2e:null 2f:["$","title",null,{"children":"beanbaggenetics | Kevin R. Thornton | Observable"}] 34:T4d6,function make_diploid_frequency_trajectory(N, initial_copies, wAA, wAa, waa, number_of_generations, label) { if (wAA < 0.0) { throw new Error("wAA must be >= 0.0") } if (wAa < 0.0) { throw new Error("wAa must be >= 0.0") } if (waa < 0.0) { throw new Error("waa must be >= 0.0") } let initial_frequency = initial_copies/(2*N); if (initial_frequency <= 0.0 || initial_frequency >= 1.0) { throw new Error("initial_frequency must be 0 < x < 1") } if (number_of_generations < 1) { throw new Error("number_of_generations must be > 0") } let current_frequency = initial_frequency; let generation = 1; let traj = [{generation: generation, frequency: current_frequency, label: label}]; while (generation <= number_of_generations && current_frequency > 0.0 && current_frequency < 1.0) { ++generation; let q = current_frequency; let delta_q = diploid_allele_frequency_change(q, wAA, wAa, waa); let expected_next_freq = current_frequency + delta_q; let copies = d3random.randomBinomial(2*N, expected_next_freq)(); current_frequency = copies/ (2*N); traj.push({generation: generation, frequency: current_frequency, label: label}); } return traj; }35:[] 32:{"id":"fd2915a5ace4d912","slug":"beanbaggenetics","title":"beanbaggenetics","thumbnail":"f8390bfbe2743cec010e4dec8247240bcf7e202b25f98460cc763b03259d0f02","access_level":"public","create_time":"$D2021-11-15T15:51:41.047Z","update_time":"$D2021-11-15T17:37:45.245Z","view_time":null,"first_public_time":"$D2021-11-15T15:58:39.466Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"10f23817881a3073","login":"molpopgen","name":"Kevin R. 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Thornton"}},"type":"notebook","body":{"title":"beanbaggenetics","cells":[{"id":0,"value":"# beanbaggenetics","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":65,"value":"## Examples","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":62,"value":"## Functions","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":47,"value":"diploid_allele_frequency_change = function(q, wAA, wAa, waa){\n let p = 1.0 - q;\n let pAA = p*p;\n let pAa = 2.0 * p * q;\n let paa = q*q;\n let wbar = pAA*wAA + pAa*wAa + paa*waa;\n let delta_q = p*q*(p*(wAa - wAA) + q*(waa - wAa))/wbar;\n return delta_q;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":24,"value":"function make_haploid_frequency_trajectory(N, initial_copies, mutant_fitness, number_of_generations, label) {\n let current_frequency = initial_copies / N;\n let generation = 1;\n let traj = [{generation: generation, frequency: current_frequency, label: label}];\n\n while (generation <= number_of_generations && current_frequency > 0.0 && current_frequency < 1.0)\n {\n ++generation;\n let wbar = 1.0 * (1.0 - current_frequency) + mutant_fitness*current_frequency;\n let copies = d3.randomBinomial(N, current_frequency*mutant_fitness/wbar)();\n current_frequency = copies/N;\n traj.push({generation: generation, frequency: current_frequency, label: label});\n }\n\n return traj;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":56,"value":"diploid_fixation_trajectory = function(N, s, h, initial_copies, label) {\n let wAA = 1.0;\n let wAa = 1+2*s*h;\n let waa = 1+2*s;\n let traj = null;\n let done = false;\n\n do {\n let t = make_diploid_frequency_trajectory(N, initial_copies, wAA, wAa, waa, 100*N, label);\n let last = t[t.length - 1];\n if (last.frequency == 1) {\n traj = t;\n done = true;\n }\n }\n while(done == false);\n\n return traj;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":20,"value":"## External dependencies","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10,"value":"d3random = require (\"d3-random@>=2.2\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W35","stdlib":"1","titling":"auto"}} 33:"$32:body"