Handling Atlantis layers whilst importing

[lentinj]

@bthe @erlasturl Currently when importing Atlantis tracers into MFDB, I'm ignoring the depth layers, as a result of any query each layers for a Box will be combined:

https://github.com/mareframe/mfdbatlantis/blob/56e05a3/demo/iceland.R#L32

Options:

• This is absolutely fine, we don't really care about depth outside Atlantis anyway.
• Import each layer with a different data_source, so it's possible to pick apart the depth information ~manually.
• Invent tows (with the right depth set) to assign each layer information to.
• Expand the database to directly represent the layer (either in meter depth or layer box), and have some ability to query this.

Any thoughts?

[bthe]

I would suggest that the depths would either by represented through tows or as actual layers in the database. In relation to this note that Gadget is meant to fit to observed data and those observations will be in the form of aggregated tows from different fishing vessels/gears.

A sidenote: it would be interesting to import information from the oceanographic model by these boxes/depth layers.

[lentinj]

@bthe Given that, does it actually make sense to import the entirety of the tracer input? It's not exactly realistic to observe the state of all fish in an ecosystem after all.

There is the (total tonnes) fisheries output to import also, you could assume that the fishery caught a random selection of the specimens that would have been available in that Area/Layer/Time.

[bthe]

First para: Not really, we should try limit ourselves to data that we will actually use.

Second para: Yes, this sounds reasonable and is the idea behind the definition of the subdivisions on the Icelandic continental shelve.

[lentinj]

@erlasturl Is it possible that Atlantis can output more detail on the specimens that a predator / fishery catches, rather than trying to derive it from the total weight? I can't see it in either the Sicily or Lake Victoria output I have, but there could be an extra output option I guess.