Tuna and migratory species

[Philipp-Neubauer]

The assessment table does not seem to contain Tuna and other billfish or migratory species. These do appear in the landings and thus appear as not-assessed. Yayx.

Not sure if we've been through this or I missed something; how should we handle it? Exclude them? OR get assessment year values? Clearly they could have a large impact in terms of size, price etc.

[Philipp-Neubauer]

Also, these are not region specific, so would be hard to assign a region, unless we add a migratory category. Seems fundamental enough to consider.

[James-Thorson]

Hmm. I suggest dropping "highly migratory species" (which we then define however we need to keep the analysis tractible, presumably could be defined as tunas and billfishes).

Sorry that we didn't think of this earlier!

[mcmelnychuk]

With the possible exception of Pacific albacore, I think all the tuna & billfishes are assessed by the RFMOs, typically have ocean basin-size stock definition boundaries, and typically involve many countries catching them. I agree that it's probably easiest to drop these.

An alternative would be to include all the stocks in ICCAAT, IATTC, and WCPTC for which the US has a big fishing stake. Maite Pons has already collected year of first assessment information for those tuna & billfish stocks; if we wanted to include these stocks and use that information we would probably want to offer co-authorship to her.

There are some sharks that are assessed by RFMOs as well, but other sharks (including some labelled as highly migratory) that are pretty much coastal and caught & assessed by the US. Those ones would be fine to include even if we exclude all RFMO stocks from the analysis.

If we decide to exclude all stocks assessed by RFMOs, I can compile a list of these so that we can exclude them and ignore their landings data.

[Philipp-Neubauer]

I don't really have a preference either way. Tuna and billfishes seem important enough that it would seem worthwhile keeping them in the analysis; but then again they may skew the analysis as factors in our analysis wouldn't affect their assessment in the same way as for stocks that are under US jurisdiction ...

[Philipp-Neubauer]

Excluding them might be the most consistent thing to do...

[mcmelnychuk]

Let's plan on excluding them, and can always decide later to bring them in if we or reviewers think that's a big gap that would be worth filling.

Similar to their exclusion, we'll also want to exclude all salmon. We've only recently started incorporating them into RAM, and we don't have any management attribute data (ie. first assessment) for any salmon yet.

[Philipp-Neubauer]

Right; are most of those assessed locally (e.g., catchment by catchment?) or do they have RFMOs (excuse my ignorance :)

[mcmelnychuk]

Assessment units are usually for lakes or streams, but occasionally for river systems. Some are carried out by NOAA (so are in SIS), but many are by state agencies. I don't think there's really anything regional like a RFMO, except maybe for the Columbia River.

On 2016-10-26 12:57 PM, Philipp Neubauer wrote:

Right; are most of those assessed locally (e.g., catchment by catchment?) or do they have RFMOs (excuse my ignorance :)

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[Philipp-Neubauer]

Cool; thanks Mike.

is there anything beyond Pacific Halibut that would need excluding from your list with the exclusion of highly migratory species and salmon?

For the sharks, I don't have that great a handle on which species could be considered coastal/resident vs highly migratory. Can you/we come up with a list/definition for those?

Thanks

On Thu, Oct 27, 2016 at 9:03 AM, Michael Melnychuk <notifications@github.com

wrote:

Assessment units are usually for lakes or streams, but occasionally for river systems. Some are carried out by NOAA (so are in SIS), but many are by state agencies. I don't think there's really anything regional like a RFMO, except maybe for the Columbia River.

On 2016-10-26 12:57 PM, Philipp Neubauer wrote:

Right; are most of those assessed locally (e.g., catchment by catchment?) or do they have RFMOs (excuse my ignorance :)

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Phil

[mcmelnychuk]

I would say that if the assessment is carried out by NOAA, by a management council (except Hawaii's), or by a state agency (except Hawaii) that it should be considered, not only for sharks but for species in general. Exceptions:

• If it's carried out by a high seas RFMO, exclude
• if it's a salmon, exclude

This should exclude the oceanic sharks (RFMO-assessed) but include the coastal ones (NOAA-assessed). I've asked Nicole to go through the landings database to check for assessments we might have missed, and during that she can look through all the shark species. Is there anything to add to this request?

"...I'm wondering if you could collect some assessment-related information from management council websites and state management agency websites. We have a project underway and we're trying to account for all stock assessments in the US.

This would involve two components, and I'm not sure whether it would be most efficient to do these one at a time or at the same time.

1) going through all management council websites (except Hawaii) and compiling a list of species that have been assessed since 2011. We have a pretty strict definition of assessment - generally involving a population model. We know about most of them, but might be missing some. Then, same thing for management agencies of all coastal states (excluding Hawaii).

2) taking a list of unassessed species that we have and searching for stock assessments for these to ensure that indeed they are not assessed."

[Philipp-Neubauer]

Agreed, and the request looks good to me.

Would be great to have a categorisation of sharks in the landings as "are or would be assessed by RFMOs" or "are or would be assessed by NOAA" - which I guess boils down to Oceanic vs coastal. Then I can jstu apply a filter on the landings DB to remove all these along with the salmon and tuna/billfishes.

On Thu, Oct 27, 2016 at 10:21 AM, Michael Melnychuk < notifications@github.com> wrote:

I would say that if the assessment is carried out by NOAA, by a management council (except Hawaii's), or by a state agency (except Hawaii) that it should be considered, not only for sharks but for species in general. Exceptions:

• If it's carried out by a high seas RFMO, exclude
• if it's a salmon, exclude

This should exclude the oceanic sharks (RFMO-assessed) but include the coastal ones (NOAA-assessed). I've asked Nicole to go through the landings database to check for assessments we might have missed, and during that she can look through all the shark species. Is there anything to add to this request?

"...I'm wondering if you could collect some assessment-related information from management council websites and state management agency websites. We have a project underway and we're trying to account for all stock assessments in the US.

This would involve two components, and I'm not sure whether it would be most efficient to do these one at a time or at the same time.

1) going through all management council websites (except Hawaii) and compiling a list of species that have been assessed since 2011. We have a pretty strict definition of assessment - generally involving a population model. We know about most of them, but might be missing some. Then, same thing for management agencies of all coastal states (excluding Hawaii).

2) taking a list of unassessed species that we have and searching for stock assessments for these to ensure that indeed they are not assessed."

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Phil

[mcmelnychuk]

I've gone through 'SpeciesCrossReference.csv' and added a column, "exclude". In this column I made suggestions for which species to exclude, attributed to:

• HMS (tuna, billfish, and oceanic sharks that are or would typically be assessed by RFMOs)
• salmon
• freshwater fish
• reptiles
• worms
• sponges

I did not do a systematic search of the species list to look for other species that should be excluded, I only wrote those exclusion suggestions for species following ad-hoc searches. (I probably didn't catch all freshwater fish, for example, and there may be other categories I didn't list that should be excluded.) I think I remember seeing somewhere in your code Phil that you'd already done such exclusions so I didn't go through this too thoroughly. If that's not in there already, I can do a more systematic search of this list to look for other exclusions.

[Philipp-Neubauer]

Great! Thanks Mike. Yes, I do have some filters in the code - similarly ad-hoc, jsut excluding things that seemed obvious at the time. Have added a few now (seaweed, roe on kelp etc...).

I'll spend some time now to try and get a final data-set together and re-run the model - think I can sort the remaining matching issues out now. I'll also try and tick off a few of the issues while I'm at it - then we can hopefully finalise the results.

cheers Phil

On Fri, Oct 28, 2016 at 6:26 PM, Michael Melnychuk <notifications@github.com

wrote:

I've gone through 'SpeciesCrossReference.csv' and added a column, "exclude". In this column I made suggestions for which species to exclude, attributed to:

• HMS (tuna, billfish, and oceanic sharks that are or would typically be assessed by RFMOs)
• salmon
• freshwater fish
• reptiles
• worms
• sponges

I did not do a systematic search of the species list to look for other species that should be excluded, I only wrote those exclusion suggestions for species following ad-hoc searches. (I probably didn't catch all freshwater fish, for example, and there may be other categories I didn't list that should be excluded.) I think I remember seeing somewhere in your code Phil that you'd already done such exclusions so I didn't go through this too thoroughly. If that's not in there already, I can do a more systematic search of this list to look for other exclusions.

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Phil

[mcmelnychuk]

Sounds good. Nicole has started looking for potentially-missing assessments. I expect she'll get through the list by mid next week. We can add some more assessments if necessary if she finds any we didn't account for before.