package phylogenetics

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Module Iupac_nucleotide.MatrixSource

Sourcetype symbol = t
include Linear_algebra.Matrix with type t = matrix and type vec := vector
Sourcetype t = matrix
Sourceval dim : t -> int * int
Matrix and vector creation
Sourceval diagm : vector -> t

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

Sourceval mul : t -> t -> t

Matrix element-wise multiplication

Sourceval add : t -> t -> t

Matrix addition.

Sourceval scal_mul : float -> t -> t

Multiplication of a matrix by a scalar.

Sourceval inplace_scal_mul : float -> t -> unit

Inplace multiplication of a matrix by a scalar.

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

Matrix multiplication

Sourceval apply : ?trans:[ `N | `T ] -> t -> vector -> vector

Matrix-vector product

Sourceval pow : t -> int -> t

Matrix exponentiation

Sourceval expm : t -> t

Matrix exponential

Sourceval log : t -> t

Element-wise logarithm of matrix

Sourceval 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

Sourceval get : t -> int -> int -> float

Access a specific element of a matrix.

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

Set a specific element of a matrix.

Sourceval row : t -> int -> vector

Copy row from a matrix

Sourceval diagonalize : t -> vector * t

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

Sourceval transpose : t -> t
Sourceval inverse : t -> t

Computes the inverse of a matrix.

Sourceval zero_eigen_vector : t -> vector

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

Sourceval pp : Format.formatter -> t -> unit

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

Sourceval init : (symbol -> symbol -> float) -> matrix
Sourceval init_sym : (symbol -> symbol -> float) -> matrix
Sourceval of_arrays : float array array -> matrix option
Sourceval of_arrays_exn : float array array -> matrix