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Improvements in the use of Chemtax to estimate Pigment Biomass of different Phytoplankton Groups

Improvements in the use of Chemtax to estimate Pigment Biomass of different Phytoplankton Groups. Input. CHEMTAX: a program to estimate the contribution of each phytoplankton group to the Chl a pool. Output. The program adjusts pigment ratios to reach a minimum variance

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Improvements in the use of Chemtax to estimate Pigment Biomass of different Phytoplankton Groups

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  1. Improvements in the use of Chemtax to estimate Pigment Biomass of different Phytoplankton Groups

  2. Input CHEMTAX: a program to estimate the contribution of each phytoplankton group to the Chl a pool

  3. Output

  4. The program adjusts pigment ratios to reach a minimum variance • Neural networks: The problem of the local minima Local minima CHEMTAX: the output is VERY dependent of the seed values WHY? 2. The settings are adjusted to optimize computer effort / results (5-9 hours to make a single run in 1996)

  5. So, CHEMTAX is 1) dependent of the seed values 2) optimized for the computer effort Alternative: I increase the computer effort (1-7 min) to - try to avoid the local minima and, therefore, - make the output independent from the seed values

  6. “Standard” conditions +------------- CHEMTAX Preprocessor -------------- (c) 1996 CSIRO -------------------------+ Data File: aro1\data.txt View Data Ratio File:aro1\ratio1.txt View Ratios Ratio Limit File:aro1\aro500.rlm View Limits Diary File:data.txt Output options Weighting: Bounded relative error by pigment Comments Iteration Limit: 500 Verbosity: Normal Epsilon Limit: 0.0500 Elements varied: 5 Initial Step Size: 10 Subiterations: 5 Step ratio: 1.3000 Weight Bound: 30 Cutoff Step: 1000 Save as default Output <Enter> to overwrite, <F2> to edit, <F1> for help or <ESC> to exit +----------------------------------------------------------------------------------------------------+

  7. “Modified” conditions +------------- CHEMTAX Preprocessor -------------- (c) 1996 CSIRO -------------------------+ Data File: aro1\data.txt View Data Ratio File:aro1\ratio1.txt View Ratios Ratio Limit File:aro1\aro500.rlm View Limits Diary File:data.txt Output options Weighting: Bounded relative error by pigment Comments Iteration Limit: 500 10000 Verbosity: Normal Epsilon Limit: 0.05000.0001 Elements varied: 510 (all pigments) Initial Step Size: 1025 Subiterations: 51 Step ratio: 1.3000 2 Weight Bound:30 5-10 Cutoff Step: 1000 30000 Save as default Output <Enter> to overwrite, <F2> to edit, <F1> for help or <ESC> to exit +----------------------------------------------------------------------------------------------------+

  8. Material and methods An artificial randomly generated pigment dataset based on specific pigment ratios Several (9) initial pigment: chlorophyll ratios were used as seed values. 1: Double of the true ratios 2: Half of the true ratios 3: A mixture of 1 and 2 4: Random but “reasonable” ratios (some times 10 times the true ratios) 5: Ratios were 0.75, 0.50 and 0.25 for dominant, important and minor pigments, respectively 6: A mixture of ratios from the literature 7: Ratios from Letelier et al (1994) for the DCM of Hawaii 8: Ratios from Mackey et al (1996) for the Southern Ocean 9: Ratios from Everitt et al (1990) for the western Equatorial Pacific 8-12 successive runs of CHEMTAX were performed starting with each of these initial values The output of one run was the modified seed matrix for the next run

  9. Simplifications: - No methodological errors were introduced (no noise) - The user identified correctly all and only the pigment groups that were present

  10. 1.062 0.229 Results

  11. 0.945 0.315

  12. Zea:Chl a (Pras) 0.100 Serie1 0.090 Serie2 Serie3 0.080 Serie4 0.070 Serie5 Serie6 0.060 Serie7 Serie8 Ratio 0.050 Serie9 0.040 0.030 0.010 0.348 0.020 0.010 0.000 1 2 3 4 5 6 7 8 9 10 11 12 Runs

  13. 0.585 0.754

  14. 0.246 1.703

  15. 70 Original Rat310 60 Rat711 50 40 Chl a 30 20 10 0 PRAS DINO CRYP HAPT3 HAPT4 SYN DIAT 70 Original 60 Rat32 Rat72 50 Chl a 40 30 20 10 0 PRAS DINO CRYP HAPT3 HAPT4 SYN DIAT

  16. Conclusions Mackey et al (1996) limit the "validity" of CHEMTAX to the use of initial seeds within a 25% of the true value The successive runs of CHEMTAX, under the used conditions, greatly improved initial guesses and, therefore, biomass estimates Groups with single pigment markers adjusted perfectly their pigment ratios Problems appeared for groups sharing common pigments. In this case the less abundant group had a tendency to become underestimated A very clear indication that the new values were “wrong” could be seen in that the output for these ratios did not stabilize, contrarily to what occurred with the other ratios Therefore, when the ratios for a single group keep diverging with successive runs, an educated guess for those values is proposed The work is still in progress…

  17. 70 Original 60 Rat712 50 40 Chl a 30 20 10 0 PRAS DINO CRYP HAPT3 HAPT4 SYN DIAT

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