Estimate Chla Concentrations of Phytoplankton Groups
Add weights to the data, bound at a maximum.
Cluster things
Calculate the mean condition number for randomized F matrices
Conduit between minimise_elements function and Fac_F_R of steepest des...
Convergence Figure
Sets the default minimum and maximum values for phytoplankton groups p...
Part of the steepest descent algorithm that works to reduce error give...
Remove any column values that average 0. Further to this, also remove ...
Part of the steepest descent algorithm
Perform matrix factorisation for phytoplankton pigments and pigments r...
Performs the non-negative matrix factorisation for given phytoplankton...
This function normalises each column in F to row sum
Normalise matrix to row sum
Phytoplankton Class Abundance Figure
Normalize F matrix specifically for Prochlorococcus pigments
Selects a random neighbour for a subset of non-zero pigments that are ...
Prochloro Wrangling
Select a random neighbour when the previous random neighbour is beyond...
Randomise value by applying scaling factors within specified bounds. S...
Select the new F matrix element with lowest error in the steepest desc...
Apply the steepest descent algorithm to optimize pigment ratios in phy...
Perform simulated annealing algorithm for samples with divinyl chlorop...
This is the main phytoclass algorithm. It performs simulated annealing...
Stand-alone version of steepest descent algorithm. This is similar to ...
Performs the steepest descent algorithm for a set number of iterations...
Vectorise a matrix and keep non-zero elements
Apply weights to F/S matrices by diagonal multiplication
Wrangle data to vectors
Determine the chlorophyll a (Chl a) concentrations of different phytoplankton groups based on their pigment biomarkers. The method uses non-negative matrix factorisation and simulated annealing to minimise error between the observed and estimated values of pigment concentrations (Hayward et al. (2023) <doi:10.1002/lom3.10541>). The approach is similar to the widely used 'CHEMTAX' program (Mackey et al. 1996) <doi:10.3354/meps144265>, but is more straightforward, accurate, and not reliant on initial guesses for the pigment to Chl a ratios for phytoplankton groups.
Useful links