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:	2.0.0
Depends:	R (≥ 3.8)
Imports:	bestNormalize, dplyr, dynamicTreeCut, ggplot2, Metrics, RcppML, stats, tidyr
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0)
Published:	2024-11-14
DOI:	10.32614/CRAN.package.phytoclass
Author:	Alexander Hayward [aut, cre, cph], Tylar Murray [aut], Andy McKenzie [aut]
Maintainer:	Alexander Hayward <phytoclass at outlook.com>
BugReports:	https://github.com/phytoclass/phytoclass/issues/
License:	MIT + file LICENSE
URL:	https://github.com/phytoclass/phytoclass/
NeedsCompilation:	no
Materials:	README NEWS
CRAN checks:	phytoclass results

Documentation:

Reference manual:	phytoclass.pdf
Vignettes:	The phytoclass package (source, R code)

Downloads:

Package source:	phytoclass_2.0.0.tar.gz
Windows binaries:	r-devel: phytoclass_2.0.0.zip, r-release: phytoclass_2.0.0.zip, r-oldrel: phytoclass_2.0.0.zip
macOS binaries:	r-release (arm64): phytoclass_2.0.0.tgz, r-oldrel (arm64): phytoclass_2.0.0.tgz, r-release (x86_64): phytoclass_2.0.0.tgz, r-oldrel (x86_64): phytoclass_2.0.0.tgz
Old sources:	phytoclass archive

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