilities for green scales (green line) and black scales (black line) as\n// a function of nearest-neighbour scales matching their colour, estimated from discrete RD (dRD)\n// simulations (mean ± s.d. among 100 simulations).”\n//\n// Data from Figure 6a.\nprobability = [\n [\n 0, // 0 black neighbors\n 0, // 1 black neighbor\n 0,\n 0,\n 0.00063,\n 0.04796,\n 0.20283, // 6 black neighbors\n ],\n [\n 0, // 0 green neighbors\n 0, // 1 green neighbor\n 0,\n 0,\n 0.02138,\n 0.23098,\n 0.99905, // 6 geen neighbors\n ],\n]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":143,"value":"next = (state) =>\n state.map(scale => ({...scale, colorIndex: nextColorIndex(state, scale)}))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"nextColorIndex = (state, scale) =>\n Math.random() <= probability[scale.colorIndex][alikeNeighbors(state, scale)]\n ? invertColor(scale.colorIndex)\n : scale.colorIndex","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":601,"value":"invertColor = (colorIndex) => {\n mutable colorInversions++;\n return colorIndex^1;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"height = Math.round(width * 0.8) // Math.round(width * 0.4)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":34,"value":"radius = 14 // Math.round(height / 24)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":29,"value":"hexgrid = d3.hexbin()\n .extent([[0,0], [width, height]])\n .radius(radius)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":527,"value":"debug","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"d3 = require(\n 'd3-hexbin',\n 'd3-shape',\n);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W31","stdlib":"1","titling":"auto"}} 30:"$2f:body"