New diagnostic plot?

[cddesja]

I wanted to suggest a diagnostic plot that would be extremely useful in the calibration phase.
I am not so sure what would be the best way to implement it, but the basic idea is to visualize whether predator distribution (by box and layer) matches its preys (defined in the diet matrix of the biom.prm). I find that trophic interaction is one of the most critical but also tricky bit in Atlantis.
Maybe a way to do it could be to add in the spatial plots a prey-pred overlap, for which by selecting a predator, you can see in which boxes and layers preys are available.
Please let me know what you think.

[cddesja]

@mcgregorv @erlasturl, do either one of you have any code to do this? I feel like the plots @erlasturl made get at this. This sounds like this this is beyond my capacity (i.e., time) at the moment..

[mcgregorv]

This sounds like a great idea Chris. I'm looking at predator-prey interactions at the moment, so I might try putting something like this together. Will keep you updated.
Vidette

[erlasturl]

The spatial plot "within a box distribution" are helpful when looking at this and they may be improved be also including the layers in that plot. I like the idea of being able to look at prey distribution for each predator and I think this would be a good addition but I don't have a code for it at the moment.

[mcgregorv]

Hey, I’ve put together some code for a summary predator-prey encounter plot. I think this would be a useful place to start, then drill down into layer and time and perhaps age. I added a small change to create_vadt() to have it read in the pPREY from biol.prm and output it and also added fgcodes for the output obj. Then I created create_pred_prey_encounter() which reads in the object created in create_vadt() and adds to it the encounter rates. I just put this separately because it was easier for testing, but it can be added to the main one as an option (it takes quite a long time to run). Then I have vadt_pred_prey() which is a copy of vadt() but with only the predator/prey encounter tab (again I pulled this bit out for testing, and can add it to the main one). I’ve attached the code, try it if you like and if it works I can add it to a branch. I’ve attached a screen shot of the plot too. Vidette

From: Christopher David Desjardins [mailto:[email protected]]
Sent: Monday, 29 February 2016 8:42 a.m.
To: mareframe/vat
Cc: Vidette McGregor
Subject: Re: [vat] New diagnostic plot? (#16)

@mcgregorvhttps://github.com/mcgregorv @erlasturlhttps://github.com/erlasturl, do either one of you have any code to do this? I feel like the plots @erlasturlhttps://github.com/erlasturl made get at this. This sounds like this this is beyond my capacity (i.e., time) at the moment..

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/16#issuecomment-189931981.

Vidette McGregor
Ecosystem Modeller

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[cddesja]

Hi Vidette, I don't actually see the attachments. Would you be able to send them again?