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 + fileLICENSE |
| URL: | https://github.com/phytoclass/phytoclass/ |
| NeedsCompilation: | no |
| Materials: | README,NEWS |
| CRAN checks: | phytoclass results |
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