6.4. List of variables to calibrate

The next step is to create a table containing the list of the Osmose parameters to calibrate (see Table 6.5).

Table 6.5 Parameters to calibrate
  paropt parmin parmax parphase
mortality.natural.larva.rate.sp0 0.476013813 0.2 1.6 2
mortality.natural.larva.rate.sp1 1.578997873 0.6 2.0 2
mortality.natural.larva.rate.sp2 1.19819857 0.4 1.6 2
mortality.natural.larva.rate.sp3 0.586048506 0.2 1.2 2
mortality.natural.larva.rate.sp4 0.2 0.2 1.2 2
mortality.natural.larva.rate.sp5 0.904776806 0.4 1.6 2
mortality.natural.larva.rate.sp6 0.859194349 0.4 1.6 2
mortality.natural.larva.rate.sp7 1.281004774 0.4 1.6 2
mortality.natural.larva.rate.sp8 0.010436663 0.005 0.02 2
mortality.natural.larva.rate.sp9 0.416166226 0.2 1.2 2
mortality.natural.larva.rate.sp10 1.530131413 0.6 1.8 2
plankton.accessibility2fish.plk0 0.1 0.05 1.9 1
plankton.accessibility2fish.plk1 0.1 0.05 1.9 1
plankton.accessibility2fish.plk2 0.05 0.05 1.9 1
plankton.accessibility2fish.plk3 0.1 0.05 1.9 1
plankton.accessibility2fish.plk4 0.1 0.05 1.9 1
plankton.accessibility2fish.plk5 1.45 0.05 1.9 1
mortality.fishing.rate.sp0 0.130877451 0.1 0.5 3
mortality.fishing.rate.sp1 0.382709506 0.175 0.7 3
mortality.fishing.rate.sp2 0.499612516 0.227 0.908 3
mortality.fishing.rate.sp3 0.2 0.125 0.5 3
mortality.fishing.rate.sp4 0.6 0.175 0.7 3
mortality.fishing.rate.sp5 0.5 0.125 0.6 3
mortality.fishing.rate.sp6 0.006662997 0.003 0.012 3
mortality.fishing.rate.sp7 0.6 0.225 0.9 3
mortality.fishing.rate.sp8 0.15 0.037723225 0.2 3
mortality.fishing.rate.sp9 0.09638775 0.05 0.2 3
mortality.fishing.rate.sp10 0.5 0.2 0.694 3
q.sp0 0.959522483 0.5 1.3 4
q.sp1 1.007415552 0.5 1.3 4
q.sp2 0.998406705 0.5 1.3 4
q.sp3 0.897712618 0.5 1.3 4
q.sp4 0.936632054 0.5 1.3 4
q.sp5 0.929764322 0.5 1.3 4
q.sp6 0.838034913 0.5 1.3 4
q.sp7 0.848811769 0.5 1.3 4
q.sp8 0.956199768 0.5 1.3 4
q.sp9 0.948716213 0.5 1.3 4
q.sp10 0.829510129 0.5 1.3 4

This table is as follows:

  • the first column contains the parameters to calibrate.
  • paropt is the parameter initial guess. If NA, the values are initialized as the mean of parmin and parmax (if both are defined). Else, initialized as 0.
  • parmin is the minimum possible value of the parameter
  • parmax is the maximum possible value of the parameter
  • parphase is the calibration phase in which the parameter will be calibrated. If NA, the parameter is not calibrated.

Hint

Here, the table format do not matter since this table will be read by the user prior to run the calibration. However, it is recommended to keep this format.

In this example, all the parameters except the q.spX ones, are OSMOSE Java parameters. The q.spX parameters can be viewed as “capturability indexes”. Since observation datasets may not be on the same spatial scale as model outputs (survey zone, etc.), this index is used to convert Osmose outputs into observational dataset.

Danger

The names of the OSMOSE Java calibrated parameters must be properly set, in order to be insure that they will be used by the model.