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'))

Peer review:

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

Datasets:

On CRAN:

4.78 score 1 stars 6 scripts 159 downloads 7 exports 86 dependencies

Last updated 9 days agofrom:d0e781697e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winOKNov 14 2024
R-4.4-macOKNov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:Bounded_weightsClusterMatrix_checksNNLS_MFsimulated_annealingsimulated_annealing_ProchloroSteepest_Desc

Dependencies:bestNormalizebutcherclasscliclockcodetoolscolorspacecpp11crayondata.tablediagramdigestdoParalleldoRNGdplyrdynamicTreeCutfansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelingLambertWlamWlatticelavalifecyclelistenvlobstrlubridatemagrittrMASSMatrixMetricsmgcvmunsellnlmennetnortestnumDerivparallellypillarpkgconfigplyrprettyunitsprodlimprogressrpurrrR6RColorBrewerRcppRcppEigenRcppMLRcppParallelrecipesreshape2rlangrngtoolsrpartscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

The phytoclass package

Rendered fromphytoclass-vignette.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-04-30
Started: 2023-08-29