Estimate Chla Concentrations of Phytoplankton Groups
Add weights to the data, bound at a maximum.
Cluster things
Calculate the condition number ...
Conduit between minimise_elements function and Fac_F_R of steepest des...
Conduit between minimise_elements function and Fac_F_R of steepest des...
Conduit between minimise_elements function and Fac_F_R of steepest des...
Sets the default minimum and maximum values for phytoplankton groups p...
Part of the steepest descent algorithm and work to reduce error given ...
Part of the steepest descent algorithm and work to reduce error given ...
Part of the steepest descent algorithm and work to reduce error given ...
Remove any column values that average 0. Further to this, also remove ...
Part of the steepest descent algorithm
A function that reduces every for every element that didn't reduce in ...
A function that reduces every for every element that didn't reduce in ...
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
This function normalises each column in S to row sum
Final step for MF with prochlorococcus
Normalise F for prochloro
Selects a random neighbour for the simulated annealing algorithm.
Prochloro random neighbour
Prochloro Wrangling
Select a random neighbour when the previous random neighbour is beyond...
Selects a random neighbour for the simulated annealing algorithm.
Randomise individual elements in the F matrix.
Select the new F matrix element with lowest error in the steepest desc...
Apply the steepest descent algorithm
Perform simulated annealing algorithm for S and F matrices
Phytoclass - simualted annealing
Stand-alone version of steepest descent algorithm. This is similar to ...
Performs the steepest descent algorithm for a set number of iterations
Title
Turn each non-zero element of the F-matrix into a vector
Apply weights to F/S matrices
Converts data-types and selects data for randomisation in the simulate...
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