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Pacific-salmon-assess / samSim

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Question about extinction threshold when computing catch #24

Open catarinawor opened 3 years ago

catarinawor commented 3 years ago

The realized catches are computed here. The catches are computed sequentially: American, mixed stock then single stock catch. So the catches get subtracted from the returns before the next fisheries occur. But why do we subtract the extinction threshold (extinctThresh) after the mixed stock fishery? Is it to indicate that the single stock fishery only occurs after some escapement has happened? I need some help explaining this, please!

carrieholt commented 3 years ago

Good question. I think this might be one for Cam. We didn't use the single-stock fishery in our application of samSim to LRPs, so the remRec2 (in the line you highlighted above) and remRec3 are inconsequential for our purposes. It looks like you're correct though. Including extinctThresh in that line means that a small number of fish (= extinctThresh) could not be caught by the single-stock fishery.

catarinawor commented 3 years ago

Thanks for he reminder about no single stock fisheries!

CamFreshwater commented 3 years ago

Sorry for the delay I was out chasing Chinook Thursday/Friday.

Yes this was a workaround to stop single stock fisheries from triggering extirpation. I don't remember the specific behaviour in simulations that triggered us inserting it, but I vaguely recall having a discussion where we decided it would be more realistic to assume that since these are near-terminal freshwater fisheries, when enumeration is presumably easier, there would be management measures in place to stop extirpation. Whether or not this is actually appropriate is up for debate!