Improve default for metabolic rate about mizer HOT 9 CLOSED

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@Kenhasteandersen , what I am looking for is a good default value for ks. I believe the philosophy of mizer is that when people have only partial knowledge of their species, i.e., only know some of the parameters, mizer tries to provide defaults for the unknown parameters in such a way that the species is at least viable. The current choice of ks = 0.2 * h does not do that. Assume for example that it is known that the species has a low assimilation efficiency of alpha = 0.1. In that case the current default for ks says that the species has a higher metabolic demand than it could ever cover by feeding. Such a species would never have evolved. So I am looking for a better default value for ks.

Do you know what the motivation for the choice ks = 0.2 * h was?

In my previous post by feeding_level I meant the f0 specified by the user.

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This is a very interesting topic. Assuming that critical feeding level is 0.2 and alpha is 0.6, then ks should be 0.12 of h (the default is 0.2*h, I believe, which is too high). For the Tasmanian model and other papers I have looked at various energy budgets, and parameterised ks to give metabolism at 30-50% of daily intake in equilibrium conditions (not necessarily maximum intake, but realised daily intake).

I think the above rule of thumb (ks = f_calphah) makes lots of sense for a start. Although if you look at literature you find that standard metabolism level (ks) is often higher in small bodied species, whereas h could be expected to be larger in large bodied species. In which case h and ks would be negatively correlated (which is the case in the Tasmanian model). But this could perhaps be left for further explorations :)

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Good. I'll change the default in the new version to ks = 0.2 * alpha * h then. I will also add a warning when a user has specified a value for f0 that is less than the critical feeding level of 0.2.

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Or how about setting the default to ks = 0.2 * alpha * h * w_mat^(n-p) so that the critical feeding level is equal to 0.2 at w_mat also when n != p?

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@Kenhasteandersen , I agree with you that it is tricky to give good defaults when p != n. For example the default for h that leads to the right maturity age will become difficult. We should definitely issue a stark warning when we provide any defaults for this case. However I would like mizer to provide some default so that the user can then use shiny gadgets to start investigating the system and interactively explore better parameter values. All I require of the defaults for that purpose is that they allow every species to reach maturity size in order to have some reproduction.

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