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clads2.tppl

function clads2​

Main model function

model function clads2(tree: Tree, rho: Real) => Real[]

type Globals​

type Globals = Globals {
    lambda:     Real,
    mu:         Real,
    sigma:      Real,
    logAlpha:   Real,
    rho:        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 (unsampled)

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

function simHiddenSpeciation​

Simulate hidden speciation along an observed branch

function simHiddenSpeciation(g: Globals, multiplier: Real, startTime: Real, endTime: Real) => Real

type alias Tree​

type alias Tree = ClockTree

function walk​

Simulate process ("walk") along the observed tree

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