Package: phytoclass 2.0.0

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], Andy McKenzie [aut]

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phytoclass.pdf |phytoclass.html✨
phytoclass/json (API)
NEWS

# 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:

5.88 score 2 stars 9 scripts 624 downloads 7 exports 87 dependencies

Last updated 21 days agofrom:5646df6dd4. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 06 2025
R-4.5-winOKMar 06 2025
R-4.5-macOKMar 06 2025
R-4.5-linuxOKMar 06 2025
R-4.4-winOKMar 06 2025
R-4.4-macOKMar 06 2025
R-4.4-linuxOKMar 06 2025
R-4.3-winOKMar 06 2025
R-4.3-macOKMar 06 2025

Exports:Bounded_weightsClusterMatrix_checksNNLS_MFsimulated_annealingsimulated_annealing_ProchloroSteepest_Desc

Dependencies:bestNormalizebutcherclasscliclockcodetoolscolorspacecpp11crayondata.tablediagramdigestdoParalleldoRNGdplyrdynamicTreeCutfansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelingLambertWlamWlatticelavalifecyclelistenvlobstrlubridatemagrittrMASSMatrixMetricsmgcvmunsellnlmennetnortestnumDerivparallellypillarpkgconfigplyrprettyunitsprodlimprogressrpurrrR6RColorBrewerRcppRcppEigenRcppMLRcppParallelrecipesreshape2rlangrngtoolsrpartscalesshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Common Issues : F Matrix

Rendered fromcommon-issues-f-matrix.Rmdusingknitr::rmarkdownon Mar 06 2025.

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

Example Usage : custom F & MinMax Matrices

Rendered fromcustom-example.Rmdusingknitr::rmarkdownon Mar 06 2025.

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

Example : Minimal

Rendered fromminimal-example.Rmdusingknitr::rmarkdownon Mar 06 2025.

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

Table of Default F MinMax Values

Rendered fromminmax.Rmdusingknitr::rmarkdownon Mar 06 2025.

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

The phytoclass package

Rendered fromphytoclass-vignette.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-18
Started: 2023-08-29