phytoclass (version 2.3.1)

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.

Description

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.

Usage

simulated_annealing_Prochloro(
  S,
  Fmat = NULL,
  user_defined_min_max = NULL,
  do_matrix_checks = TRUE,
  niter = 500,
  step = 0.009,
  weight.upper.bound = 30,
  verbose = TRUE,
  seed = NULL,
  check_converge = 100
)

Value

A list containing

1. Fmat matrix

2. RMSE (Root Mean Square Error)

3. condition number

4. Class abundances

5. Figure (plot of results)

6. MAE (Mean Absolute Error)

7. Error

Arguments

S

Sample data matrix – a matrix of pigment samples

Fmat

Pigment to Chl a matrix

user_defined_min_max

data frame with some format as min_max built-in data

do_matrix_checks

This should only be set to TRUE when using the default values. This will remove pigment columns that have column sums of 0. Set to FALSE if using customised names for pigments and phytoplankton groups

niter

Number of iterations (default is 500)

step

Step ratio used (default is 0.009)

weight.upper.bound

Upper limit of the weights applied (default value is 30).

verbose

Logical value. Output error and temperature at each iteration. Default value of TRUE

seed

Set seed number to reproduce the same results

check_converge

TRUE/FALSE/integer; set the number of F matrices to for convergence checking

Examples

# Using the built-in matrices Sp and Fp.
set.seed(5326)
sa.example <- simulated_annealing_Prochloro(Sp, Fp, niter = 1)
sa.example$Figure