In what follows, we define a set of ocean test cases for Active Transfer Learning. The test cases are intended to be not too simple but not too complicated, so that ideas can be generated and tested, and algorithms and methods evaluated, in fast but relevant enough situations. We provide three types of cases, as well as software to run them and/or actual data sets.This page presents a simplified (e.g., largely non-mathematical) version of the setup and underlying "story" for example 0 of test case 2 (Learning for 2-D Biogeochemical Dynamical Systems). It is not definitive, but it may serve as a useful conceptual introduction.
This is the fraction of the Phytoplankton that becomes part of the the grazing Zooplankton; the rest returns to the stock of Nutrients.
This controls the fraction of Phytoplankton that is available for grazing (in the Ivlev predation model).
This controls the amount of light that is available at a given depth and thus the maximum amount of photosynthesis that Phytoplankton can perform.
This is the daily grazing rate by Zooplankton of Phytoplankton.
This is the daily death rate for Phytoplankton (Zooplankton). The resulting biomass returns to the stock of Nutrients.
This is the maximum daily uptake rate by Phytoplankton of Nutrients.
Together with the amount of available Nutrients, this controls the actual uptake rate by Phytoplankton of Nutrients.
dZ). This is calculated based on four common terms (
Z_deatheach appear twice, with opposite signs.
Z_grazeappears three times, but the mass taken from Phytoplankton is split between the Zooplankton and Nutrients:
dN = - P_uptake + P_death + Z_death + Z_graze * (1-a) dP = + P_uptake - P_death - Z_graze dZ = - Z_death + Z_graze * aNow, let's look at the definitions and effects of these terms:
P_uptake(uptake by Phytoplankton of Nutrients)
This depends on the ratio of Phytoplankton to Nutrients and the amount of sunlight at this depth. It decreases the mass of Nutrients and increases the mass of Phytoplankton.
P_death(natural death of Phytoplankton)
This depends on the mass of Phytoplankton. It increases the mass of Nutrients and decreases the mass of Phytoplankton.
Z_death(natural death of Zooplankton)
This depends on the mass of Zooplankton. It increases the mass of Nutrients and decreases the mass of Zooplankton.
Z_graze(grazing by Zooplankton on Phytoplankton)
This depends on the relative masses of Zooplankton and Phytoplankton. It increases the masses of Nutrients and Zooplankton and decreases the mass of Phytoplankton.
P_uptake = U * exp(z/h) * (P*N) / (N+ks) # P uptake of N P_death = P * dp # P natural death Z_death = Z * dz # Z natural death Z_graze = Z * gv * (1-exp(-v*P)) # Z grazing on PNote: The NPZ Equations section is adapted, with thanks, from work done by Gene Dronek.
The final solution fields for the three different regimes of biological dynamics ... is plotted in Fig. 11. The results show that idealized strait bathymetry effectively perturbs the biology away from the inlet conditions. The case with single stable points (bio case 1) adjusts back to the stable equilibrium, whereas the two cases with limit cycles show complex structures in the vertical. In all cases, a phytoplankton bloom over the bump is observed. -- High Order Schemes for 2D Unsteady Biogeochemical Ocean Models, section 4.4 (Full NPZ equations)Q: The heading for the image matrix is "Three simulations with increased biomass". However, the description for these images in the paper speaks of single stable points, stable limit cycles, etc. Is the heading incorrect? If not, how does it relate to the paper's description? Q: Is the "a)" annotation in the upper-left corner of the image set an accidental and irrelevant inclusion from the source paper?
1.5. Each data set (e.g., y-0.5.csv) is a four-column array, containing a header row and 200 data rows. (The file names and some plots refer to depth as
Y; this is an artifact of the plotting software.) The columns contain time values (
t, ranging from
40.0) and corresponding concentrations of Nutrients (
N), Phytoplankton (
P), and Zooplankton (
Z). The data sets provide a general picture of the simulation over time. The image columns, in contrast, provide a detailed snapshot, taken halfway through the simulation run (i.e., t=20). Q: It appears that the (N, P, Z) values for t=20 in each data file correspond to the false colors shown at the appropriate
-0.5) in the corresponding images. However, what
11.5) is used?