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bdd2.tppl

function bdd2​

Model function for BDD2

model function bdd2(tree: Tree, rho: Real, numIntervals: Int) => Real[]

function bddCase​

Help function to determine BDD case

function bddCase(timeSegment: Real, waitingTime: Real, deltaT: Real) => BDDCase

type BDDCase​

Type for capturing BDD time segment cases

type BDDCase =
    | DeltaT {timeSegment:Real}
    | Event {timeSegment:Real}
    | EndOfBranch {timeSegment:Real}

type Globals​

Type for global model parameters

type Globals = Globals {
  lambda   : Real,
  mu       : Real,
  sigma    : Real,
  logAlpha : Real,
  rho      : Real,
  deltaT   : Real
}

function isDetected​

Forward simulation determining whether a tree survives and is detected (sampled)

function isDetected(g: Globals, multiplier: Real, tBegin: Real) => Bool

function numTrialsUntilMRCADetection​

Get an estimate of the probability of the MRCA being detected under given parameter values

function numTrialsUntilMRCADetection(g: Globals, tRoot: Real, mMax: Int) => Int

function predictUndetectedProb​

Help function to predict the prob that a tree goes undetected

function predictUndetectedProb(g: Globals, multiplier: Real, time: Real) => Real

function shiftDivRates​

Help function to let lambda and mu change according to Brownian motion on the log scale

function shiftDivRates(g: Globals, timeSegment: Real) => Real

function simHiddenSpeciation​

Simulate hidden speciation process along a branch in the reconstructed tree

function simHiddenSpeciation(g: Globals, multiplier: Real, tBegin:Real, tEnd: Real) => Real

type alias Tree​

We use clock tree representation

type alias Tree = ClockTree

function walk​

Simulate ("walk") along the reconstructed tree

function walk(g: Globals, multiplier: Real, parentAge: Real, node: Tree)