Wrangling

Converts data-types and selects data for randomisation in
the simulated annealing algorithm

internal

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.

Alexander Hayward

phytoclass

Estimate Chla Concentrations of Phytoplankton Groups

Tylar Murray

Sebastian Di Geronimo

Mohd Aasim Maqsood Khan

Andy McKenzie

Wrangling function

<dl><dt>Fl</dt>
<dd>A matrix of the initial F matrix (i.e. pigment ratio matrix)</dd>
<dt>min.val</dt>
<dd>A vector of the minimum values for each non-zero pigment ratios</dd>
<dt>max.val</dt>
<dd>A vector of the maximum values for each non-zero pigment ratios</dd></dl>

Arguments

Wrangle data to vectors — Wrangling

<dl>

<dt>Fl</dt>
<dd>A matrix of the initial F matrix (i.e. pigment ratio matrix)</dd>


<dt>min.val</dt>
<dd>A vector of the minimum values for each non-zero pigment ratios</dd>


<dt>max.val</dt>
<dd>A vector of the maximum values for each non-zero pigment ratios</dd>

</dl>

Wrangling: Wrangle data to vectors

Description

Usage

Value

Arguments