package phylogenetics

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Matrix and vector creation

phylogenetics
- Phylogenetics
  - Alignment
    
    Fasta
    
    Make
    
    S
    
    Phylip
  - Alphabet
    
    Make
    
    Matrix
    
    Table
    
    Vector
    
    X
    
    S
    
    Matrix
    
    Table
    
    Vector
    
    S_int
    
    Matrix
    
    Table
    
    Vector
  - Amino_acid
    
    Matrix
    
    Table
    
    Vector
  - Birth_death
  - Bppsuite
    
    Cmd
  - Codon
    
    Genetic_code
    
    NS
    
    Matrix
    
    Table
    
    Vector
    
    Matrix
    
    S
    
    Matrix
    
    Table
    
    Vector
    
    Table
    
    Universal_genetic_code
    
    NS
    
    Matrix
    
    Table
    
    Vector
    
    Vector
  - Discrete_pd
  - Dna
  - Felsenstein
    
    Alignment
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Align
    
    E
  - Fitch
  - ID_monad
  - Iupac_nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Linear_algebra
    
    Matrix
    
    S
    
    Matrix
    
    Vector
    
    Vector
  - Linear_algebra_tools
    
    Lacaml
    
    Mat
    
    Vec
  - List1
  - MCMC
    
    M
    
    Alignment
    
    Felsenstein
  - MG94
    
    NSCodon_rate_matrix
  - Mutsel
    
    NSCodon_rate_matrix
  - Nelder_mead
  - Newick
    
    Tree_repr
  - Newick_ast
  - Newick_lexer
  - Newick_parser
    
    Incremental
    
    MenhirInterpreter
  - Newick_parser_errors
  - Nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Nucleotide_process
    
    Random
  - Phylip
  - Phylo_ctmc
    
    Ambiguous
    
    Path_sampler
    
    SV
    
    Uniformized_process
  - Phylogenetic_tree
  - Rate_matrix
    
    Amino_acid
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Nucleotide
    
    S
  - Rejection_sampling
    
    Make
    
    Align
  - Seq
    
    Base
    
    DNA
    
    Make
    
    B
    
    Make_list
    
    B
    
    S
  - Sequence_generation
    
    Base
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Align
    
    E
    
    Seq
    
    Sequence
  - Sequence_simulator
    
    Alphabet
    
    Vector
    
    Make
    
    A
    
    Vector
  - Sigs
    
    ALIGNMENT
    
    BASE
    
    EVOL_MODEL
    
    SEQUENCE
  - Simulator
    
    Branch_info
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    BI
    
    NSCodon
    
    BI
  - Site_evolution_model
    
    Diagonalizable_rate_matrix
    
    JC69
    
    JC69_numerical
    
    K80
    
    K80_numerical
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    M
    
    Make_diag
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    M
    
    Nucleotide_S_with_reduction
    
    Rate_matrix
    
    S
    
    S_with_reduction
  - Stat_tools
  - TKF91
    
    Make_simulator
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    BI
  - Tree
  - Utils
  - Wag
  - Zipper

Legend:
Library
Module
Module type
Parameter
Class
Class type

type t = mat

val dim : t -> int * int

Matrix and vector creation

val init : int -> f:(int -> int -> float) -> t

Initialises a square matrix from a int->int->float function.

val init_sym : int -> f:(int -> int -> float) -> t

init_sym n ~f creates a symetric square matrix by calling f only for elements s.t. i <= j

val diagm : vec -> t

Initializes a square diagonal matrix from the vector of its diagonal elements.

val mul : t -> t -> t

Matrix element-wise multiplication

val add : t -> t -> t

Matrix addition.

val scal_mul : float -> t -> t

Multiplication of a matrix by a scalar.

val inplace_scal_mul : float -> t -> unit

Inplace multiplication of a matrix by a scalar.

val dot : ?transa:[ `N | `T ] -> ?transb:[ `N | `T ] -> t -> t -> t

Matrix multiplication

val apply : ?trans:[ `N | `T ] -> t -> vec -> vec

Matrix-vector product

val pow : t -> int -> t

Matrix exponentiation

val expm : t -> t

Matrix exponential

val log : t -> t

Element-wise logarithm of matrix

val robust_equal : tol:float -> t -> t -> bool

Compares two matrices and tolerates a certain relative difference. Let f be the float parameter, it returns true iff the elements of the second matrix are between 1-f and 1+f times the corresponding elements of the first

val get : t -> int -> int -> float

Access a specific element of a matrix.

val set : t -> int -> int -> float -> unit

Set a specific element of a matrix.

val row : t -> int -> vec

Copy row from a matrix

val diagonalize : t -> vec * t

Diagonalizes a matrix M so that M = PxDxP^T; returns (v,P) where v is the diagonal vector of D.

val transpose : t -> t

val inverse : t -> t

Computes the inverse of a matrix.

val zero_eigen_vector : t -> vec

zero_eigen_vector m is a vector v such that Vec.sum v = 1 and mat_vec_mul m v = zero

val of_arrays : float array array -> t option

val of_arrays_exn : float array array -> t

val pp : Stdlib.Format.formatter -> t -> unit

Prints a matrix to the standard output (display may be messy).