package phylogenetics

  1. Overview
  2. Docs
package phylogenetics
Legend:
Page
Library
Module
Module type
Parameter
Class
Class type
Source

Module Phylogenetics.Phylo_ctmcSource

Sourcetype shifted_vector =
  1. | SV of Linear_algebra.vec * float
Sourceval pruning : ('n, 'l, 'b) Tree.t -> nstates:int -> transition_matrix:('b -> Linear_algebra.mat) -> leaf_state:('l -> int) -> root_frequencies:Linear_algebra.vec -> float
Sourceval pruning_with_missing_values : ('n, 'l, 'b) Tree.t -> nstates:int -> transition_matrix:('b -> Linear_algebra.mat) -> leaf_state:('l -> int option) -> root_frequencies:Linear_algebra.vec -> float
Sourceval conditionial_likelihoods : ('n, 'l, 'b) Tree.t -> nstates:int -> leaf_state:('l -> int) -> transition_matrix:('b -> Linear_algebra.mat) -> (shifted_vector, int, 'b * Linear_algebra.mat) Tree.t
Sourceval conditional_simulation : Gsl.Rng.t -> (shifted_vector, int, 'b * Linear_algebra.mat) Tree.t -> root_frequencies:Linear_algebra.vec -> (int, int, 'b * Linear_algebra.mat) Tree.t
Sourcetype uniformized_process
Sourceval uniformized_process : Linear_algebra.mat -> uniformized_process
Sourceval conditional_simulation_along_branch : Gsl.Rng.t -> uniformized_process -> branch_length:float -> start_state:int -> end_state:int -> nstates:int -> (int * float) array
Sourceval substitution_mapping : nstates:int -> branch_length:('b -> float) -> rng:Gsl.Rng.t -> process:('b -> uniformized_process) -> (int, int, 'b * Linear_algebra.mat) Tree.t -> (int, int, 'b * (int * float) array) Tree.t