NNLS_MF: Performs the non-negative matrix factorisation for given...

In phytoclass: Estimate Chla Concentrations of Phytoplankton Groups

Performs the non-negative matrix factorisation for given phytoplankton pigments and pigment ratios, to attain an estimate of phytoplankton class abundances.

Description

Performs the non-negative matrix factorisation for given phytoplankton pigments and pigment ratios, to attain an estimate of phytoplankton class abundances.

Usage

NNLS_MF(Fn, S, cm = NULL)

Arguments

Fn	Pigment to Chl a matrix
S	Sample data matrix – a matrix of pigment samples
cm	Weights for each column

Value

A list containing

1. The F matrix (pigment: Chl a) ratios

2. The root mean square error (RMSE)

3. The C matrix (class abundances for each group)

Examples

MC <- Matrix_checks(Sm,Fm)
Snew <- MC$Snew
Fnew <- MC$Fnew
cm <- Bounded_weights(Snew, weight.upper.bound = 30)
NNLS_MF(Fnew, Snew, cm)

phytoclass documentation built on April 4, 2025, 4:02 a.m.