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).
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.
paroptis the parameter initial guess. IfNA, the values are initialized as the mean ofparminandparmax(if both are defined). Else, initialized as 0.parminis the minimum possible value of the parameterparmaxis the maximum possible value of the parameterparphaseis the calibration phase in which the parameter will be calibrated. IfNA, 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.