Cluster

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

Cluster function

<dl><dt>Data</dt>
<dd>S (sample) matrix</dd>
<dt>minSamplesPerCluster</dt>
<dd>the minimum number of samples required for a cluster</dd>
<dt>row_ids</dt>
<dd>A vector of custom row names to be added to dendrogram</dd>
<dt>dist_method</dt>
<dd>Distance metric to be used in <code><a href="/link/stats%3A%3Adist?package=phytoclass&version=2.3.1" data-mini-rdoc="phytoclass::stats::dist">stats::dist</a></code>. This should
be one of "euclidean", "maximum", "manhattan", "canberra",
"binary" or "minkowski".</dd>
<dt>hclust_method</dt>
<dd>Cluster method to be used in <code><a href="/link/stats%3A%3Ahclust?package=phytoclass&version=2.3.1" data-mini-rdoc="phytoclass::stats::hclust">stats::hclust</a></code>. This
should be one of "ward.D", "ward.D2", "single",
"complete", "average" (= UPGMA), "mcquitty" (= WPGMA),
"median" (= WPGMC) or "centroid" (= UPGMC).</dd></dl>

Arguments

Cluster things — Cluster

<dl>

<dt>Data</dt>
<dd>S (sample) matrix</dd>


<dt>minSamplesPerCluster</dt>
<dd>the minimum number of samples required for a cluster</dd>


<dt>row_ids</dt>
<dd>A vector of custom row names to be added to dendrogram</dd>


<dt>dist_method</dt>
<dd>Distance metric to be used in <code><a href='https://rdrr.io/r/stats/dist.html'>stats::dist</a></code>. This should
be one of "euclidean", "maximum", "manhattan", "canberra",
"binary" or "minkowski".</dd>


<dt>hclust_method</dt>
<dd>Cluster method to be used in <code><a href='https://rdrr.io/r/stats/hclust.html'>stats::hclust</a></code>. This
should be one of "ward.D", "ward.D2", "single",
"complete", "average" (= UPGMA), "mcquitty" (= WPGMA),
"median" (= WPGMC) or "centroid" (= UPGMC).</dd>

</dl>

Cluster things

Cluster: Cluster things

Description

Usage

Value

Arguments

Examples