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container-types.tppl

type BranchSample​

Container type for the history along a branch, along with the debt from the independence model

type BranchSample = BranchSample {
  history: Event[][], success: Bool
}

type CorrectedBranchSample​

Like the above but with the excess from the full model too

type CorrectedBranchSample = CorrectedBranchSample {
  history: Event[],
  logDebt: Real,
  logExcess: Real,
  success: Bool
}

type EmbeddedMarkovChainMatrix​

Container type for a CTMC in jump chain form

type EmbeddedMarkovChainMatrix = EmbeddedMarkovChainMatrix {
  totalRates: Real[],
  transitionProbs: Real[][],
  mat: Matrix[Real]
}

type Event​

Container type for a single event in a host

type Event = Event {eventTime: Real, fromState: Int, toState: Int, host: Int}

type HistoryTree​

This is the final tree with node repertoires and branch histories

type HistoryTree =
  | HistoryLeaf {age: Real, label: Int, repertoire: Int[], history: Event[]}
  | HistoryNode {age: Real, left: HistoryTree, right: HistoryTree, label: Int, repertoire: Int[], history: Event[]}

type HostBranchSample​

type HostBranchSample = HostBranchSample {
  history: Event[], success: Bool
}

type ModelParams​

Container type for all model params

type ModelParams = ModelParams {
  beta: Real,
  hostMetric: Matrix[Real],
  embeddedQMatrix: EmbeddedMarkovChainMatrix,
  meanDist: Real
}

type MsgTree​

The result from postorder message passing

type MsgTree =
  | MsgLeaf{

type TreeLabeled​

Types shared by several files Tree with labels

type TreeLabeled =
  | Leaf{age: Real, label: Int}
  | Node{age: Real, left: TreeLabeled, right: TreeLabeled, label: Int}