Phytoclass uses three input matrices:
S : The pigment values from field samples.F : Defines which pigments are present in each
taxa.min_max : Specifies limits of taxa contributions for
each pigment.The F and min_max matrices built into
phytoclass are designed for general use. Specifying maxtrices tailored
to a specific study region can improve accuracy of results.
In this example we provide an F and min_max
matrices which have been derived from a standard deviation calculation
on pigment-to-chlorophyll ratios found in literature about the Southern
Ocean.
## here() starts at /tmp/Rtmp3VGVUk/Rbuild13d91b36abed/phytoclass
# Load the sample matrix from a file
# If your file does not contain sample names (e.g., Sample_1, Sample_2), you may omit `row.names = 1`
# In that case, do: S_matrix <- read.csv(here("vignettes/custom-example-S.csv"))
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"), row.names = 1)# === 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]]
}phytoclass::simulated_annealing(
S_matrix,
Fmat = F_matrix,
user_defined_min_max = min_max_matrix,
verbose = FALSE
)## $`F matrix`
## Per X19but Fuco Neox Pra
## Prasinophytes 0.0000000 0.0000000 0.00000000 0.102428436 0.2421075
## Chlorophytes 0.0000000 0.0000000 0.00000000 0.009413437 0.0000000
## Cryptophytes 0.0000000 0.0000000 0.00000000 0.000000000 0.0000000
## Diatoms-2 0.0000000 0.0000000 0.78701366 0.000000000 0.0000000
## Dinoflagellates-1 0.3451638 0.0000000 0.00000000 0.000000000 0.0000000
## Haptophytes 0.0000000 0.1971387 0.03493175 0.000000000 0.0000000
## Pelagophytes 0.0000000 0.4193069 0.74492589 0.000000000 0.0000000
## Syn 0.0000000 0.0000000 0.00000000 0.000000000 0.0000000
## Viol X19hex Allo Zea Chl_b Tchla
## Prasinophytes 0.08260286 0.000000 0.0000000 0.05660803 0.9012857 1
## Chlorophytes 0.01538102 0.000000 0.0000000 0.00688907 0.1666030 1
## Cryptophytes 0.00000000 0.000000 0.4061315 0.00000000 0.0000000 1
## Diatoms-2 0.00000000 0.000000 0.0000000 0.00000000 0.0000000 1
## Dinoflagellates-1 0.00000000 0.000000 0.0000000 0.00000000 0.0000000 1
## Haptophytes 0.00000000 1.262069 0.0000000 0.00000000 0.0000000 1
## Pelagophytes 0.00000000 0.000000 0.0000000 0.00000000 0.0000000 1
## Syn 0.00000000 0.000000 0.0000000 1.20685098 0.0000000 1
##
## $RMSE
## [1] 0.01530537
##
## $`condition number`
## [1] 1628.089
##
## $`Class abundances`
## Prasinophytes Chlorophytes Cryptophytes Diatoms-2 Dinoflagellates-1
## Sample_1 0.05650641 0.241887091 5.092608e-03 0.04168265 0.0002568489
## Sample_2 0.01486470 0.052820847 5.169872e-03 0.02744531 0.0004875421
## Sample_3 0.03730465 0.206832547 1.739272e-02 0.29741004 0.0009658856
## Sample_4 0.04816692 0.178828079 1.619352e-02 0.31749748 0.0009596431
## Sample_5 0.05777593 0.048031927 3.808512e-03 0.34413004 0.0002545762
## Sample_6 0.04687670 0.016063488 5.078412e-05 0.25022875 0.0301706271
## Sample_7 0.03059019 0.000000000 1.641580e-03 0.13729116 0.0000000000
## Sample_8 0.01610296 0.000000000 1.058378e-02 0.50026471 0.0000000000
## Sample_9 0.02237900 0.000000000 1.494261e-01 0.72919178 0.0001592983
## Sample_10 0.03255430 0.003808178 6.912803e-03 0.09563034 0.0000000000
## Sample_11 0.14206800 0.065543072 7.118349e-02 0.57388394 0.0000000000
## Sample_12 0.08631156 0.031883878 0.000000e+00 0.28571727 0.0000000000
## Sample_13 0.08060284 0.032143280 0.000000e+00 0.15765177 0.0000000000
## Sample_14 0.15524890 0.000000000 1.991379e-02 0.26778265 0.0000000000
## Sample_15 0.23381934 0.047863082 9.043753e-02 0.86363134 0.0018633317
## Sample_16 0.23534714 0.000000000 1.790728e-02 0.23620442 0.0000621864
## Sample_17 0.48452817 0.183930085 4.295104e-02 0.79766849 0.0011283355
## Sample_18 0.15893472 0.000000000 2.442882e-02 0.22977039 0.0000000000
## Sample_19 0.31566277 0.000000000 5.055630e-02 0.50252749 0.0005791177
## Sample_20 0.20021133 0.163107981 5.684902e-02 0.34331679 0.0000000000
## Sample_21 0.28597498 0.000000000 4.279399e-02 0.43124487 0.0003036162
## Sample_22 0.13497710 0.179813012 4.416667e-02 0.72684444 0.0000000000
## Sample_23 0.11180382 0.134830364 3.529374e-02 0.49709397 0.0001040103
## Sample_24 0.05703512 0.015541322 2.608724e-02 0.14866929 0.0000000000
## Sample_25 0.07331180 0.079931463 3.084222e-02 0.18534866 0.0000000000
## Sample_26 0.08713494 0.000000000 2.013930e-02 0.18907121 0.0000000000
## Sample_27 0.04458766 0.000000000 1.378258e-02 0.10766478 0.0000000000
## Sample_28 0.04698013 0.000000000 1.170658e-02 0.10190682 0.0000000000
## Sample_29 0.07834034 0.067780574 2.016809e-02 0.04747516 0.0000000000
## Haptophytes Pelagophytes Syn
## Sample_1 0.06912237 0.04396202 0.0000000000
## Sample_2 0.01620345 0.02752672 0.0011915564
## Sample_3 0.01628856 0.03586986 0.0006357385
## Sample_4 0.01762811 0.04095719 0.0004690620
## Sample_5 0.01762445 0.05491635 0.0036582245
## Sample_6 0.01534686 0.04671551 0.0002472775
## Sample_7 0.01821820 0.02395887 0.0000000000
## Sample_8 0.10264686 0.05779052 0.0011111629
## Sample_9 0.10634553 0.07548920 0.0019090993
## Sample_10 0.03146268 0.03483737 0.0007943281
## Sample_11 0.09223684 0.06978273 0.0249626623
## Sample_12 0.02228901 0.03534118 0.0196614308
## Sample_13 0.02032674 0.04034348 0.0098397806
## Sample_14 0.01553645 0.02386164 0.0069467456
## Sample_15 0.09177748 0.02841859 0.0233535118
## Sample_16 0.03220316 0.04910133 0.0002894285
## Sample_17 0.11796140 0.11144949 0.0017224710
## Sample_18 0.06295087 0.09530365 0.0062822327
## Sample_19 0.09229812 0.10902582 0.0032813412
## Sample_20 0.09633776 0.12570538 0.0053727292
## Sample_21 0.07358933 0.11506647 0.0030751431
## Sample_22 0.10039250 0.05622890 0.0070458544
## Sample_23 0.07396266 0.06109376 0.0048841622
## Sample_24 0.04447610 0.04950782 0.0073388844
## Sample_25 0.03982645 0.04088648 0.0054951992
## Sample_26 0.01710939 0.03145979 0.0048589559
## Sample_27 0.01678360 0.04782461 0.0060752978
## Sample_28 0.01699483 0.02834233 0.0057763943
## Sample_29 0.03435180 0.05012387 0.0032291334
##
## $Figure
##
## $MAE
## Per X19but Fuco Neox Pra Viol
## 6.621820e-05 5.007408e-06 2.538870e-03 2.698336e-03 2.405541e-03 3.329999e-03
## X19hex Allo Zea Chl_b Tchla
## 7.373981e-05 9.072222e-05 2.198464e-04 5.633395e-03 3.533571e-02
##
## $Error
## Per X19but Fuco Neox Pra
## Sample_1 -1.113648e-04 -4.902467e-06 -0.0024856620 -0.0027136690 1.550716e-03
## Sample_2 -5.521565e-04 -2.430687e-05 -0.0123241371 -0.0016785001 3.840329e-03
## Sample_3 -3.018133e-04 -1.328634e-05 -0.0067364749 0.0015514377 1.560145e-03
## Sample_4 -2.894579e-04 -1.274243e-05 -0.0064607015 0.0013487251 1.524782e-03
## Sample_5 -8.692333e-05 -3.826513e-06 -0.0019401291 0.0039961030 -3.152600e-04
## Sample_6 -3.171644e-05 -1.396212e-06 -0.0007079111 0.0036443472 -5.885990e-04
## Sample_7 0.000000e+00 7.268680e-06 0.0036853860 0.0012034547 -4.495797e-04
## Sample_8 0.000000e+00 1.196558e-06 0.0006066823 0.0015100694 1.893495e-03
## Sample_9 -2.729377e-05 -1.201518e-06 -0.0006091972 0.0013327705 1.092047e-03
## Sample_10 0.000000e+00 3.858570e-06 0.0019563825 0.0010120742 -7.678029e-04
## Sample_11 0.000000e+00 2.492320e-06 0.0012636632 0.0008203519 -5.481197e-04
## Sample_12 0.000000e+00 4.818828e-06 0.0024432555 0.0082225602 -2.460981e-03
## Sample_13 0.000000e+00 4.119812e-06 0.0020888384 0.0045906498 -1.594415e-03
## Sample_14 0.000000e+00 6.746104e-06 0.0034204279 0.0030814606 5.829817e-03
## Sample_15 -2.278117e-04 -1.002866e-05 -0.0050847589 0.0071488326 -6.574673e-05
## Sample_16 -1.794752e-05 -7.900803e-07 -0.0004005887 0.0005217023 8.388577e-03
## Sample_17 -1.106977e-04 -4.873101e-06 -0.0024707729 -0.0011577252 9.633602e-04
## Sample_18 0.000000e+00 1.020403e-06 0.0005173677 -0.0003321671 6.614821e-03
## Sample_19 -8.894506e-05 -3.915513e-06 -0.0019852542 -0.0012722459 2.508512e-03
## Sample_20 0.000000e+00 4.091135e-06 0.0020742985 -0.0031114624 7.650853e-05
## Sample_21 -5.313422e-05 -2.339059e-06 -0.0011859560 -0.0034372647 4.853818e-03
## Sample_22 0.000000e+00 9.099757e-07 0.0004613784 -0.0014479157 1.769530e-04
## Sample_23 -2.106552e-05 -9.273402e-07 -0.0004701826 0.0010892932 -9.971933e-05
## Sample_24 0.000000e+00 3.266431e-06 0.0016561547 0.0099728998 -2.577082e-03
## Sample_25 0.000000e+00 6.576747e-06 0.0033345602 0.0010274511 -1.157925e-03
## Sample_26 0.000000e+00 9.613220e-07 0.0004874121 -0.0003217127 7.735417e-03
## Sample_27 0.000000e+00 3.196360e-06 0.0016206272 0.0046523391 3.981807e-03
## Sample_28 0.000000e+00 2.000197e-06 0.0010141453 0.0027552718 4.663389e-03
## Sample_29 0.000000e+00 8.155293e-06 0.0041349188 0.0032972763 -1.880957e-03
## Viol X19hex Allo Zea Chl_b
## Sample_1 -0.0004298167 -7.219442e-05 -9.464688e-05 -3.434797e-03 0.0007344641
## Sample_2 -0.0002745570 -3.579465e-04 -4.692678e-04 -1.579188e-04 -0.0071620186
## Sample_3 -0.0056696162 -1.956565e-04 -2.565056e-04 -8.631970e-05 -0.0013092408
## Sample_4 -0.0058805682 -1.876468e-04 -2.460050e-04 -8.278601e-05 -0.0009122801
## Sample_5 -0.0054518304 -5.634978e-05 -7.387455e-05 -2.486039e-05 0.0006933311
## Sample_6 -0.0053834859 -2.056081e-05 -2.695522e-05 -9.071016e-06 0.0015895356
## Sample_7 -0.0004465512 1.070396e-04 1.403289e-04 -2.076379e-03 0.0015389136
## Sample_8 -0.0010089627 1.762069e-05 2.310072e-05 7.773894e-06 -0.0040685655
## Sample_9 0.0010992201 -1.769373e-05 -2.319648e-05 -7.806118e-06 -0.0039112796
## Sample_10 0.0002209585 5.682185e-05 7.449343e-05 2.506865e-05 0.0007250114
## Sample_11 -0.0065529828 3.670227e-05 4.811667e-05 1.619230e-05 0.0047542800
## Sample_12 -0.0084410460 7.096275e-05 0.000000e+00 3.130734e-05 0.0038033165
## Sample_13 -0.0109401673 6.066894e-05 0.000000e+00 2.676592e-05 0.0066423036
## Sample_14 -0.0025249594 9.934409e-05 1.302401e-04 4.382861e-05 -0.0114685257
## Sample_15 0.0070456829 -1.476835e-04 -1.936130e-04 -6.515498e-05 -0.0107277598
## Sample_16 0.0066093419 -1.163484e-05 -1.525327e-05 -5.133055e-06 -0.0205938866
## Sample_17 0.0074450253 -7.176198e-05 -9.407994e-05 -3.165994e-05 -0.0059842829
## Sample_18 -0.0016103286 1.502661e-05 1.969988e-05 6.629436e-06 -0.0111462235
## Sample_19 0.0002865825 -5.766041e-05 -7.559278e-05 -2.543861e-05 -0.0041398909
## Sample_20 0.0003972449 6.024664e-05 7.898333e-05 2.657960e-05 0.0023274566
## Sample_21 -0.0001302521 -3.444532e-05 -4.515780e-05 -1.519658e-05 -0.0064822338
## Sample_22 -0.0002542666 1.340043e-05 1.756796e-05 5.912001e-06 0.0010410841
## Sample_23 -0.0003640991 -1.365614e-05 -1.790320e-05 -6.024816e-06 -0.0005021954
## Sample_24 0.0050610187 4.810193e-05 6.306162e-05 2.122160e-05 -0.0061809272
## Sample_25 0.0013215744 9.685011e-05 1.269705e-04 4.272832e-05 0.0008990225
## Sample_26 -0.0009442533 1.415656e-05 1.855925e-05 6.245591e-06 -0.0137072429
## Sample_27 0.0012149722 4.707005e-05 6.170883e-05 2.076636e-05 -0.0118508532
## Sample_28 0.0053146335 2.945518e-05 3.861574e-05 1.299503e-05 -0.0143372562
## Sample_29 -0.0042459727 1.200960e-04 1.574458e-04 5.298394e-05 0.0041350802
## Tchla
## Sample_1 0.034595172
## Sample_2 0.171525988
## Sample_3 0.093757518
## Sample_4 0.089919335
## Sample_5 0.027002504
## Sample_6 0.009852629
## Sample_7 -0.051292798
## Sample_8 -0.008443738
## Sample_9 0.008478740
## Sample_10 -0.027228718
## Sample_11 -0.017587525
## Sample_12 -0.034004962
## Sample_13 -0.029072224
## Sample_14 -0.047605141
## Sample_15 0.070769116
## Sample_16 0.005575350
## Sample_17 0.034387947
## Sample_18 -0.007200668
## Sample_19 0.027630550
## Sample_20 -0.028869860
## Sample_21 0.016506006
## Sample_22 -0.006421414
## Sample_23 0.006543949
## Sample_24 -0.023050180
## Sample_25 -0.046410043
## Sample_26 -0.006783748
## Sample_27 -0.022555711
## Sample_28 -0.014114763
## Sample_29 -0.057549346
##
## $F_mat_iter
## iter phyto pigment ratio
## 1 0 Dinoflagellates-1 Per 1.000000000
## 2 0 Haptophytes X19but 1.000000000
## 3 0 Pelagophytes X19but 1.000000000
## 4 0 Diatoms-2 Fuco 1.000000000
## 5 0 Haptophytes Fuco 1.000000000
## 6 0 Pelagophytes Fuco 1.000000000
## 7 0 Prasinophytes Neox 1.000000000
## 8 0 Chlorophytes Neox 1.000000000
## 9 0 Prasinophytes Pra 1.000000000
## 10 0 Prasinophytes Viol 1.000000000
## 11 0 Chlorophytes Viol 1.000000000
## 12 0 Haptophytes X19hex 1.000000000
## 13 0 Cryptophytes Allo 1.000000000
## 14 0 Prasinophytes Zea 1.000000000
## 15 0 Chlorophytes Zea 1.000000000
## 16 0 Syn Zea 1.000000000
## 17 0 Prasinophytes Chl_b 1.000000000
## 18 0 Chlorophytes Chl_b 1.000000000
## 19 0 Prasinophytes Tchla 1.000000000
## 20 0 Chlorophytes Tchla 1.000000000
## 21 0 Cryptophytes Tchla 1.000000000
## 22 0 Diatoms-2 Tchla 1.000000000
## 23 0 Dinoflagellates-1 Tchla 1.000000000
## 24 0 Haptophytes Tchla 1.000000000
## 25 0 Pelagophytes Tchla 1.000000000
## 26 0 Syn Tchla 1.000000000
## 27 6 Dinoflagellates-1 Per 0.450500000
## 28 6 Haptophytes X19but 0.186800000
## 29 6 Pelagophytes X19but 1.186800000
## 30 6 Diatoms-2 Fuco 0.814600000
## 31 6 Haptophytes Fuco 0.368000000
## 32 6 Pelagophytes Fuco 0.927700000
## 33 6 Prasinophytes Neox 0.061700000
## 34 6 Chlorophytes Neox 0.028600000
## 35 6 Prasinophytes Pra 0.221500000
## 36 6 Prasinophytes Viol 0.029900000
## 37 6 Chlorophytes Viol 0.036300000
## 38 6 Haptophytes X19hex 0.668800000
## 39 6 Cryptophytes Allo 0.378900000
## 40 6 Prasinophytes Zea 0.031500000
## 41 6 Chlorophytes Zea 0.018400000
## 42 6 Syn Zea 0.919900000
## 43 6 Prasinophytes Chl_b 0.754600000
## 44 6 Chlorophytes Chl_b 0.303900000
## 45 6 Prasinophytes Tchla 1.000000000
## 46 6 Chlorophytes Tchla 1.000000000
## 47 6 Cryptophytes Tchla 1.000000000
## 48 6 Diatoms-2 Tchla 1.000000000
## 49 6 Dinoflagellates-1 Tchla 1.000000000
## 50 6 Haptophytes Tchla 1.000000000
## 51 6 Pelagophytes Tchla 1.000000000
## 52 6 Syn Tchla 1.000000000
## 53 11 Dinoflagellates-1 Per 0.450500000
## 54 11 Haptophytes X19but 0.186800000
## 55 11 Pelagophytes X19but 1.186800000
## 56 11 Diatoms-2 Fuco 0.814600000
## 57 11 Haptophytes Fuco 0.368000000
## 58 11 Pelagophytes Fuco 0.927700000
## 59 11 Prasinophytes Neox 0.061700000
## 60 11 Chlorophytes Neox 0.028600000
## 61 11 Prasinophytes Pra 0.221500000
## 62 11 Prasinophytes Viol 0.029900000
## 63 11 Chlorophytes Viol 0.036300000
## 64 11 Haptophytes X19hex 0.668800000
## 65 11 Cryptophytes Allo 0.378900000
## 66 11 Prasinophytes Zea 0.031500000
## 67 11 Chlorophytes Zea 0.018400000
## 68 11 Syn Zea 0.919900000
## 69 11 Prasinophytes Chl_b 0.754600000
## 70 11 Chlorophytes Chl_b 0.303900000
## 71 11 Prasinophytes Tchla 1.000000000
## 72 11 Chlorophytes Tchla 1.000000000
## 73 11 Cryptophytes Tchla 1.000000000
## 74 11 Diatoms-2 Tchla 1.000000000
## 75 11 Dinoflagellates-1 Tchla 1.000000000
## 76 11 Haptophytes Tchla 1.000000000
## 77 11 Pelagophytes Tchla 1.000000000
## 78 11 Syn Tchla 1.000000000
## 79 16 Dinoflagellates-1 Per 0.344800000
## 80 16 Haptophytes X19but 0.208500000
## 81 16 Pelagophytes X19but 1.431367770
## 82 16 Diatoms-2 Fuco 0.908600000
## 83 16 Haptophytes Fuco 0.132700000
## 84 16 Pelagophytes Fuco 0.502900000
## 85 16 Prasinophytes Neox 0.100300000
## 86 16 Chlorophytes Neox 0.037900000
## 87 16 Prasinophytes Pra 0.167100000
## 88 16 Prasinophytes Viol 0.029400000
## 89 16 Chlorophytes Viol 0.029700000
## 90 16 Haptophytes X19hex 1.061100000
## 91 16 Cryptophytes Allo 0.274900000
## 92 16 Prasinophytes Zea 0.136200000
## 93 16 Chlorophytes Zea 0.028100000
## 94 16 Syn Zea 0.633800000
## 95 16 Prasinophytes Chl_b 0.594400000
## 96 16 Chlorophytes Chl_b 0.241800000
## 97 16 Prasinophytes Tchla 1.000000000
## 98 16 Chlorophytes Tchla 1.000000000
## 99 16 Cryptophytes Tchla 1.000000000
## 100 16 Diatoms-2 Tchla 1.000000000
## 101 16 Dinoflagellates-1 Tchla 1.000000000
## 102 16 Haptophytes Tchla 1.000000000
## 103 16 Pelagophytes Tchla 1.000000000
## 104 16 Syn Tchla 1.000000000
## 105 21 Dinoflagellates-1 Per 0.344800000
## 106 21 Haptophytes X19but 0.208500000
## 107 21 Pelagophytes X19but 1.431367770
## 108 21 Diatoms-2 Fuco 0.908600000
## 109 21 Haptophytes Fuco 0.132700000
## 110 21 Pelagophytes Fuco 0.502900000
## 111 21 Prasinophytes Neox 0.100300000
## 112 21 Chlorophytes Neox 0.037900000
## 113 21 Prasinophytes Pra 0.167100000
## 114 21 Prasinophytes Viol 0.029400000
## 115 21 Chlorophytes Viol 0.029700000
## 116 21 Haptophytes X19hex 1.061100000
## 117 21 Cryptophytes Allo 0.274900000
## 118 21 Prasinophytes Zea 0.136200000
## 119 21 Chlorophytes Zea 0.028100000
## 120 21 Syn Zea 0.633800000
## 121 21 Prasinophytes Chl_b 0.594400000
## 122 21 Chlorophytes Chl_b 0.241800000
## 123 21 Prasinophytes Tchla 1.000000000
## 124 21 Chlorophytes Tchla 1.000000000
## 125 21 Cryptophytes Tchla 1.000000000
## 126 21 Diatoms-2 Tchla 1.000000000
## 127 21 Dinoflagellates-1 Tchla 1.000000000
## 128 21 Haptophytes Tchla 1.000000000
## 129 21 Pelagophytes Tchla 1.000000000
## 130 21 Syn Tchla 1.000000000
## 131 26 Dinoflagellates-1 Per 0.350400000
## 132 26 Haptophytes X19but 0.097800000
## 133 26 Pelagophytes X19but 0.715900000
## 134 26 Diatoms-2 Fuco 0.875200000
## 135 26 Haptophytes Fuco 0.078900000
## 136 26 Pelagophytes Fuco 0.902100000
## 137 26 Prasinophytes Neox 0.072200000
## 138 26 Chlorophytes Neox 0.013400000
## 139 26 Prasinophytes Pra 0.208100000
## 140 26 Prasinophytes Viol 0.082600000
## 141 26 Chlorophytes Viol 0.028700000
## 142 26 Haptophytes X19hex 0.947300000
## 143 26 Cryptophytes Allo 0.309400000
## 144 26 Prasinophytes Zea 0.063100000
## 145 26 Chlorophytes Zea 0.007900000
## 146 26 Syn Zea 0.446200000
## 147 26 Prasinophytes Chl_b 0.750600000
## 148 26 Chlorophytes Chl_b 0.179952011
## 149 26 Prasinophytes Tchla 1.000000000
## 150 26 Chlorophytes Tchla 1.000000000
## 151 26 Cryptophytes Tchla 1.000000000
## 152 26 Diatoms-2 Tchla 1.000000000
## 153 26 Dinoflagellates-1 Tchla 1.000000000
## 154 26 Haptophytes Tchla 1.000000000
## 155 26 Pelagophytes Tchla 1.000000000
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## 2516 485 Chlorophytes Tchla 1.000000000
## 2517 485 Cryptophytes Tchla 1.000000000
## 2518 485 Diatoms-2 Tchla 1.000000000
## 2519 485 Dinoflagellates-1 Tchla 1.000000000
## 2520 485 Haptophytes Tchla 1.000000000
## 2521 485 Pelagophytes Tchla 1.000000000
## 2522 485 Syn Tchla 1.000000000
## 2523 490 Dinoflagellates-1 Per 0.345163767
## 2524 490 Haptophytes X19but 0.197138664
## 2525 490 Pelagophytes X19but 0.419306873
## 2526 490 Diatoms-2 Fuco 0.787013661
## 2527 490 Haptophytes Fuco 0.034931748
## 2528 490 Pelagophytes Fuco 0.744925892
## 2529 490 Prasinophytes Neox 0.102428436
## 2530 490 Chlorophytes Neox 0.009413437
## 2531 490 Prasinophytes Pra 0.242107505
## 2532 490 Prasinophytes Viol 0.082602860
## 2533 490 Chlorophytes Viol 0.015381019
## 2534 490 Haptophytes X19hex 1.262069226
## 2535 490 Cryptophytes Allo 0.406131519
## 2536 490 Prasinophytes Zea 0.056608032
## 2537 490 Chlorophytes Zea 0.006889070
## 2538 490 Syn Zea 1.206850980
## 2539 490 Prasinophytes Chl_b 0.901285691
## 2540 490 Chlorophytes Chl_b 0.166603044
## 2541 490 Prasinophytes Tchla 1.000000000
## 2542 490 Chlorophytes Tchla 1.000000000
## 2543 490 Cryptophytes Tchla 1.000000000
## 2544 490 Diatoms-2 Tchla 1.000000000
## 2545 490 Dinoflagellates-1 Tchla 1.000000000
## 2546 490 Haptophytes Tchla 1.000000000
## 2547 490 Pelagophytes Tchla 1.000000000
## 2548 490 Syn Tchla 1.000000000
## 2549 495 Dinoflagellates-1 Per 0.345163767
## 2550 495 Haptophytes X19but 0.197138664
## 2551 495 Pelagophytes X19but 0.419306873
## 2552 495 Diatoms-2 Fuco 0.787013661
## 2553 495 Haptophytes Fuco 0.034931748
## 2554 495 Pelagophytes Fuco 0.744925892
## 2555 495 Prasinophytes Neox 0.102428436
## 2556 495 Chlorophytes Neox 0.009413437
## 2557 495 Prasinophytes Pra 0.242107505
## 2558 495 Prasinophytes Viol 0.082602860
## 2559 495 Chlorophytes Viol 0.015381019
## 2560 495 Haptophytes X19hex 1.262069226
## 2561 495 Cryptophytes Allo 0.406131519
## 2562 495 Prasinophytes Zea 0.056608032
## 2563 495 Chlorophytes Zea 0.006889070
## 2564 495 Syn Zea 1.206850980
## 2565 495 Prasinophytes Chl_b 0.901285691
## 2566 495 Chlorophytes Chl_b 0.166603044
## 2567 495 Prasinophytes Tchla 1.000000000
## 2568 495 Chlorophytes Tchla 1.000000000
## 2569 495 Cryptophytes Tchla 1.000000000
## 2570 495 Diatoms-2 Tchla 1.000000000
## 2571 495 Dinoflagellates-1 Tchla 1.000000000
## 2572 495 Haptophytes Tchla 1.000000000
## 2573 495 Pelagophytes Tchla 1.000000000
## 2574 495 Syn Tchla 1.000000000
## 2575 500 Dinoflagellates-1 Per 0.345163767
## 2576 500 Haptophytes X19but 0.197138664
## 2577 500 Pelagophytes X19but 0.419306873
## 2578 500 Diatoms-2 Fuco 0.787013661
## 2579 500 Haptophytes Fuco 0.034931748
## 2580 500 Pelagophytes Fuco 0.744925892
## 2581 500 Prasinophytes Neox 0.102428436
## 2582 500 Chlorophytes Neox 0.009413437
## 2583 500 Prasinophytes Pra 0.242107505
## 2584 500 Prasinophytes Viol 0.082602860
## 2585 500 Chlorophytes Viol 0.015381019
## 2586 500 Haptophytes X19hex 1.262069226
## 2587 500 Cryptophytes Allo 0.406131519
## 2588 500 Prasinophytes Zea 0.056608032
## 2589 500 Chlorophytes Zea 0.006889070
## 2590 500 Syn Zea 1.206850980
## 2591 500 Prasinophytes Chl_b 0.901285691
## 2592 500 Chlorophytes Chl_b 0.166603044
## 2593 500 Prasinophytes Tchla 1.000000000
## 2594 500 Chlorophytes Tchla 1.000000000
## 2595 500 Cryptophytes Tchla 1.000000000
## 2596 500 Diatoms-2 Tchla 1.000000000
## 2597 500 Dinoflagellates-1 Tchla 1.000000000
## 2598 500 Haptophytes Tchla 1.000000000
## 2599 500 Pelagophytes Tchla 1.000000000
## 2600 500 Syn Tchla 1.000000000
##
## $converge_plot