The phytoclass package uses non-negative matrix factorization and simulated annealing to determine the biomass of different phytoplankton groups from pigment concentrations.
It can be installed from CRAN with:
install.packages("phytoclass")Or the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("AndyMcKenzieFromNZ/phytoclass")For the built-in samples matrix Sm of pigment samples:
library(phytoclass)
set.seed("84545")
Results <- simulated_annealing(Sm, niter = 5)
#>
#> Condition number = 390
#> Current error: 0.0283
#> Neighbour's error: 0.0283
#> Temperature (%): 99.1
#> [1] " "
#> Current error: 0.024
#> Neighbour's error: 0.024
#> Temperature (%): 98.21
#> [1] " "
#> Current error: 0.024
#> Neighbour's error: 0.0248
#> Temperature (%): 97.32
#> [1] " "
#> Current error: 0.024
#> Neighbour's error: 0.0266
#> Temperature (%): 96.45
#> [1] " "
#> Current error: 0.024
#> Neighbour's error: 0.0257
#> Temperature (%): 95.58
#> [1] " "
Results$RMSE
#> [1] 0.02402553
Results$MAE
#> Per X19but Fuco Neox Pra Viol
#> 3.471209e-03 1.423318e-05 5.395220e-04 8.540243e-03 6.235006e-03 2.153819e-02
#> X19hex Allo Zea Chl.b Tchla
#> 9.868784e-05 6.901592e-04 1.529518e-02 3.024765e-03 3.555499e-03
Results$Error
#> Per X19but Fuco Neox Pra
#> 1257 -2.016832e-04 2.555861e-05 -0.0089617928 -0.0088573156 0.0057854981
#> 1278 -4.000933e-04 5.070243e-05 -0.0177781490 -0.0050287416 0.0029692048
#> 1908 -2.629452e-04 3.332212e-05 -0.0116839694 -0.0022869672 0.0036127567
#> 1909 -2.343801e-04 2.970217e-05 -0.0104146790 -0.0020856447 0.0039330735
#> 1914 -5.734420e-05 7.267031e-06 -0.0025480900 0.0014803626 0.0022605199
#> 1915 -2.691132e-05 3.410378e-06 -0.0011958046 0.0015754724 0.0036692934
#> 5614 0.000000e+00 -1.441622e-05 0.0050548609 -0.0003748107 0.0039785042
#> 5647 0.000000e+00 -1.907135e-06 0.0006687121 0.0012341398 0.0020925046
#> 5653 0.000000e+00 -4.937718e-07 0.0001731347 0.0010131425 0.0011489899
#> 6770 0.000000e+00 -1.031987e-05 0.0036185272 -0.0009429398 0.0024941454
#> 8425 0.000000e+00 -4.826104e-06 0.0016922106 -0.0015747921 0.0009532809
#> 8426 0.000000e+00 -1.185224e-05 0.0041558352 0.0042948847 0.0015547195
#> 9538 0.000000e+00 -7.970628e-06 0.0027947972 0.0002394925 0.0018553239
#> 9568 0.000000e+00 -1.451985e-05 0.0050911975 -0.0001082795 0.0095320268
#> 9625 -8.283923e-05 -6.988029e-05 -0.0036809615 0.0042735702 0.0004537920
#> 9626 0.000000e+00 -5.766038e-06 0.0020217863 -0.0024167071 0.0143167572
#> 9838 -3.677364e-05 4.660196e-06 -0.0016340370 -0.0044467202 0.0057361770
#> 9839 0.000000e+00 -6.087732e-06 0.0021345842 -0.0027920763 0.0098255906
#> 9845 -3.619323e-06 4.586642e-07 -0.0001608246 -0.0033778541 0.0067249902
#> 9860 0.000000e+00 -3.437891e-06 0.0012054518 -0.0065380900 0.0035195542
#> 9861 0.000000e+00 -1.350248e-06 0.0004734470 -0.0055708210 0.0092787207
#> 9904 -2.734102e-05 3.464832e-06 -0.0012148983 -0.0039355274 0.0015618060
#> 9913 -3.292737e-05 4.172771e-06 -0.0014631278 -0.0017724637 0.0021516319
#> 9938 0.000000e+00 -1.236979e-05 0.0043373057 0.0063476391 -0.0001607775
#> 9980 0.000000e+00 -6.567464e-06 0.0023027958 -0.0029623708 0.0008925982
#> 10081 0.000000e+00 -5.246794e-06 0.0018397200 -0.0029268007 0.0102797984
#> 10082 0.000000e+00 -6.889093e-06 0.0024155710 0.0020369517 0.0047177666
#> 10089 0.000000e+00 -7.131170e-06 0.0025004522 -0.0003558590 0.0054162953
#> 10121 0.000000e+00 -1.334807e-05 0.0046803262 -0.0023168271 0.0041727702
#> Viol X19hex Allo Zea Chl.b
#> 1257 -0.0024269941 -3.711938e-04 -4.409828e-04 -1.120497e-02 0.015353185
#> 1278 -0.0021616075 -7.363636e-04 -8.748092e-04 -2.370467e-03 0.002087823
#> 1908 -0.0067722402 -4.839452e-04 -5.749329e-04 -3.373919e-03 0.005189338
#> 1909 -0.0071833294 -4.313717e-04 -5.124750e-04 -4.215064e-03 0.006222377
#> 1914 -0.0075942703 -1.055408e-04 -1.253838e-04 -1.743049e-03 0.003904737
#> 1915 -0.0072936003 -4.952973e-05 -5.884194e-05 -5.185266e-03 0.006005577
#> 5614 -0.0026324549 2.093703e-04 2.487345e-04 -9.104614e-03 0.009501780
#> 5647 -0.0014681990 2.769778e-05 3.290531e-05 -3.594214e-04 -0.003185980
#> 5653 0.0006155274 7.171168e-06 8.519438e-06 -2.165362e-04 -0.003564019
#> 6770 -0.0024095732 1.498779e-04 1.780568e-04 -5.719746e-03 0.007581382
#> 8425 -0.0093803479 7.009066e-05 8.326859e-05 2.827730e-05 0.009681932
#> 8426 -0.0123283981 1.721330e-04 0.000000e+00 6.944515e-05 0.005687787
#> 9538 -0.0158033847 1.157593e-04 0.000000e+00 4.670183e-05 0.012753453
#> 9568 -0.0082235070 2.108753e-04 2.505225e-04 -9.037484e-03 0.004185448
#> 9625 0.0033144315 -9.905241e-05 -1.811290e-04 -2.966061e-04 -0.009022583
#> 9626 0.0006596631 8.374155e-05 9.948601e-05 -1.996796e-02 0.003618368
#> 9838 0.0031349282 -6.768114e-05 -8.040604e-05 -1.372653e-02 0.010039291
#> 9839 -0.0061039172 8.841360e-05 1.050365e-04 -8.019459e-03 0.002309205
#> 9845 -0.0039680721 -6.661290e-06 -7.913696e-06 -1.273194e-02 0.013087472
#> 9860 -0.0031299818 4.992932e-05 5.931665e-05 -8.148555e-03 0.015364147
#> 9861 -0.0044837767 1.960998e-05 2.329690e-05 -1.301483e-02 0.011566731
#> 9904 -0.0023630976 -5.032059e-05 -5.978149e-05 -3.089930e-03 0.007837740
#> 9913 -0.0027060704 -6.060215e-05 -7.199611e-05 -3.810046e-03 0.005754947
#> 9938 0.0012556180 1.796494e-04 2.134258e-04 7.247757e-05 -0.007040581
#> 9980 -0.0022312429 9.538085e-05 1.133136e-04 -2.360653e-03 0.007530935
#> 10081 -0.0054650329 7.620044e-05 9.052708e-05 -5.481875e-03 -0.002786379
#> 10082 -0.0028179810 1.000520e-04 1.188630e-04 4.036486e-05 -0.007959213
#> 10089 0.0005513200 1.035677e-04 1.230397e-04 4.178324e-05 -0.010184592
#> 10121 -0.0091840014 1.938572e-04 2.303048e-04 -7.841625e-03 0.015989165
#> Tchla
#> 1257 0.130654395
#> 1278 0.259188462
#> 1908 0.170341134
#> 1909 0.151836089
#> 1914 0.037148723
#> 1915 0.017433690
#> 5614 -0.073695053
#> 5647 -0.009749185
#> 5653 -0.002524139
#> 6770 -0.052754676
#> 8425 -0.024670817
#> 8426 -0.060588115
#> 9538 -0.040745478
#> 9568 -0.074224805
#> 9625 0.053664909
#> 9626 -0.029475716
#> 9838 0.023822701
#> 9839 -0.031120203
#> 9845 0.002344670
#> 9860 -0.017574337
#> 9861 -0.006902406
#> 9904 0.017712059
#> 9913 0.021331008
#> 9938 -0.063233782
#> 9980 -0.033572568
#> 10081 -0.026821364
#> 10082 -0.035216723
#> 10089 -0.036454209
#> 10121 -0.068234694
Results$`F matrix`
#> Per X19but Fuco Neox Pra Viol X19hex Allo
#> Prasinophytes 0.0000 0.0000 0.0000 0.0960 0.1734 0.0923 0.0000 0.0000
#> Chlorophytes 0.0000 0.0000 0.0000 0.0502 0.0000 0.0311 0.0000 0.0000
#> Cryptophytes 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3292
#> Diatoms-B 0.0000 0.0000 0.8244 0.0000 0.0000 0.0000 0.0000 0.0000
#> Dinoflagellates-A 0.7198 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
#> Haptophytes 0.0000 0.2513 0.0637 0.0000 0.0000 0.0000 0.9634 0.0000
#> Pelagophytes 0.0000 0.3376 0.8734 0.0000 0.0000 0.0000 0.0000 0.0000
#> Syn 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
#> Zea Chl.b Tchla
#> Prasinophytes 0.1305 0.6366 1
#> Chlorophytes 0.0228 0.2891 1
#> Cryptophytes 0.0000 0.0000 1
#> Diatoms-B 0.0000 0.0000 1
#> Dinoflagellates-A 0.0000 0.0000 1
#> Haptophytes 0.0000 0.0000 1
#> Pelagophytes 0.0000 0.0000 1
#> Syn 0.9694 0.0000 1
Results$`Class abudances`
#> NULL
Results$Figure