Rev Language Reference

SiteMixtureModel - SiteMixtureModel

A weighted collection of discrete character evolution models.

Details

The SiteMixtureModel datatype is a mixture distribution where each component is a model of discrete character evolution. Each character evolves according to one of the component models. However, the specific model for each character is not specified in advance. Instead, each character has some probability of choosing each component. These probabilities are specified by the mixture weights.

Example

M := fnInvASRV(fnGammaASRV(fnJC(4),alpha=1),pInv=0.1)
M.weights()
M.nComponents()
M.rootFrequencies(1)

# It possible to express nested models using pipes.
M := fnJC(4) |> fnGammaASRV(alpha=1) |> fnInvASRV(pInv=0.1)

Methods

  • getTransitionProbabilities(Tree tree, Natural node, RealPos rate)
  • nComponents()
  • nStates()
  • rate()
  • rootFrequencies(Natural index)
  • weights()

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