convergence_figure

A figure to show the pigment ratios for each phytoplankton group for each
iteration.

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

convergence_figure function

<dl><dt>fm_iter</dt>
<dd>A data.frame with columns of iter, phyto, pigment and ratio</dd>
<dt>niter</dt>
<dd>Optional: the number of iterations on the x axis.
If <code>NULL</code>, will extract from the <code>iter</code> column of <code>fm_iter</code>.</dd></dl>

Arguments

Convergence Figure — convergence_figure

<dl>

<dt>fm_iter</dt>
<dd>A data.frame with columns of iter, phyto, pigment and ratio</dd>


<dt>niter</dt>
<dd>Optional: the number of iterations on the x axis.
If <code>NULL</code>, will extract from the <code>iter</code> column of <code>fm_iter</code>.</dd>

</dl>

convergence_figure: Convergence Figure

Description

Usage

Value

Arguments

Examples