phytoclass: Estimate Chla Concentrations of Phytoplankton Groups

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.

Version: 1.2.0
Depends: R (≥ 3.8)
Imports: bestNormalize, dplyr, dynamicTreeCut, ggplot2, Metrics, RcppML, stats, tidyr
Suggests: knitr, rmarkdown
Published: 2024-05-11
Author: Alexander Hayward [aut, cre, cph], Andy McKenzie [aut]
Maintainer: Alexander Hayward <phytoclass at>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: README NEWS
CRAN checks: phytoclass results


Reference manual: phytoclass.pdf
Vignettes: The phytoclass package


Package source: phytoclass_1.2.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): phytoclass_1.2.0.tgz, r-oldrel (arm64): phytoclass_1.2.0.tgz, r-release (x86_64): phytoclass_1.2.0.tgz, r-oldrel (x86_64): phytoclass_1.2.0.tgz
Old sources: phytoclass archive


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