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subroot-HRM.tppl

function compAge​

function compAge(left: Event, right: Event) => Int

function rejectAcceptSubroot​

model function rejectAcceptSubroot(
  symbiont_tree: TreeLabeled,
  ntips: Int,
  nhosts: Int,
  interactions: Int[],
  host_distances: Real[],
  dMean: Real,
  subrootLength: Real
) => ReturnType

type ReturnType​

type ReturnType = ReturnType{
  lambda: Real[], mu: Real, beta: Real, tree: HistoryTree
}

function sampleBranch​

function sampleBranch(
  startRep: Int[],
  finalRep: Int[],
  startAge: Real,
  finalAge: Real,
  nhosts: Int,
  modelParams: ModelParams,
  branchKernel: Matrix[Real],
  rejectionDepth: Int
) => CorrectedBranchSample

function sampleHostHistory​

function sampleHostHistory(
  startState: Int,
  finalState: Int,
  startAge: Real,
  finalAge: Real,
  host: Int,
  embeddedQMatrix: EmbeddedMarkovChainMatrix,
  stepIndex: Int
) => HostBranchSample

function sampleTreeHistory​

function sampleTreeHistory(
  tree: MsgTree,
  nhosts: Int,
  preorderMsg: Matrix[Real],
  parentRep: Int[],
  parentAge: Real,
  modelParams: ModelParams,
  branchKernel: Matrix[Real]
) => HistoryTree

function sampleTruncatedExponential​

function sampleTruncatedExponential(rate: Real, maxT: Real) => Real

function sampleUnorderedBranch​

function sampleUnorderedBranch(
  startRep: Int[],
  finalRep: Int[],
  startAge: Real,
  finalAge: Real,
  hostIndex: Int,
  nhosts: Int,
  embeddedQMatrix: EmbeddedMarkovChainMatrix,
  rejectionDepth: Int
) => BranchSample

function suggestRepAligned​

function suggestRepAligned(msg: Matrix[Real], i: Int, max: Int) => Int[]

function suggestRepRS​

function suggestRepRS(msg: Matrix[Real], max: Int, initialRep: Int[], depth: Int) => Int[]

function suggestRepUnaligned​

function suggestRepUnaligned(msg: Matrix[Real], i: Int, max: Int) => Int[]