Add function for seasonality to mizer...

[SamikDatta]

A paper I did with Julia following the last two chapters of my Ph.D. (link given below) was about adding seasonality in both the resource spectrum and species-specific reproduction to an early version of mizer:

[https://cdnsciencepub.com/doi/pdf/10.1139/cjfas-2015-0468]

It was a bit of a hack, but a fairly straightforward one to implement at the time. I though, given the discussion which occurred at the workshop during the World Fisheries Congress yesterday, it would be good to resurrect that code and get it implemented into mizer.

The resource dynamics are the place to start. It may be possible without actually touching the code base itself, but rather using the function setResource. I will investigate and update this issue.

[SamikDatta]

@gustavdelius - you can assign this issue to me 🙂

[gustavdelius]

Hi Samik, you are right that time-dependence can be implemented without thouching the mizer code. All the rate functions and the dynamics functions are being passed the current time in the t argument, so you just need to write your own versions of those functions that need to take time into account and register them with setRates() or setResource().

The problem with seasonality that it is difficult to handle is that in mizer reproduction is strictly proportional to income at the time of reproduction. With pulsed reproduction, which is what you would probably want in a seasonal context, you probably want to be able to build up gonadic mass throughout the year, and that is not possible in mizer.

[Kenhasteandersen]

I have also hacked in seasonal variation in the resource. You actually don’t really need pulsed reproduction to have it work. The reason is that in large parts of the year there is too little resource for the larve to grow, so they just die. It’s not fully satisfactory, I know, but it works. Another questions is whether it is useful for people. It is great as an illustrative research paper, but is it useful in practise? If we have the feature, do we then risk that people think it is works perfectly and can be used? Ken

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--------------------------------------------------------------------------------------------------------------- Ken H. Andersen, http://ken.haste.dk<http://ken.haste.dk/>, twitter: @69kno Professor in theoretical marine ecology, head of section and phd school, and deputy director of Centre for Ocean Life http://www.oceanlifecentre.dk<http://www.oceanlifecentre.dk/> Try my plankton simulator: http://oceanlife.dtuaqua.dk/Plankton/ New book: Fish Ecology, Evolution, and Exploitation - A New Theoretical Synthesis https://press.princeton.edu/titles/13516.html ***@***.*** On 21 Sep 2021, at 07.11, Gustav W Delius ***@***.******@***.***>> wrote: Hi Samik, you are right that time-dependence can be implemented without thouching the mizer code. All the rate functions and the dynamics functions are being passed the current time in the t argument, so you just need to write your own versions of those functions that need to take time into account and register them with setRates() or setResource(). The problem with seasonality that it is difficult to handle is that in mizer reproduction is strictly proportional to income at the time of reproduction. With pulsed reproduction, which is what you would probably want in a seasonal context, you probably want to be able to build up gonadic mass throughout the year, and that is not possible in mizer. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADFHLAKTGVZPWS2E4VMJMCDUDAHWRANCNFSM5ENPGB3A>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[SamikDatta]

Hi both. I thought I would let you know that I have a Masters student doing a project with me for a few months, investigating seasonality and its impacts on multispecies mizer models. We'll just be sticking to the resource spectrum (i.e. phytoplankton blooms), so can do the same thing as Ken did, but hopefully it can lay the foundation for building in more concrete seasonality into the code base if people think it would be useful to them.

[Kenhasteandersen]

Hi Samik, Sounds interesting. Looking forward to hear what comes out of it. Ken

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--------------------------------------------------------------------------------------------------------------- Ken H. Andersen, http://ken.haste.dk<http://ken.haste.dk/>, twitter: @69kno Professor in theoretical marine ecology, head of section and phd school, and deputy director of Centre for Ocean Life http://www.oceanlifecentre.dk<http://www.oceanlifecentre.dk/> ASLO 2021 talk: Scaling from first principles to global ecosystems<https://vimeo.com/566908694>. Fish Ecology, Evolution, and Exploitation - A New Theoretical Synthesis https://press.princeton.edu/titles/13516.html ***@***.*** On 8 Nov 2021, at 21.25, Samik Datta ***@***.******@***.***>> wrote: Hi both. I thought I would let you know that I have a Masters student doing a project with me for a few months, investigating seasonality and its impacts on multispecies mizer models. We'll just be sticking to the resource spectrum (i.e. phytoplankton blooms), so can do the same thing as Ken did, but hopefully it can lay the foundation for building in more concrete seasonality into the code base if people think it would be useful to them. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADFHLAMZVZ56MBNMORVF4W3ULAW2XANCNFSM5ENPGB3A>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[gustavdelius]

Hi Samik, that'll be interesting. Your student will probably discover interesting resonance effects between the time it takes to maturity and the yearly seasons. I am looking forward to hearing what you find out. Best, Gustav

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On Mon, Nov 8, 2021 at 8:25 PM Samik Datta ***@***.***> wrote: Hi both. I thought I would let you know that I have a Masters student doing a project with me for a few months, investigating seasonality and its impacts on multispecies mizer models. We'll just be sticking to the resource spectrum (i.e. phytoplankton blooms), so can do the same thing as Ken did, but hopefully it can lay the foundation for building in more concrete seasonality into the code base if people think it would be useful to them. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#31 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKHKKKLD2XDQAZLGOBOYUDULAW2XANCNFSM5ENPGB3A> .

[gustavdelius]

If there is more work done on seasonality, it could build on https://github.com/gustavdelius/mizerSeasonal which implements the accumulation of gonadic mass throughout the year and its release during spawning season.