phytoclass (version 2.3.1)

Conduit: Conduit between minimise_elements function and Fac_F_R of steepest descent algorithm.

Description

Conduit between minimise_elements function and Fac_F_R of steepest descent algorithm.

Usage

Conduit(Fmat, place, S, cm, c_num = c(1, 2, 3))

Value

A list containing three elements: 1: The modified F matrix 2: Number of iterations or modifications made 3: The original F matrix before modifications

Arguments

Fmat

A matrix of contribution values for each pigment and taxa pair

place

Indices of elements to be modified

S

Matrix of pigment sample measurements

cm

Vector of weights for each column

c_num

A numeric value (1, 2, or 3) to select which scaler values to use

Examples

Fmat <- as.matrix(phytoclass::Fm)
S <- as.matrix(phytoclass::Sm)
S_weights <- as.numeric(phytoclass:::Bounded_weights(S))
place <- which(Fmat[, seq(ncol(Fmat) - 2)] > 0)

# Get F_initial from NNLS_MF as done in Steepest_Descent
F_initial <- phytoclass::NNLS_MF(Fmat, S, S_weights)

result <- phytoclass:::Conduit(F_initial[[1]], place, S, S_weights, c_num = 3)