R: Estimate Chla Concentrations of Phytoplankton Groups

# Estimate Chla Concentrations of Phytoplankton Groups

## Documentation for package ‘phytoclass’ version 2.3.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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.