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phytoclass
View on CRAN: Click
here
Download and install phytoclass package within the R console
Install from CRAN:
install.packages("phytoclass")
Install from Github:
library("remotes")
install_github("cran/phytoclass") Install by package version:
library("remotes")
install_version("phytoclass", "2.0.0") Attach the package and use:
library("phytoclass")
Maintained by
Alexander Hayward
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-09-29
Latest Update: 2024-11-14
Description:
Determine the chlorophyll a (Chl a) biomass 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) ).
The approach is similar to the widely used 'CHEMTAX' program
(Mackey et al. 1996) , but is more straightforward,
accurate, and not reliant on initial guesses for the pigment to Chl a
ratios for each phytoplankton group.
How to cite:
Alexander Hayward (2023). phytoclass: Estimate Chla Concentrations of Phytoplankton Groups. R package version 2.0.0, https://cran.r-project.org/web/packages/phytoclass. Accessed 25 Aug. 2026.
Previous versions and publish date:
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imports, suggests or enhances
Complete documentation for phytoclass
Functions, R codes and Examples using
the phytoclass R package
Some associated functions: Bounded_weights . Cluster . Condition_test . Conduit_1 . Conduit_2 . Conduit_3 . Default_min_max . Fac_F_RR1 . Fac_F_RR2 . Fac_F_RR3 . Fm . Matrix_checks . Minimise_elements . Minimise_elements1 . Minimise_elements2 . NNLS_MF . NNLS_MF_Final . Normalise_F . Normalise_S . Random_neighbour . Random_neighbour2 . Randomise_elements . Replace_Rand . SAALS . Sm . Steepest_Desc . Steepest_Descent . Weight_error . Wrangling . min_max . simulated_annealing . target . vectorise .
Some associated R codes: Bounded_weights.R . Cluster.R . Condition_test.R . Conduit_1.R . Conduit_2.R . Conduit_3.R . Default_min_max.R . Fac_F_RR1.R . Fac_F_RR2.R . Fac_F_RR3.R . Matrix_checks.R . Minimise_elements.R . Minimise_elements1.R . Minimise_elements2.R . NNLS_MF.R . NNLS_MF_Final.R . Normalise_F.R . Normalise_S.R . Random_neighbour.R . Random_neighbour2.R . Randomise_elements.R . Replace_Rand.R . SAALS.R . Steepest_Desc.R . Steepest_Descent.R . Weight_error.R . Wrangling.R . data.R . simulated_annealing.R . target.R . vectorise.R . Full phytoclass package functions and examples
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