Rsim.run function output questions

[andybeet]

I have been using one of the lazy loaded data objects (Ecosense.EBS) and extracting some info for squids. (see below)

library(Rpath)
Rpath <- rpath(Ecosense.EBS)
Rsim.scenario <- rsim.scenario(Rpath, Ecosense.EBS, years = 1:50)
Rsim.output <- rsim.run(Rsim.scenario, method = "RK4", years = 1:50)
groups <- extract.node(Rsim.output,Rpath$Group['Squids'])
head(groups$Discards)
#>           Total Fishery/Subsistence Fishery/Subsistence
#> 1: 3.323654e-05        1.661827e-05         5.63144e-05
#> 2: 3.323654e-05        1.661827e-05         5.63144e-05
#> 3: 3.323654e-05        1.661827e-05         5.63144e-05
#> 4: 3.323654e-05        1.661827e-05         5.63144e-05
#> 5: 3.323654e-05        1.661827e-05         5.63144e-05
#> 6: 3.323654e-05        1.661827e-05         5.63144e-05
Rpath$NUM_GEARS
#> [1] 1

^{Created on 2025-02-03 with reprex v2.1.0}

The output for groups$Discards i think indicates (with my limited understanding) that there are TWO fisheries/gears that create discards for SQUID (... and both fisheries have the same name!) . But, when i look at the Rpath object above (Rpath$NUM_GEARS) there is only one fishery specified in the model.

This (error?) seems to result in propogating the Rsim.output$Gear_Catch_sp, Rsim.output$Gear_Catch_gear, Rsim.output$Gear_Catch_disp

Is this correct? Can someone verify? Thanks

[SarahJWeisberg]

OK I looked at the model a bit and I have a thought -- in this system, there are two fates for the discards: pelagic detritus and benthic detritus. So I think we have two columns here representing the amount of biomass flowing to each detrital compartment. BUT this is definitely not clear from the way the output is labeled / named so I wonder if we can adjust that. Also I am still trying to figure out why the total does not reflect the sum of the other two columns here...

I quickly tried the extract.node function on my Gulf of Maine model and I got an expected result (but I only have one detrital pathway in my model).

@kaydin curious for your thoughts

[andybeet]

All 3 example models Ecosense.GOA, Ecosense.CBS, Ecosense.EBS have two detrital components

[SarahJWeisberg]

But the Anchovy Bay model AB.params only has one - right?

[andybeet]

Ah, i didnt realize that was another model (naming is different).

But, yes, this has one detrital component, and 5 fishing gears. But the Discards field has one column, Total, of which all values are zero (for all groups), which i think is expected since there are no discards in this model ( Rsim.output$Gear_Catch_disp are all "Landing"). So i think this isn't a good example for this function

[SarahJWeisberg]

Yes that's right - looks like no one is discarding in Anchovy Bay.