2c:null 2d:["$","title",null,{"children":"Demographic helper functions | JT McCrone | Observable"}] 32:T4b1,function processSkyGrid(burnin){ const cutoff = burnin[0]["skygrid.cutOff"]; const popKeys = Object.keys(burnin[0]).filter(d=>d.includes("skygrid.logPopSize")) const numGridPoints = popKeys.length; const data = d3.range(numGridPoints).reduce((acc,cur)=>{acc.push([]);return acc;},[]) const origin=burnin[0]["treeModel.rootHeight"]+burnin[0]["age(root)"]; for(const entry of burnin){ for(let i=0; i< popKeys.length; i++){ const popsize = entry[popKeys[i]] const point = parseGridPoint(popKeys[i]); data[point].push(popsize) } } const sorted = data.map(d=>d.sort(d3.ascending)) return sorted.map((Ne,i)=>{ const Upper = Math.exp(d3.quantile(Ne,0.975)); const Lower = Math.exp(d3.quantile(Ne,0.025)); const Median = Math.exp(d3.median(Ne)); const Mean = Math.exp(d3.mean(Ne)); const height = (i/(numGridPoints-1))*cutoff; const t = origin-height return {Upper,Lower,Median,Mean,height,t} }); }33:[] 30:{"id":"6734eba57871e94e","slug":"demographic-helper-functions","title":"Demographic helper functions","thumbnail":"6675c9377292616bd819c12d2853a95404ec60ca804c8d9e81b116fb64f43803","access_level":"public","create_time":"$D2020-06-08T11:53:59.262Z","update_time":"$D2020-07-27T12:00:04.188Z","view_time":null,"first_public_time":"$D2020-06-08T15:21:56.293Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"3800e1e175aef818","login":"jtmccr1","name":"JT McCrone","avatar_url":"https://avatars-next.observableusercontent.com/576c91e5885cf3eb97e629abccc219cea3b1518d73c5bf46dfebcda63a4bd7ba","tier":"starter_2024"},"version":139,"publish_version":139,"role":null,"authored":false,"authors":[{"type":"individual","id":"4deab1691aa12820","login":"jtmccr1","name":"JT McCrone","avatar_url":"https://avatars-next.observableusercontent.com/576c91e5885cf3eb97e629abccc219cea3b1518d73c5bf46dfebcda63a4bd7ba","tier":null}],"members":[{"type":"individual","id":"4deab1691aa12820","login":"jtmccr1","name":"JT McCrone","avatar_url":"https://avatars-next.observableusercontent.com/576c91e5885cf3eb97e629abccc219cea3b1518d73c5bf46dfebcda63a4bd7ba","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Demographic helper functions","cells":[{"id":0,"value":"md`# Demographic helper functions \n\nThis notebook contains useful functions for parsing and processing demographic trace files from BEAST. Nothing here is sacred it should develop and change dramatically.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2,"value":"parseLog = function(text,burnin=null){\n \n text = text.replace(/^[#@][^\\r\\n]+[\\r\\n]+/mg, '');\n \nconst data = d3.tsvParse(text,d3.autoType)\n if(burnin){\n return data.filter((d,i)=>i>burnin)\n }\n return data.filter((d,i)=>i>data.length*0.1)\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"pipe = (...fns)=>x=>fns.reduce((v,f)=>f(v),x)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"html`

Exponetial Exponetial demographic plot

The parameters for the model are :

N0: population size at the present momement
r: current growth rate.
r1: ancestral growth rate.
transistion time : the point at which the growth rates change

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"md` The population size at time t (into the past) is given by \n${tex.block`N_0e^{(-r * t)}`}\n\nWhere t< transition time and \n\n${tex.block`N_1 * e^{-r_1*(t- \\text{transition time})}`}\nWhere N1 is the population size at the transition point and is given by equation 1 where t=transtion time.\n` ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"getExpExpPopSize = function(state,height){\n const N0 = state[\"exponential.popSize\"];\n const r = state[\"exponential.growthRate\"];\n const r1 = state[\"exponential.ancestralGrowthRate\"];\n const changeTime = state[\"transition.time\"];\n \n if(height>state[\"treeModel.rootHeight\"]){\n return null\n }\n if(height(height)=>{\n const Ne=burnin.map(d=>getExpExpPopSize(d,height)).filter(d=>d).sort(d3.ascending)\n const Upper = d3.quantile(Ne,0.975);\n const Lower = d3.quantile(Ne,0.025);\n const Median = d3.median(Ne);\n const Mean = d3.mean(Ne);\n \n \n return {height,Upper,Lower,Median,Mean, Ne}\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"processExpExpData = function(burnin){\n \n const heights= d3.range(50).map(d=>(d/50)*d3.mean(burnin,d=>d[\"treeModel.rootHeight\"]))\n const popSizes= heights.map(getExpExpPopulationSizes(burnin))\n const origin=burnin[0][\"treeModel.rootHeight\"]+burnin[0][\"age(root)\"];\n popSizes.forEach(d=>d.t=origin-d.height)\n return popSizes;\n \n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"processExpLog = pipe(parseLog,processExpExpData)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":44,"value":"html`

SkyGrid Nonparameteric model

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":54,"value":"function parseGridPoint(text){\n return parseInt(text.split(\"skygrid.logPopSize\")[1])-1\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":53,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":61,"value":"baseStyles = html`\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":122,"value":"d3.quantile([-1,-3,-5,-6],0.975)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":47,"value":"processSkyGridLog=pipe(parseLog,processSkyGrid)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"d3= require(\"d3\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1"}} 31:"$30:body"