Estimate Chla Concentrations of Phytoplankton Groups

Documentation for package ‘phytoclass’ version 2.3.1

Bounded_weights	Add weights to the data, bound at a maximum.
Cluster	Cluster things
convergence_figure	Convergence Figure
Fm	Fm data
Fp	Fp data
Matrix_checks	Remove any column values that average 0. Further to this, also remove phytoplankton groups from the F matrix if their diagnostic pigment isn’t present.
min_max	min_max data
NNLS_MF	Performs the non-negative matrix factorisation for given phytoplankton pigments and pigment ratios, to attain an estimate of phytoplankton class abundances.
phyto_figure	Phytoplankton Class Abundance Figure
simulated_annealing	This is the main phytoclass algorithm. It performs simulated annealing algorithm for S and F matrices. See the examples (Fm, Sm) for how to set up matrices, and the vignette for more detailed instructions. Different pigments and phytoplankton groups may be used.
simulated_annealing_Prochloro	Perform simulated annealing algorithm for samples with divinyl chlorophyll and prochlorococcus. Chlorophyll must be the final column of both S and F matrices, with Divinyl Chlorophyll a the 2nd to last column. See how the example Sp and Fp matrices are organised.
Sm	Sm data
Sp	Sp data
Steepest_Desc	Stand-alone version of steepest descent algorithm. This is similar to the CHEMTAX steepest descent algorithm. It is not required to use this function, and as results are not bound by minimum and maximum, results may be unrealistic.