Skip to main content

tree_inference.tppl

function buildForest​

Build forest of trees from leaves, recursively

function buildForest(data: Int[][], forest: SeqTree[], index: Int, dataLen: Int) => SeqTree[]

function cluster​

function cluster(q: Matrix[Real], trees: SeqTree[], maxAge: Real, seqLen: Int) => SeqTree[]

function ctmc​

Note: this is not optimal, in terms of repeated calculation of matrix exp

function ctmc(initialstate: Int, q: Matrix[Real], t: Real) => Real[]

function myModel​

model function myModel(data: Int[][]) => SeqTree[]

function pickpair​

Randomly sample two indices in the trees vector, to be combined. Avoiding mirror cases.

  function pickpair(n: Int) => Int[]

type SeqTree​

type SeqTree =
  | Leaf {age: Real, seq: Int[]}
  | Node {age: Real, seq: Int[], left: SeqTree, right: SeqTree}