Question regarding warning messages

DanOvando / GUM

Run Global Upside Model in the manner of Costello et al 2016

MIT License

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Question regarding warning messages #10

Open traceybit opened 7 years ago

traceybit commented 7 years ago

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages:
1: In min(k1[g1 < 1.1 * parbound$g[1]], na.rm = T) :
  no non-missing arguments to min; returning Inf
2: In min(k1[g1 < 1.1 * parbound$g[1]], na.rm = T) :
  no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

tclavelle commented 7 years ago

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin notifications@github.com wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10, or mute the thread https://github.com/notifications/unsubscribe-auth/AHyNJ_lCAnT1uhOgPHnbay5o-_CmUQ6vks5roUI6gaJpZM4MlaFe .

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

traceybit commented 7 years ago

Sort of, but I wouldn't know how to use either in this situation. The only columns that return NAs are MaxLength, AgeMat, VonVertK, and Temp (for some species).

But more generally, let's just say what you said is true (CMSY didn’t work and there’s only NA values for k1), what does that mean, and what would be the appropriate next step?

On Wed, Mar 22, 2017 at 9:00 AM, Tyler Clavelle notifications@github.com wrote:

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin notifications@github.com wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10, or mute the thread https://github.com/notifications/unsubscribe- auth/AHyNJ_lCAnT1uhOgPHnbay5o-_CmUQ6vks5roUI6gaJpZM4MlaFe .

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288447495, or mute the thread https://github.com/notifications/unsubscribe-auth/ALOpsFiIDR0OBlINMbrpCzhqX3jco1Dhks5roUWpgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 Skype: traceymangin

tclavelle commented 7 years ago

Are you on campus at all today? It's probably just easier to go over this in person so we can both look at the code/results at the same time.

On Wed, Mar 22, 2017 at 9:11 AM, Tracey Mangin notifications@github.com wrote:

Sort of, but I wouldn't know how to use either in this situation. The only columns that return NAs are MaxLength, AgeMat, VonVertK, and Temp (for some species).

But more generally, let's just say what you said is true (CMSY didn’t work and there’s only NA values for k1), what does that mean, and what would be the appropriate next step?

On Wed, Mar 22, 2017 at 9:00 AM, Tyler Clavelle notifications@github.com wrote:

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin <notifications@github.com

wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10, or mute the thread https://github.com/notifications/unsubscribe- auth/AHyNJ_lCAnT1uhOgPHnbay5o-_CmUQ6vks5roUI6gaJpZM4MlaFe .

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288447495, or mute the thread https://github.com/notifications/unsubscribe-auth/ ALOpsFiIDR0OBlINMbrpCzhqX3jco1Dhks5roUWpgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 <(201)%20400-0157> Skype: traceymangin

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288451213, or mute the thread https://github.com/notifications/unsubscribe-auth/AHyNJ2HuNXQ8Qc1KRGFEogi4GxXS30Azks5roUgugaJpZM4MlaFe .

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

traceybit commented 7 years ago

I'm not and I don't have a car today. I could come tomorrow afternoon or Friday anytime.

I'm happy to come in and work this out, but I have a more general question about troubleshooting: if the idea is that the package is public, what's the plan for troubleshooting for people who are not in Santa Barbara? The work that I'm doing is to support Cuban researchers working with EDF, but I can imagine a time when I won't be working on their project. Is the idea that the user will have a more in-depth knowledge of the inner workings of the GUM package? Or is it not really meant for external use?

On Wed, Mar 22, 2017 at 9:54 AM, Tyler Clavelle notifications@github.com wrote:

Are you on campus at all today? It's probably just easier to go over this in person so we can both look at the code/results at the same time.

On Wed, Mar 22, 2017 at 9:11 AM, Tracey Mangin notifications@github.com

wrote:

Sort of, but I wouldn't know how to use either in this situation. The only columns that return NAs are MaxLength, AgeMat, VonVertK, and Temp (for some species).

But more generally, let's just say what you said is true (CMSY didn’t work and there’s only NA values for k1), what does that mean, and what would be the appropriate next step?

On Wed, Mar 22, 2017 at 9:00 AM, Tyler Clavelle < notifications@github.com> wrote:

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin < notifications@github.com

wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10, or mute the thread https://github.com/notifications/unsubscribe- auth/AHyNJ_lCAnT1uhOgPHnbay5o-_CmUQ6vks5roUI6gaJpZM4MlaFe .

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288447495, or mute the thread https://github.com/notifications/unsubscribe-auth/ ALOpsFiIDR0OBlINMbrpCzhqX3jco1Dhks5roUWpgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 <(201)%20400-0157> <(201)%20400-0157> Skype: traceymangin

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.

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288465247, or mute the thread https://github.com/notifications/unsubscribe-auth/ALOpsDbavzhyxz-18VNOvSwbC2lHBnMmks5roVJHgaJpZM4MlaFe .

tclavelle commented 7 years ago

Dan, correct me if I’m wrong here, but I don’t think the original intent of creating the GUM package was to make it freely and publicly available to other users. We created it to facilitate our own projects that use the upside projection modeling, but we don’t necessarily want anyone to use it because it wasn’t meant to be used as an individual fishery assessment tool. It sounds like Chris has you doing just that though, so it probably warrants a broader discussion between the larger group.

There’s no way to make the package error proof and error message are quite often hard to diagnose. We can certainly try to improve the GUM package, but unless we can be sure that the errors are a result of the code and not the underlying data that people are passing to the functions it’s hard to know where to start.

On Wed, Mar 22, 2017 at 10:09 AM, Tracey Mangin notifications@github.com wrote:

I'm not and I don't have a car today. I could come tomorrow afternoon or Friday anytime.

I'm happy to come in and work this out, but I have a more general question about troubleshooting: if the idea is that the package is public, what's the plan for troubleshooting for people who are not in Santa Barbara? The work that I'm doing is to support Cuban researchers working with EDF, but I can imagine a time when I won't be working on their project. Is the idea that the user will have a more in-depth knowledge of the inner workings of the GUM package? Or is it not really meant for external use?

On Wed, Mar 22, 2017 at 9:54 AM, Tyler Clavelle notifications@github.com

wrote:

Are you on campus at all today? It's probably just easier to go over this in person so we can both look at the code/results at the same time.

On Wed, Mar 22, 2017 at 9:11 AM, Tracey Mangin <notifications@github.com

wrote:

Sort of, but I wouldn't know how to use either in this situation. The only columns that return NAs are MaxLength, AgeMat, VonVertK, and Temp (for some species).

But more generally, let's just say what you said is true (CMSY didn’t work and there’s only NA values for k1), what does that mean, and what would be the appropriate next step?

On Wed, Mar 22, 2017 at 9:00 AM, Tyler Clavelle < notifications@github.com> wrote:

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin < notifications@github.com

wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10, or mute the thread https://github.com/notifications/unsubscribe- auth/AHyNJ_lCAnT1uhOgPHnbay5o-_CmUQ6vks5roUI6gaJpZM4MlaFe .

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288447495, or mute the thread https://github.com/notifications/unsubscribe-auth/ ALOpsFiIDR0OBlINMbrpCzhqX3jco1Dhks5roUWpgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 <(201)%20400-0157> <(201)%20400-0157> <(201)%20400-0157> Skype: traceymangin

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288451213, or mute the thread https://github.com/notifications/unsubscribe-auth/ AHyNJ2HuNXQ8Qc1KRGFEogi4GxXS30Azks5roUgugaJpZM4MlaFe

.

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288465247, or mute the thread https://github.com/notifications/unsubscribe-auth/ALOpsDbavzhyxz- 18VNOvSwbC2lHBnMmks5roVJHgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 <(201)%20400-0157> Skype: traceymangin

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288470231, or mute the thread https://github.com/notifications/unsubscribe-auth/AHyNJxXn7KEWXhP445EdtFNtpcvQgaXrks5roVXKgaJpZM4MlaFe .

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

traceybit commented 7 years ago

Ok -- when are you available tomorrow or Friday?

On Wed, Mar 22, 2017 at 10:30 AM, Tyler Clavelle notifications@github.com wrote:

Dan, correct me if I’m wrong here, but I don’t think the original intent of creating the GUM package was to make it freely and publicly available to other users. We created it to facilitate our own projects that use the upside projection modeling, but we don’t necessarily want anyone to use it because it wasn’t meant to be used as an individual fishery assessment tool. It sounds like Chris has you doing just that though, so it probably warrants a broader discussion between the larger group.

There’s no way to make the package error proof and error message are quite often hard to diagnose. We can certainly try to improve the GUM package, but unless we can be sure that the errors are a result of the code and not the underlying data that people are passing to the functions it’s hard to know where to start.

On Wed, Mar 22, 2017 at 10:09 AM, Tracey Mangin notifications@github.com

wrote:

I'm not and I don't have a car today. I could come tomorrow afternoon or Friday anytime.

I'm happy to come in and work this out, but I have a more general question about troubleshooting: if the idea is that the package is public, what's the plan for troubleshooting for people who are not in Santa Barbara? The work that I'm doing is to support Cuban researchers working with EDF, but I can imagine a time when I won't be working on their project. Is the idea that the user will have a more in-depth knowledge of the inner workings of the GUM package? Or is it not really meant for external use?

On Wed, Mar 22, 2017 at 9:54 AM, Tyler Clavelle < notifications@github.com>

wrote:

Are you on campus at all today? It's probably just easier to go over this in person so we can both look at the code/results at the same time.

On Wed, Mar 22, 2017 at 9:11 AM, Tracey Mangin < notifications@github.com

wrote:

Sort of, but I wouldn't know how to use either in this situation. The only columns that return NAs are MaxLength, AgeMat, VonVertK, and Temp (for some species).

But more generally, let's just say what you said is true (CMSY didn’t work and there’s only NA values for k1), what does that mean, and what would be the appropriate next step?

On Wed, Mar 22, 2017 at 9:00 AM, Tyler Clavelle < notifications@github.com> wrote:

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin < notifications@github.com

wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10, or mute the thread https://github.com/notifications/unsubscribe- auth/AHyNJ_lCAnT1uhOgPHnbay5o-_CmUQ6vks5roUI6gaJpZM4MlaFe .

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/DanOvando/GUM/issues/10#issuecomment-288447495 , or mute the thread https://github.com/notifications/unsubscribe-auth/ ALOpsFiIDR0OBlINMbrpCzhqX3jco1Dhks5roUWpgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 <(201)%20400-0157> <(201)%20400-0157> <(201)%20400-0157> <(201)%20400-0157> Skype: traceymangin

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288451213, or mute the thread https://github.com/notifications/unsubscribe-auth/ AHyNJ2HuNXQ8Qc1KRGFEogi4GxXS30Azks5roUgugaJpZM4MlaFe

.

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288465247, or mute the thread https://github.com/notifications/unsubscribe-auth/ALOpsDbavzhyxz- 18VNOvSwbC2lHBnMmks5roVJHgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 <(201)%20400-0157> <(201)%20400-0157> Skype: traceymangin

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.

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10#issuecomment-288476959, or mute the thread https://github.com/notifications/unsubscribe-auth/ALOpsOmgxl-rfsPjEvDo9_OVM1tAW194ks5roVrDgaJpZM4MlaFe .

tclavelle commented 7 years ago

Friday works best for me. Dan?

On Wed, Mar 22, 2017 at 10:35 AM, Tracey Mangin notifications@github.com wrote:

Ok -- when are you available tomorrow or Friday?

On Wed, Mar 22, 2017 at 10:30 AM, Tyler Clavelle <notifications@github.com

wrote:

Dan, correct me if I’m wrong here, but I don’t think the original intent of creating the GUM package was to make it freely and publicly available to other users. We created it to facilitate our own projects that use the upside projection modeling, but we don’t necessarily want anyone to use it because it wasn’t meant to be used as an individual fishery assessment tool. It sounds like Chris has you doing just that though, so it probably warrants a broader discussion between the larger group.

There’s no way to make the package error proof and error message are quite often hard to diagnose. We can certainly try to improve the GUM package, but unless we can be sure that the errors are a result of the code and not the underlying data that people are passing to the functions it’s hard to know where to start.

On Wed, Mar 22, 2017 at 10:09 AM, Tracey Mangin < notifications@github.com>

wrote:

I'm not and I don't have a car today. I could come tomorrow afternoon or Friday anytime.

I'm happy to come in and work this out, but I have a more general question about troubleshooting: if the idea is that the package is public, what's the plan for troubleshooting for people who are not in Santa Barbara? The work that I'm doing is to support Cuban researchers working with EDF, but I can imagine a time when I won't be working on their project. Is the idea that the user will have a more in-depth knowledge of the inner workings of the GUM package? Or is it not really meant for external use?

On Wed, Mar 22, 2017 at 9:54 AM, Tyler Clavelle < notifications@github.com>

wrote:

Are you on campus at all today? It's probably just easier to go over this in person so we can both look at the code/results at the same time.

On Wed, Mar 22, 2017 at 9:11 AM, Tracey Mangin < notifications@github.com

wrote:

Sort of, but I wouldn't know how to use either in this situation. The only columns that return NAs are MaxLength, AgeMat, VonVertK, and Temp (for some species).

But more generally, let's just say what you said is true (CMSY didn’t work and there’s only NA values for k1), what does that mean, and what would be the appropriate next step?

On Wed, Mar 22, 2017 at 9:00 AM, Tyler Clavelle < notifications@github.com> wrote:

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin < notifications@github.com

wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/DanOvando/GUM/issues/10, or mute the thread https://github.com/notifications/unsubscribe- auth/AHyNJ_lCAnT1uhOgPHnbay5o-_CmUQ6vks5roUI6gaJpZM4MlaFe .

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/DanOvando/GUM/issues/10#issuecomment- 288447495 , or mute the thread https://github.com/notifications/unsubscribe-auth/ ALOpsFiIDR0OBlINMbrpCzhqX3jco1Dhks5roUWpgaJpZM4MlaFe .

-- Tracey Mangin Master of Environmental Science and Management 2013 Bren School of Environmental Science & Management University of California, Santa Barbara traceymangin@gmail.com | 201.400.0157 <(201)%20400-0157> <(201)%20400-0157> <(201)%20400-0157> <(201)%20400-0157> <(201)%20400-0157> Skype: traceymangin

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/DanOvando/GUM/issues/10#issuecomment-288451213 , or mute the thread https://github.com/notifications/unsubscribe-auth/ AHyNJ2HuNXQ8Qc1KRGFEogi4GxXS30Azks5roUgugaJpZM4MlaFe

.

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

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DanOvando commented 7 years ago

Friday works for me. Broadly, you guys are currently the only ones using this package ha. So, trying to figure out how much time and effort we want to dedicate to doing a more careful build and debug of GUM. Let's discuss Friday

On Wed, Mar 22, 2017 at 11:42 AM, Tyler Clavelle notifications@github.com wrote:

Friday works best for me. Dan?

On Wed, Mar 22, 2017 at 10:35 AM, Tracey Mangin notifications@github.com

wrote:

Ok -- when are you available tomorrow or Friday?

On Wed, Mar 22, 2017 at 10:30 AM, Tyler Clavelle < notifications@github.com

wrote:

Dan, correct me if I’m wrong here, but I don’t think the original intent of creating the GUM package was to make it freely and publicly available to other users. We created it to facilitate our own projects that use the upside projection modeling, but we don’t necessarily want anyone to use it because it wasn’t meant to be used as an individual fishery assessment tool. It sounds like Chris has you doing just that though, so it probably warrants a broader discussion between the larger group.

There’s no way to make the package error proof and error message are quite often hard to diagnose. We can certainly try to improve the GUM package, but unless we can be sure that the errors are a result of the code and not the underlying data that people are passing to the functions it’s hard to know where to start.

On Wed, Mar 22, 2017 at 10:09 AM, Tracey Mangin < notifications@github.com>

wrote:

I'm not and I don't have a car today. I could come tomorrow afternoon or Friday anytime.

I'm happy to come in and work this out, but I have a more general question about troubleshooting: if the idea is that the package is public, what's the plan for troubleshooting for people who are not in Santa Barbara? The work that I'm doing is to support Cuban researchers working with EDF, but I can imagine a time when I won't be working on their project. Is the idea that the user will have a more in-depth knowledge of the inner workings of the GUM package? Or is it not really meant for external use?

On Wed, Mar 22, 2017 at 9:54 AM, Tyler Clavelle < notifications@github.com>

wrote:

Are you on campus at all today? It's probably just easier to go over this in person so we can both look at the code/results at the same time.

On Wed, Mar 22, 2017 at 9:11 AM, Tracey Mangin < notifications@github.com

wrote:

Sort of, but I wouldn't know how to use either in this situation. The only columns that return NAs are MaxLength, AgeMat, VonVertK, and Temp (for some species).

But more generally, let's just say what you said is true (CMSY didn’t work and there’s only NA values for k1), what does that mean, and what would be the appropriate next step?

On Wed, Mar 22, 2017 at 9:00 AM, Tyler Clavelle < notifications@github.com> wrote:

That error looks like it probably means CMSY didn’t work and there’s only NA values for k1. Hard to say though.

Do you know how to use browser() to debug? If not, I can show you since it will probably make figuring out these errors easier.

Cheers, Tyler

On Wed, Mar 22, 2017 at 8:46 AM, Tracey Mangin < notifications@github.com

wrote:

Hi there!

Just ran the GUM package for a handful of species and got the following warning message:

Warning messages: 1: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf 2: In min(k1[g1 < 1.1 parbound$g[1]], na.rm = T) : no non-missing arguments to min; returning Inf

Just wanted to get some clarity on how to interpret this warning message, and if it suggests that there is a problem with the catch history data.

Thanks! Tracey

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jennifercouture commented 7 years ago

Hey! Just letting you know that I've been using GUM as well as Kristin but not sure who else has this package (I did receive approval from you guys and/or Chris to send the GUM package to a scientist in Japan back in the fall - Gaku - who you guys are meeting with in April I believe). Just an FYI

traceybit commented 7 years ago

Thanks for chiming in, Jenny!

I'm free all of Friday, so just let me know when is a good time for both of you.

Dan -- maybe we can also look at the alternative method that I wrote to you about today?

On Wed, Mar 22, 2017 at 12:16 PM, Jennifer Couture <notifications@github.com

wrote:

Hey! Just letting you know that I've been using GUM as well as Kristin but not sure who else has this package (I did receive approval from you guys and/or Chris to send the GUM package to a scientist in Japan back in the fall - Gaku - who you guys are meeting with in April I believe). Just an FYI

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DanOvando commented 7 years ago

Thanks for the update Jenny, good to know.

I just pushed some updates to GUM that 1) try and fill in the species category if only a scientific name is provided (that was part of the problem with the lobster.csv), and 2) fixes an issue that was occurring finding a "nearest neighbor" for the regression. Works on Tracey's lobster_catch.csv now.

Always best to at least pass it the ISSCAAP species codes, as SpeciesCat and SpeciesCatName if possible.

That should hopefully iron out some of the kinks. We're going to have a discussion soon about the best way to maintain and update this thing, if at all

I would really encourage people that are using this to

1) submit problems or questions directly to GitHub at https://github.com/DanOvando/GUM/issues . Can't promise we'll get to them, but it helps a lot as opposed to keeping track of emails. If they feel comfortable, even better have them submit pull requests to actually fix the problems that they encounter (if that phrase doesn't mean anything to them, then unfortunately they probably can't do this on their own)

2) remind users that this is a very beta tool that was mostly designed for internal consumption. It hasn't been designed as a bullet-proof package yet, and so it very well might fail if the data it gets aren't formatted in the way we try and format things. We're happy to share it, but can't guarantee its performance at this time

3) caveat emptor! We accept no responsibility for the use or results of this model (as it says in the license that you agree to when you use this code), and any results produced are the sole responsibility of the people using the model (i.e. SFG does not "endorse" results that are produced by GUM).

Thanks for the feedback all, good luck!

Dan

On Wed, Mar 22, 2017 at 12:42 PM, Tracey Mangin notifications@github.com wrote:

Thanks for chiming in, Jenny!

I'm free all of Friday, so just let me know when is a good time for both of you.

Dan -- maybe we can also look at the alternative method that I wrote to you about today?

On Wed, Mar 22, 2017 at 12:16 PM, Jennifer Couture < notifications@github.com

wrote:

Hey! Just letting you know that I've been using GUM as well as Kristin but not sure who else has this package (I did receive approval from you guys and/or Chris to send the GUM package to a scientist in Japan back in the fall - Gaku - who you guys are meeting with in April I believe). Just an FYI

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traceybit commented 7 years ago

Hey Dan! Thanks for this. Just so you know, I did pass ISSCAAP species code, SpeciesCat, SpeciesCatName, when trying to run the package for the lobster catch series, although we have been using "SpeciesGroup" as the column name, as opposed to "SpeciesCatName." Is the correct column name "SpeciesCatName"? I thought I tried using this column header at some point, but maybe not.

Thanks a bunch!

On Fri, Mar 24, 2017 at 2:12 PM, Dan Ovando notifications@github.com wrote:

Thanks for the update Jenny, good to know.

I just pushed some updates to GUM that 1) try and fill in the species category if only a scientific name is provided (that was part of the problem with the lobster.csv), and 2) fixes an issue that was occurring finding a "nearest neighbor" for the regression. Works on Tracey's lobster_catch.csv now.

Always best to at least pass it the ISSCAAP species codes, as SpeciesCat and SpeciesCatName if possible.

That should hopefully iron out some of the kinks. We're going to have a discussion soon about the best way to maintain and update this thing, if at all

I would really encourage people that are using this to

1) submit problems or questions directly to GitHub at https://github.com/DanOvando/GUM/issues . Can't promise we'll get to them, but it helps a lot as opposed to keeping track of emails. If they feel comfortable, even better have them submit pull requests to actually fix the problems that they encounter (if that phrase doesn't mean anything to them, then unfortunately they probably can't do this on their own)

2) remind users that this is a very beta tool that was mostly designed for internal consumption. It hasn't been designed as a bullet-proof package yet, and so it very well might fail if the data it gets aren't formatted in the way we try and format things. We're happy to share it, but can't guarantee its performance at this time

3) caveat emptor! We accept no responsibility for the use or results of this model (as it says in the license that you agree to when you use this code), and any results produced are the sole responsibility of the people using the model (i.e. SFG does not "endorse" results that are produced by GUM).

Thanks for the feedback all, good luck!

Dan

On Wed, Mar 22, 2017 at 12:42 PM, Tracey Mangin notifications@github.com wrote:

Thanks for chiming in, Jenny!

I'm free all of Friday, so just let me know when is a good time for both of you.

Dan -- maybe we can also look at the alternative method that I wrote to you about today?

On Wed, Mar 22, 2017 at 12:16 PM, Jennifer Couture < notifications@github.com

wrote:

Hey! Just letting you know that I've been using GUM as well as Kristin but not sure who else has this package (I did receive approval from you guys and/or Chris to send the GUM package to a scientist in Japan back in the fall - Gaku - who you guys are meeting with in April I believe). Just an FYI

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DanOvando commented 7 years ago

Either should work, there were two different errors that were interacting in two interesting ways with the lobster-by-itself example. Best case, pass it a scientific name, a column called SpeciesCat which is the numerical ISSCAAP species category, and SpeciesCatName, which is the name of that group. If you just pass it scientific name now, it will try and look up the others if they aren't included

Dan

On Fri, Mar 24, 2017 at 2:31 PM, Tracey Mangin notifications@github.com wrote:

Hey Dan! Thanks for this. Just so you know, I did pass ISSCAAP species code, SpeciesCat, SpeciesCatName, when trying to run the package for the lobster catch series, although we have been using "SpeciesGroup" as the column name, as opposed to "SpeciesCatName." Is the correct column name "SpeciesCatName"? I thought I tried using this column header at some point, but maybe not.

Thanks a bunch!

On Fri, Mar 24, 2017 at 2:12 PM, Dan Ovando notifications@github.com wrote:

Thanks for the update Jenny, good to know.

I just pushed some updates to GUM that 1) try and fill in the species category if only a scientific name is provided (that was part of the problem with the lobster.csv), and 2) fixes an issue that was occurring finding a "nearest neighbor" for the regression. Works on Tracey's lobster_catch.csv now.

Always best to at least pass it the ISSCAAP species codes, as SpeciesCat and SpeciesCatName if possible.

That should hopefully iron out some of the kinks. We're going to have a discussion soon about the best way to maintain and update this thing, if at all

I would really encourage people that are using this to

1) submit problems or questions directly to GitHub at https://github.com/DanOvando/GUM/issues . Can't promise we'll get to them, but it helps a lot as opposed to keeping track of emails. If they feel comfortable, even better have them submit pull requests to actually fix the problems that they encounter (if that phrase doesn't mean anything to them, then unfortunately they probably can't do this on their own)

2) remind users that this is a very beta tool that was mostly designed for internal consumption. It hasn't been designed as a bullet-proof package yet, and so it very well might fail if the data it gets aren't formatted in the way we try and format things. We're happy to share it, but can't guarantee its performance at this time

3) caveat emptor! We accept no responsibility for the use or results of this model (as it says in the license that you agree to when you use this code), and any results produced are the sole responsibility of the people using the model (i.e. SFG does not "endorse" results that are produced by GUM).

Thanks for the feedback all, good luck!

Dan

On Wed, Mar 22, 2017 at 12:42 PM, Tracey Mangin < notifications@github.com> wrote:

Thanks for chiming in, Jenny!

I'm free all of Friday, so just let me know when is a good time for both of you.

Dan -- maybe we can also look at the alternative method that I wrote to you about today?

On Wed, Mar 22, 2017 at 12:16 PM, Jennifer Couture < notifications@github.com

wrote:

Hey! Just letting you know that I've been using GUM as well as Kristin but not sure who else has this package (I did receive approval from you guys and/or Chris to send the GUM package to a scientist in Japan back in the fall - Gaku - who you guys are meeting with in April I believe). Just an FYI

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