Package index • phytoclass

All functions

Bounded_weights(): Add weights to the data, bound at a maximum.

Cluster(): Cluster things

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.

NNLS_MF(): Performs the non-negative matrix factorisation for given phytoplankton pigments and pigment ratios, to attain an estimate of phytoplankton class abundances.

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.

convergence_figure(): Convergence Figure

min_max: min_max data

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.