Package: phytoclass 3.0.0

Alexander Hayward

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.

Authors:Alexander Hayward [aut, cre, cph], Tylar Murray [aut], Sebastian Di Geronimo [aut], Mohd Aasim Maqsood Khan [aut], Andy McKenzie [aut]

phytoclass_3.0.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phytoclass/json (API)

# Install 'phytoclass' in R:
install.packages('phytoclass', repos = c('https://phytoclass.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/phytoclass/phytoclass/issues

Datasets:

On CRAN:

Conda:

6.90 score 3 stars 14 scripts 154 downloads 7 exports 84 dependencies

Last updated from:3c2df0d2ea. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK166
source / vignettesOK261
linux-release-x86_64OK193
macos-release-arm64OK204
macos-oldrel-arm64OK213
windows-develOK97
windows-releaseOK94
windows-oldrelOK98
wasm-releaseOK136

Exports:Bounded_weightsClusterMatrix_checksNNLS_MFsimulated_annealingsimulated_annealing_ProchloroSteepest_Desc

Dependencies:bestNormalizebutcherclasscliclockcodetoolscpp11crayondata.tablediagramdigestdoParalleldoRNGdplyrdynamicTreeCutfarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhathmsipredisobanditeratorsKernSmoothlabelingLambertWlamWlatticelavalifecyclelistenvlobstrlubridatemagrittrMASSMatrixnnetnortestnumDerivparallellypillarpkgconfigplyrprettyunitsprodlimprogressprogressrpurrrR6RColorBrewerRcppRcppEigenRcppMLRcppParallelrecipesreshape2rlangrngtoolsrpartS7scalesshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Example Usage : Custom F & MinMax Matrices
Rendered fromcustom-example.Rmdusingknitr::rmarkdown

Last update: 2026-04-10
Started: 2025-02-18

The phytoclass package
Introduction | Main function: simulated_annealing() | Cluster function | Example without clustering | Example with clustering | Example using non-default values | Helper functions | Matrix_checks | Steep_Desc | Bounded_weights | NNLS_MF | References
Rendered fromphytoclass-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-04-10
Started: 2023-08-29

Example : Minimal
Preparing the S Matrix | Simulated Annealing | Viewing Results
Rendered fromminimal-example.Rmdusingknitr::rmarkdown

Last update: 2025-07-10
Started: 2025-02-18

Common Issues : F Matrix
non-conformable arguments | non-numeric argument to binary operator | x needs two+ dimensions | subscript out of bounds: | 'x' must be numeric
Rendered fromcommon-issues-f-matrix.Rmdusingknitr::rmarkdown

Last update: 2025-05-19
Started: 2025-02-18

Table of Default F MinMax Values
Rendered fromminmax.Rmdusingknitr::rmarkdown

Last update: 2025-05-19
Started: 2025-02-18