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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 |
Reference manual: | phytoclass.pdf |
Vignettes: |
The phytoclass package |
Package source: | phytoclass_1.2.0.tar.gz |
Windows binaries: | r-devel: phytoclass_1.2.0.zip, r-release: phytoclass_1.2.0.zip, r-oldrel: phytoclass_1.2.0.zip |
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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These binaries (installable software) and packages are in development.
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