## here() starts at /home/runner/work/phytoclass/phytoclass
# sample matrix
S_matrix <- read.csv(here("vignettes/custom-example-S.csv"), row.names = 1)
# pigment-taxa occurrence matrix (specific to an oceanographic region)
F_matrix <- read.csv(here("vignettes/custom-example-F.csv"))
# === remove numeric rownames introduced by read.csv
if (all(grepl("^[0-9]+$", rownames(F_matrix)))) {
print("dropping unneeded numeric index")
# Set the first column as row names
rownames(F_matrix) <- F_matrix[[1]]
# Remove the first column
F_matrix <- F_matrix[, -1]
}
## [1] "dropping unneeded numeric index"
min_max_matrix <- read.csv(here("vignettes/custom-example-min_max.csv"))
# === remove numeric rownames introduced by read.csv
if (all(grepl("^[0-9]+$", rownames(min_max_matrix)))) {
print("dropping unneeded numeric index")
# Set the first column as row names
rownames(min_max_matrix) <- min_max_matrix[[1]]
# Remove the first column
min_max_matrix <- min_max_matrix[, -1]
}
## [1] "dropping unneeded numeric index"
phytoclass::simulated_annealing(
S_matrix,
Fmat = F_matrix,
user_defined_min_max = min_max_matrix,
verbose = FALSE
)
## $`F matrix`
## Per X19but Fuco Neox Pra Viol
## Prasinophytes 0.0000 0.0000 0.00000000 0.1025489 0.0644515 0.09948707
## Chlorophytes 0.0000 0.0000 0.00000000 0.0141000 0.0000000 0.01500000
## Cryptophytes 0.0000 0.0000 0.00000000 0.0000000 0.0000000 0.00000000
## Diatoms-2 0.0000 0.0000 0.82131856 0.0000000 0.0000000 0.00000000
## Dinoflagellates-1 0.3529 0.0000 0.00000000 0.0000000 0.0000000 0.00000000
## Haptophytes 0.0000 0.1783 0.09899329 0.0000000 0.0000000 0.00000000
## Pelagophytes 0.0000 1.2731 1.13930000 0.0000000 0.0000000 0.00000000
## Syn 0.0000 0.0000 0.00000000 0.0000000 0.0000000 0.00000000
## X19hex Allo Zea Chl_b Tchla
## Prasinophytes 0.0000 0.0000 0.138995 0.6442477 1
## Chlorophytes 0.0000 0.0000 0.016600 0.1666537 1
## Cryptophytes 0.0000 0.3163 0.000000 0.0000000 1
## Diatoms-2 0.0000 0.0000 0.000000 0.0000000 1
## Dinoflagellates-1 0.0000 0.0000 0.000000 0.0000000 1
## Haptophytes 1.1858 0.0000 0.000000 0.0000000 1
## Pelagophytes 0.0000 0.0000 0.000000 0.0000000 1
## Syn 0.0000 0.0000 0.890600 0.0000000 1
##
## $RMSE
## [1] 0.01377313
##
## $`condition number`
## [1] 2209.591
##
## $`Class abundances`
## Prasinophytes Chlorophytes Cryptophytes Diatoms-2 Dinoflagellates-1
## Sample_1 0.03748538 0.293235675 0.005366237 0.04342503 0.000000e+00
## Sample_2 0.01353461 0.066061881 0.006326338 0.03441818 3.736584e-04
## Sample_3 0.01720883 0.279195924 0.020068214 0.26920888 3.764029e-04
## Sample_4 0.02846782 0.256104547 0.018581332 0.28779706 3.486677e-04
## Sample_5 0.07432741 0.055065488 0.005099832 0.35796337 3.089432e-04
## Sample_6 0.04940686 0.044386963 0.000000000 0.25218742 2.870037e-02
## Sample_7 0.03679178 0.001636643 0.002129818 0.14329585 0.000000e+00
## Sample_8 0.01984018 0.000000000 0.014472999 0.51957252 1.601840e-04
## Sample_9 0.02965853 0.000000000 0.192226784 0.72396695 1.678466e-04
## Sample_10 0.04304153 0.000000000 0.009133720 0.10751692 0.000000e+00
## Sample_11 0.21513807 0.000000000 0.094514369 0.59331621 0.000000e+00
## Sample_12 0.13358560 0.000000000 0.000000000 0.29835603 0.000000e+00
## Sample_13 0.12529787 0.000000000 0.000000000 0.17836029 0.000000e+00
## Sample_14 0.18639758 0.000000000 0.024347332 0.25495434 0.000000e+00
## Sample_15 0.33978072 0.000000000 0.114896803 0.81879342 1.599053e-03
## Sample_16 0.26707163 0.000000000 0.021833539 0.23363807 0.000000e+00
## Sample_17 0.62792512 0.068368932 0.056843594 0.82081996 1.389769e-03
## Sample_18 0.19270068 0.000000000 0.031147687 0.25558885 0.000000e+00
## Sample_19 0.37211329 0.000000000 0.063203430 0.50693976 3.086611e-04
## Sample_20 0.25417722 0.137666279 0.073471126 0.38002198 0.000000e+00
## Sample_21 0.33393208 0.000000000 0.053962669 0.44928263 1.478257e-04
## Sample_22 0.17958220 0.154967705 0.058048029 0.72834684 8.435887e-05
## Sample_23 0.15131737 0.108122519 0.046702637 0.51089818 3.023529e-04
## Sample_24 0.08944070 0.000000000 0.033615192 0.16142380 0.000000e+00
## Sample_25 0.12623146 0.004489137 0.044454049 0.21800281 7.746081e-05
## Sample_26 0.10589033 0.000000000 0.025385903 0.19027815 0.000000e+00
## Sample_27 0.06087435 0.000000000 0.017646123 0.12297711 0.000000e+00
## Sample_28 0.06322149 0.000000000 0.014653104 0.10617994 0.000000e+00
## Sample_29 0.11057866 0.039137465 0.027118621 0.06896198 0.000000e+00
## Haptophytes Pelagophytes Syn
## Sample_1 0.06567978 0.013317892 0.0000000000
## Sample_2 0.01633173 0.008663606 0.0000000000
## Sample_3 0.01576332 0.010878423 0.0000000000
## Sample_4 0.01701558 0.012384995 0.0000000000
## Sample_5 0.01902111 0.018413845 0.0000000000
## Sample_6 0.01591817 0.015100213 0.0000000000
## Sample_7 0.01971191 0.008133996 0.0000000000
## Sample_8 0.11399425 0.020459860 0.0000000000
## Sample_9 0.11336874 0.025511154 0.0000000000
## Sample_10 0.03435172 0.011956114 0.0000000000
## Sample_11 0.10127829 0.024245583 0.0111682098
## Sample_12 0.02451848 0.012155335 0.0125888833
## Sample_13 0.02287887 0.014153516 0.0002173421
## Sample_14 0.01590197 0.007688956 0.0000000000
## Sample_15 0.09639969 0.009694502 0.0000000000
## Sample_16 0.03285907 0.015712621 0.0000000000
## Sample_17 0.12796957 0.038022547 0.0000000000
## Sample_18 0.06664155 0.031591908 0.0000000000
## Sample_19 0.09581509 0.035550730 0.0000000000
## Sample_20 0.10328342 0.042280965 0.0000000000
## Sample_21 0.07702564 0.037697553 0.0000000000
## Sample_22 0.10897377 0.019465567 0.0000000000
## Sample_23 0.08068753 0.021035900 0.0000000000
## Sample_24 0.04753741 0.016638669 0.0000000000
## Sample_25 0.04718102 0.015206331 0.0000000000
## Sample_26 0.01791634 0.010302866 0.0000000000
## Sample_27 0.01783931 0.015833416 0.0015482170
## Sample_28 0.01770018 0.009240318 0.0007120534
## Sample_29 0.03821338 0.017458866 0.0000000000
##
## $Figure
##
## $MAE
## Per X19but Fuco Neox Pra Viol
## 4.875451e-05 9.258623e-06 1.886508e-03 2.676760e-03 1.632989e-02 5.127979e-03
## X19hex Allo Zea Chl_b Tchla
## 6.106915e-05 9.358228e-05 6.107067e-03 7.978379e-03 2.740068e-02
##
## $Error
## Per X19but Fuco Neox Pra
## Sample_1 0.000000e+00 -1.139163e-05 2.321121e-03 -0.0037941172 0.015340968
## Sample_2 -4.566398e-04 4.900642e-05 -9.985392e-03 -0.0030833660 0.012627856
## Sample_3 -1.315222e-04 1.411491e-05 -2.876010e-03 0.0011280399 0.008638287
## Sample_4 -1.179264e-04 1.265583e-05 -2.578711e-03 0.0008724480 0.009957096
## Sample_5 -1.064510e-04 1.142429e-05 -2.327776e-03 0.0020972306 0.008844578
## Sample_6 1.068012e-05 -1.146187e-06 2.335435e-04 0.0024917103 0.009978239
## Sample_7 0.000000e+00 -1.443915e-05 2.942076e-03 -0.0003043560 0.012267532
## Sample_8 -4.111363e-05 4.412301e-06 -8.990363e-04 0.0012814326 0.003920723
## Sample_9 -2.935684e-05 3.150566e-06 -6.419493e-04 0.0009632399 0.002834188
## Sample_10 0.000000e+00 -4.950896e-06 1.008779e-03 -0.0012719501 0.011899700
## Sample_11 0.000000e+00 -4.953458e-07 1.009301e-04 -0.0023823062 0.010223868
## Sample_12 0.000000e+00 -5.825544e-06 1.186994e-03 0.0036505144 0.011449773
## Sample_13 0.000000e+00 -4.815182e-07 9.811261e-05 -0.0009300230 0.016557192
## Sample_14 0.000000e+00 -2.267988e-05 4.621180e-03 -0.0011112194 0.032653739
## Sample_15 -2.025170e-04 2.173406e-05 -4.428462e-03 0.0032868651 0.012126660
## Sample_16 0.000000e+00 -4.850313e-06 9.882843e-04 -0.0031779816 0.041038328
## Sample_17 -1.368459e-04 1.468626e-05 -2.992424e-03 -0.0047952585 0.023013983
## Sample_18 0.000000e+00 -3.301445e-06 6.726919e-04 -0.0033568201 0.028539528
## Sample_19 -4.967129e-05 5.330705e-06 -1.086167e-03 -0.0042862800 0.025578424
## Sample_20 0.000000e+00 -8.447953e-06 1.721328e-03 -0.0062416164 0.017571392
## Sample_21 -2.688653e-05 2.885454e-06 -5.879308e-04 -0.0062347679 0.028865755
## Sample_22 -1.285593e-05 1.379694e-06 -2.811220e-04 -0.0035124168 0.009565478
## Sample_23 -6.111514e-05 6.558856e-06 -1.336412e-03 -0.0012074779 0.010197335
## Sample_24 0.000000e+00 -7.061633e-06 1.438856e-03 0.0053549531 0.009269251
## Sample_25 -3.029887e-05 3.251664e-06 -6.625487e-04 -0.0032175873 0.011680370
## Sample_26 0.000000e+00 -5.008646e-06 1.020546e-03 -0.0033893402 0.028375028
## Sample_27 0.000000e+00 -7.832874e-06 1.596001e-03 0.0010422497 0.018709048
## Sample_28 0.000000e+00 -8.403557e-06 1.712282e-03 -0.0015442504 0.021797436
## Sample_29 0.000000e+00 -1.159250e-05 2.362051e-03 -0.0016162205 0.020044936
## Viol X19hex Allo Zea Chl_b
## Sample_1 -0.0013138249 7.513826e-05 1.184292e-04 -1.148444e-02 0.012729446
## Sample_2 -0.0016745093 -3.232425e-04 -5.094789e-04 -1.796863e-03 -0.002650076
## Sample_3 -0.0058417911 -9.310086e-05 -1.467410e-04 -3.147349e-03 0.003276447
## Sample_4 -0.0063961357 -8.347683e-05 -1.315721e-04 -3.995547e-03 0.004577549
## Sample_5 -0.0080264408 -7.535369e-05 -1.187688e-04 -3.074494e-03 0.004406249
## Sample_6 -0.0074763084 7.560161e-06 0.000000e+00 -6.192615e-03 0.007755738
## Sample_7 -0.0032004482 9.523952e-05 1.501118e-04 -1.041510e-02 0.011519632
## Sample_8 -0.0014355804 -2.910319e-05 -4.587101e-05 -2.892551e-04 -0.002356079
## Sample_9 0.0005544567 -2.078089e-05 -3.275381e-05 -2.783851e-04 -0.003369005
## Sample_10 -0.0032723360 3.265572e-05 5.147034e-05 -7.329588e-03 0.007913348
## Sample_11 -0.0106743618 3.267262e-06 5.149697e-06 1.828935e-06 0.007089329
## Sample_12 -0.0142590445 3.842483e-05 0.000000e+00 2.150929e-05 0.003523884
## Sample_13 -0.0180560114 3.176056e-06 0.000000e+00 1.777880e-06 0.009026075
## Sample_14 -0.0093716505 1.495947e-04 2.357838e-04 -1.031677e-02 0.004921012
## Sample_15 0.0020162649 -1.433561e-04 -2.259508e-04 -2.225933e-03 -0.011817240
## Sample_16 -0.0002794560 3.199228e-05 5.042466e-05 -2.090806e-02 0.006893597
## Sample_17 0.0019083822 -9.686938e-05 -1.526807e-04 -1.595388e-02 0.010795498
## Sample_18 -0.0067924139 2.177607e-05 3.432237e-05 -8.720603e-03 0.004410311
## Sample_19 -0.0049926112 -3.516091e-05 -5.541890e-05 -1.389772e-02 0.013134761
## Sample_20 -0.0040073764 5.572203e-05 8.782632e-05 -9.969536e-03 0.014422979
## Sample_21 -0.0052754126 -1.903222e-05 -2.999765e-05 -1.384728e-02 0.013321727
## Sample_22 -0.0028472449 -9.100353e-06 -1.434353e-05 -4.231393e-03 0.006672512
## Sample_23 -0.0032797430 -4.326170e-05 -6.818695e-05 -5.363416e-03 0.005647952
## Sample_24 -0.0006806070 4.657797e-05 7.341390e-05 -2.532170e-04 -0.011151912
## Sample_25 -0.0037019255 -2.144772e-05 -3.380484e-05 -5.532622e-03 0.007691014
## Sample_26 -0.0060493409 3.303663e-05 5.207071e-05 -6.046795e-03 -0.000245508
## Sample_27 -0.0038907664 5.166502e-05 8.143186e-05 2.892084e-05 -0.009878255
## Sample_28 -0.0007278925 5.542920e-05 8.736477e-05 3.102793e-05 -0.012576418
## Sample_29 -0.0107090402 7.646323e-05 1.205176e-04 -1.174901e-02 0.017599429
## Tchla
## Sample_1 -0.033713248
## Sample_2 0.145033358
## Sample_3 0.041772756
## Sample_4 0.037454618
## Sample_5 0.033809907
## Sample_6 -0.003392114
## Sample_7 -0.042732336
## Sample_8 0.013058101
## Sample_9 0.009324027
## Sample_10 -0.014652061
## Sample_11 -0.001465964
## Sample_12 -0.017240560
## Sample_13 -0.001425042
## Sample_14 -0.067120578
## Sample_15 0.064321428
## Sample_16 -0.014354387
## Sample_17 0.043463628
## Sample_18 -0.009770549
## Sample_19 0.015776097
## Sample_20 -0.025001519
## Sample_21 0.008539432
## Sample_22 0.004083172
## Sample_23 0.019410780
## Sample_24 -0.020898736
## Sample_25 0.009623224
## Sample_26 -0.014822970
## Sample_27 -0.023181207
## Sample_28 -0.024870130
## Sample_29 -0.034307739