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: | 2.3.1 |
| Depends: | R (≥ 3.8) |
| Imports: | bestNormalize, dynamicTreeCut, ggplot2, RcppML, stats, tidyr, progress |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0), quarto, here |
| Published: | 2026-01-30 |
| DOI: | 10.32614/CRAN.package.phytoclass |
| Author: | Alexander Hayward [aut, cre, cph], Tylar Murray [aut], Sebastian Di Geronimo [aut], Mohd Aasim Maqsood Khan [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 |
| Reference manual: | phytoclass.html , phytoclass.pdf |
| Vignettes: |
Common Issues : F Matrix (source, R code) Custom F Matrices (source, R code) Minimal Example (source, R code) Default MinMax Values (source, R code) The phytoclass package (source, R code) |
| Package source: | phytoclass_2.3.1.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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