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NOAA-FIMS / FIMS-planning

:fish: :chart_with_upwards_trend: :ocean: a place to manage FIMS' planning process
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Investigation group idea: I/O file type and structure #16

Closed Cole-Monnahan-NOAA closed 2 years ago

Cole-Monnahan-NOAA commented 3 years ago

I think the I/O file type and structure is worth some thought. E.g., if we use TMB do we have ASCII files that get parsed in R, or specify things directly in R? Likewise for outputs. As an SS user I almost never look at output files b/c they get read in by r4ss. So can we skip that step? It seems unwieldly for a TMB model to create the output in R, write to file, then read it back in for analysis.

Would be curious to hear @timjmiller opinion on this with his experience with WHAM.

kellijohnson-NOAA commented 3 years ago

I don't think that we can skip writing output files. I constantly look at them and compare output across models using diff. Also, lots of people that don't know R use these output files, e.g., groundfish subcommittee, managers, etc.

k-doering-NOAA commented 3 years ago

Reading and writing is really slow, though, so it would be nice to have the option to skip it when needed. For example, I think it really slows down simulations.

timjmiller commented 3 years ago

Yeah, I agree that having it as an option seems to cover the bases.

On Thu, Aug 5, 2021 at 2:24 PM Kathryn Doering @.***> wrote:

Reading and writing is really slow, though, so it would be nice to have the option to skip it when needed. For example, I think it really slows down simulations.

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Cole-Monnahan-NOAA commented 3 years ago

That's a good idea. Ideally I suppose the user could have a lot of control of what is printed/reported. Like @k-doering-NOAA said if you're doing a simulation and just grabbing a few values you could save a lot of time. Even more time-saving would be skipping unnecessary delta method calculations.

I don't know if this is the place to hash that out. I was just proposing that a group of people could start thinking it out more carefully now. I don't think I want to volunteer for it, just proposing it!