Question regarding differing outputs for same species inputs

[traceybit]

This is a question about some of the life history parameters that the GUM package spits out at outputs. While preparing input data for a projection model, I ran a single fishery's catch history and the outputs for MaxLength, AgeMat, VonBertK, and Temp were all NAs (this didn't seem like a problem since we don't actually use any of those in the PT model for projections).

When I add catch history for three more fisheries to the same inputs used (same SciName, SpeciesCat, SpeciesGroup, and CommName) and ran the gum package, these outputs actually contain values for MaxLength, AgeMat, and VonBertK (Temp is still NA).

Is there a reason that these life history characteristics would be filled when using the second set of inputs (with more than 1 fishery), but not the first set (with only 1 fishery)? I'm mostly trying to understand this in order to answer a question that we received from the researchers in Cuba using the GUM package.

[tclavelle]

Hey Tracey,

The GUM package takes the info about the scientific name and species group and looks for a match in the FishBase data, returning NA if it cannot find that species or if no data is present for those life history variables.

Cheers, Tyler ​

On Wed, Feb 22, 2017 at 10:45 AM, Tracey Mangin notifications@github.com wrote:

This is a question about some of the life history parameters that the GUM package spits out at outputs. While preparing input data for a projection model, I ran a single fishery's catch history and the outputs for MaxLength, AgeMat, VonBertK, and Temp were all NAs (this didn't seem like a problem since we don't actually use any of those in the PT model for projections).

When I add catch history for three more fisheries to the same inputs used (same SciName, SpeciesCat, SpeciesGroup, and CommName) and ran the gum package, these outputs actually contain values for MaxLength, AgeMat, and VonBertK (Temp is still NA).

Is there a reason that these life history characteristics would be filled when using the second set of inputs (with more than 1 fishery), but not the first set (with only 1 fishery)? I'm mostly trying to understand this in order to answer a question that we received from the researchers in Cuba using the GUM package.

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-- Tyler Clavelle Project Researcher Sustainable Fisheries Group (SFG) University of California, Santa Barbara tclavelle@bren.ucsb.edu (802) 578-8701

[traceybit]

So if the species name, species group, species cat, etc. is the same for both sets of inputs, why would there be outputs for one set of inputs and not the other? The only difference between them is that one has contains four fisheries (four catch histories), but they are all for the same species, species cat, etc. etc.

[tclavelle]

Oh gotcha, I misread your question. Is the spelling exactly the same?

On Wed, Feb 22, 2017 at 11:07 AM, Tracey Mangin notifications@github.com wrote:

So if the species name, species group, species cat, etc. is the same for both sets of inputs, why would there be outputs for one set of inputs and not the other? The only difference between them is that one has contains four fisheries (four catch histories), but they are all for the same species, species cat, etc. etc.

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-- Tyler Clavelle Project Researcher Sustainable Fisheries Group (SFG) University of California, Santa Barbara tclavelle@bren.ucsb.edu (802) 578-8701

[traceybit]

Resolved! There was a space at the end of the sci name in one of the CSVs. Thanks!

[DanOvando]

Ha, that'll do it. Sorry for not responding faster. If we're going to keep using GUM it would be good to dedicate some time to improving the package. Tracey, is that something you'd want to take on?

Dan

On Wed, Feb 22, 2017 at 11:26 AM, Tracey Mangin notifications@github.com wrote:

Resolved! There was a space at the end of the sci name in one of the CSVs. Thanks!

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-- PhD Candidate, Project Researcher Sustainable Fisheries Group University of California, Santa Barbara

[traceybit]

Hmmm this is not something that I have much experience in, but would think about it if it makes sense to make changes.

Another quick question -- I was asked if they can use the model for non-fish species. I'm pretty sure this model has been used for other marine species... what are the guidelines here?

Thanks! Tracey

[tclavelle]

It will model non-fish species using the same life-history parameters and with a surplus production model (PT). If they're comfortable with that then yes, the model can be used for non-fish species. That being said, it's certainly not the best model for species like crab, lobster, shrimp, etc.

On Fri, Feb 24, 2017 at 8:17 AM, Tracey Mangin notifications@github.com wrote:

Hmmm this is not something that I have much experience in, but would think about it if it makes sense to make changes.

Another quick question -- I was asked if they can use the model for non-fish species. I'm pretty sure this model has been used for other marine species... what are the guidelines here?

Thanks! Tracey

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/8#issuecomment-282332746, or mute the thread https://github.com/notifications/unsubscribe-auth/AHyNJztPIa4SYsXALwoKnjTu-ZjdNDp3ks5rfwKVgaJpZM4MJCKt .

-- Tyler Clavelle Project Researcher Sustainable Fisheries Group (SFG) University of California, Santa Barbara tclavelle@bren.ucsb.edu (802) 578-8701

[DanOvando]

Yeah, we use it, but huge huge red flags for those species. They are realllllly underrepresented in RAM, so the fits are poor, and they really just don't seem to exhibit surplus production style pop dynamics.

Dan

On Fri, Feb 24, 2017 at 9:32 AM, Tyler Clavelle notifications@github.com wrote:

It will model non-fish species using the same life-history parameters and with a surplus production model (PT). If they're comfortable with that then yes, the model can be used for non-fish species. That being said, it's certainly not the best model for species like crab, lobster, shrimp, etc.

On Fri, Feb 24, 2017 at 8:17 AM, Tracey Mangin notifications@github.com wrote:

Hmmm this is not something that I have much experience in, but would think about it if it makes sense to make changes.

Another quick question -- I was asked if they can use the model for non-fish species. I'm pretty sure this model has been used for other marine species... what are the guidelines here?

Thanks! Tracey

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/8#issuecomment-282332746, or mute the thread https://github.com/notifications/unsubscribe- auth/AHyNJztPIa4SYsXALwoKnjTu-ZjdNDp3ks5rfwKVgaJpZM4MJCKt .

-- Tyler Clavelle Project Researcher Sustainable Fisheries Group (SFG) University of California, Santa Barbara tclavelle@bren.ucsb.edu (802) 578-8701

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-- PhD Candidate, Project Researcher Sustainable Fisheries Group University of California, Santa Barbara