Performs the non-negative matrix factorisation for given phytoplankton pigments and pigment ratios, to attain an estimate of phytoplankton class abundances.
Source:R/NNLS_MF.R
NNLS_MF.RdPerforms the non-negative matrix factorisation for given phytoplankton pigments and pigment ratios, to attain an estimate of phytoplankton class abundances.
Value
A list containing
The F matrix (pigment: Chl a) ratios
The root mean square error (RMSE)
The C matrix (class abundances for each group)
Examples
MC <- Matrix_checks(Sm,Fm)
Snew <- MC$Snew
Fnew <- MC$Fnew
cm <- Bounded_weights(Snew, weight.upper.bound = 30)
NNLS_MF(Fnew, Snew, cm)
#> $`F matrix `
#> Per X19but Fuco Neox Pra Viol X19hex Allo Zea Chl_b Tchla
#> Prasinophytes 0 0 0 1 1 1 0 0 1 1 1
#> Chlorophytes 0 0 0 1 0 1 0 0 1 1 1
#> Cryptophytes 0 0 0 0 0 0 0 1 0 0 1
#> Diatoms-2 0 0 1 0 0 0 0 0 0 0 1
#> Dinoflagellates-1 1 0 0 0 0 0 0 0 0 0 1
#> Haptophytes 0 1 1 0 0 0 1 0 0 0 1
#> Pelagophytes 0 1 1 0 0 0 0 0 0 0 1
#> Syn 0 0 0 0 0 0 0 0 1 0 1
#>
#> $RMSE
#> [1] 0.1127568
#>
#> $`C matrix`
#> Prasinophytes Chlorophytes Cryptophytes Diatoms-2 Dinoflagellates-1
#> [1,] 0.088117948 0.00000000 0.0217204089 0.4901801 0.0037567947
#> [2,] 0.055584649 0.00000000 0.0373938768 0.6222451 0.0027804911
#> [3,] 0.023402989 0.00000000 0.0237891848 0.8898721 0.0015045577
#> [4,] 0.025080760 0.00000000 0.0208394859 0.8879702 0.0013748370
#> [5,] 0.027278768 0.00000000 0.0050338409 0.8891283 0.0007088272
#> [6,] 0.024427004 0.00000000 0.0006420380 0.8482800 0.0403115206
#> [7,] 0.029818901 0.00000000 0.0056863026 0.8501687 0.0004333909
#> [8,] 0.006998486 0.00000000 0.0097623255 0.8482667 0.0004993785
#> [9,] 0.007273723 0.00000000 0.0834778062 0.8126633 0.0005630781
#> [10,] 0.041423150 0.00000000 0.0248502005 0.7213906 0.0007292296
#> [11,] 0.033785036 0.00000000 0.0480895900 0.7854960 0.0007137484
#> [12,] 0.047211598 0.00000000 0.0005753971 0.8297532 0.0005753971
#> [13,] 0.065913285 0.00000000 0.0008208615 0.7888618 0.0008208615
#> [14,] 0.088836617 0.00000000 0.0299819886 0.8287089 0.0006540520
#> [15,] 0.058417376 0.00000000 0.0440282484 0.8389594 0.0009788646
#> [16,] 0.125844391 0.00000000 0.0258929304 0.7449531 0.0010843156
#> [17,] 0.085675844 0.00000000 0.0205483370 0.7943691 0.0012253888
#> [18,] 0.080155362 0.00000000 0.0327531006 0.6997688 0.0009135323
#> [19,] 0.077226096 0.00000000 0.0355593296 0.7586179 0.0010293554
#> [20,] 0.065007214 0.00000000 0.0509516342 0.7059805 0.0011235075
#> [21,] 0.078274256 0.00000000 0.0339483113 0.7547636 0.0009751164
#> [22,] 0.031530158 0.00000000 0.0263143309 0.8543388 0.0008336558
#> [23,] 0.037075351 0.00000000 0.0290232371 0.8314658 0.0009196788
#> [24,] 0.062767108 0.00151289 0.0562106906 0.6948740 0.0008153781
#> [25,] 0.058367609 0.00000000 0.0575224093 0.7466852 0.0009684633
#> [26,] 0.069420509 0.00000000 0.0401302883 0.8048198 0.0007330733
#> [27,] 0.060138593 0.00000000 0.0395615803 0.7292408 0.0006281012
#> [28,] 0.075116512 0.00000000 0.0391858968 0.7480381 0.0007317574
#> [29,] 0.109413008 0.00000000 0.0750124557 0.5374235 0.0015472772
#> Haptophytes Pelagophytes Syn
#> [1,] 0.39622477 0.00000000 0.0000000000
#> [2,] 0.28199589 0.00000000 0.0000000000
#> [3,] 0.06143118 0.00000000 0.0000000000
#> [4,] 0.06473471 0.00000000 0.0000000000
#> [5,] 0.06518414 0.01266611 0.0000000000
#> [6,] 0.07389414 0.01244533 0.0000000000
#> [7,] 0.11389271 0.00000000 0.0000000000
#> [8,] 0.13447311 0.00000000 0.0000000000
#> [9,] 0.09602212 0.00000000 0.0000000000
#> [10,] 0.21160678 0.00000000 0.0000000000
#> [11,] 0.10185148 0.00000000 0.0300641351
#> [12,] 0.07127730 0.00000000 0.0506071021
#> [13,] 0.11859426 0.00000000 0.0249889572
#> [14,] 0.05181846 0.00000000 0.0000000000
#> [15,] 0.05761614 0.00000000 0.0000000000
#> [16,] 0.10222524 0.00000000 0.0000000000
#> [17,] 0.09818131 0.00000000 0.0000000000
#> [18,] 0.18640925 0.00000000 0.0000000000
#> [19,] 0.12756732 0.00000000 0.0000000000
#> [20,] 0.17693716 0.00000000 0.0000000000
#> [21,] 0.13203875 0.00000000 0.0000000000
#> [22,] 0.08698308 0.00000000 0.0000000000
#> [23,] 0.10151595 0.00000000 0.0000000000
#> [24,] 0.18371728 0.00000000 0.0001026917
#> [25,] 0.13645632 0.00000000 0.0000000000
#> [26,] 0.08489631 0.00000000 0.0000000000
#> [27,] 0.14672943 0.01494256 0.0087589477
#> [28,] 0.13363978 0.00000000 0.0032879586
#> [29,] 0.27660378 0.00000000 0.0000000000
#>