This function ensures S and F matrices are properly formatted and ordered for the simulated annealing function.

Some checks applied:

• drops columns with 0 values

• drops taxa with missing major pigments, which are indicated with a '2'

• drops pigments with < 1% in samples

Usage

Matrix_checks(S, Fmat)

Arguments

S

Sample data matrix – a matrix of pigment samples

Fmat

Pigment to taxa matrix

Value

Named list with new S and Fmat matrices

Examples

MC <- Matrix_checks(Sm, Fm)  
#> Removing pigments that occur in less than 1% of samples: Per, X19but, Fuco, Neox, Pra, Viol, X19hex, Allo, Zea, Chl_b, Tchla
#> Removing phytoplankton taxa that map to one pigment or less:
Snew <- MC$Snew