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 |
| DOI: |
10.32614/CRAN.package.phytoclass |
| Author: |
Alexander Hayward [aut, cre, cph],
Andy McKenzie [aut] |
| Maintainer: |
Alexander Hayward <phytoclass at outlook.com> |
| BugReports: |
https://github.com/AndyMcKenzieFromNZ/phytoclass/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/AndyMcKenzieFromNZ/phytoclass |
| NeedsCompilation: |
no |
| Materials: |
README NEWS |
| CRAN checks: |
phytoclass results |
Documentation:
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