discrepancies with SIS database

[mcmelnychuk]

There are not many discrepancies, but there are a few.

1) What should we do when a stock has previously been assessed, but currently is not classified as such under SIS? There are a few stocks that would previously have met the criteria, but currently they're assigned a low level (1 or 2) in SIS. This seems to have occurred in most cases because it's recently been thought that the input data and/or previous assessment are insufficient. These stocks are currently counted as assessed in our dataset, even though SIS does not currently count them as such. Does anyone want to revisit this classification? The stocks are:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GoMaine winter flounder 2003 Winter flounder - Gulf of Maine 1 nGeBank/GoMaine silver hake 1978 Silver hake - Gulf of Maine / Northern Georges Bank 1 sGeBank/midAtl silver hake 1978 Silver hake - Southern Georges Bank / Mid-Atlantic 1 USNE deep sea red crab 1977 Red deepsea crab - Northwestern Atlantic 1 (one-time assessment) USNE longfin inshore squid 1976 Longfin inshore squid - Georges Bank / Cape Hatteras 1 USNE northern shortfin squid 1986 Northern shortfin squid - Northwestern Atlantic Coast 2 USWC market squid 2001 Opalescent inshore squid - Pacific Coast 2

2) In contrast, there are a couple stocks that we've classified as not assessed ("only relative indices"), but SIS has a "3" assigned. (No mismatches involving a 4 or 5 in SIS). After reviewing the latest stock assessment I think it's appropriate to continue classifying these as unassessed, but here they are for interest:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GOA shortraker rockfish only relative indices Shortraker rockfish - Gulf of Alaska 3 GOA yelloweye rockfish only relative indices Yelloweye rockfish - Gulf of Alaska 3

For reference, these are the SIS categorical definitions:

11. Levels of Stock Assessment Models 0—Although some data may have been collected on this species, these data have not been examined beyond simple time series plots or tabulations of catch. 1—Either: a) time series of a (potentially imprecise) abundance index calculated as raw or standardized CPUE in commercial, recreational, or survey vessel data, or b) onetime estimation of absolute abundance made on the basis of tagging results, a depletion study, or some form of calibrated survey. 2—Simple equilibrium models applied to life history information; for example, yield per recruit or spawner per recruit functions based on mortality, growth, and maturity schedules; catch curve analysis; survival analysis; or length-based cohort analysis. 3—Equilibrium and non-equilibrium production models aggregated both spatially and over age and size; for example, the Schaefer model and the Pella-Tomlinson model. 4—Size, stage, or age structured models such as cohort analysis and untuned and tuned VPA analyses, age-structured production models, CAGEAN, stock synthesis, size or age-structured Bayesian models, modified DeLury methods, and size or age-based mark-recapture models. 5—Assesssment models incorporating ecosystem considerations and spatial and seasonal analyses in addition to Levels 3 or 4. Ecosystem considerations include one or more of the following: a) one or more time-varying parameters, either estimated as constrained series, or driven by environmental variables, b) multiple target species as state variables in the model, or c) living components of the ecosystem other than the target species included as state variables in the model.

[James-Thorson]

I'm fine classifying stocks that were previously assessed but have since been downgraded in SIS as "assessed", as we currently do

I also agree with not listing index-only models as "assessed".

So I vote for keeping our database as-is rather than updating to match SIS for these two points.

Mike -- would you be willing to write an appendix listing these detailed decisions in applying our definition of "assessments"?

On Nov 11, 2016 4:08 PM, "Michael Melnychuk" notifications@github.com wrote:

There are not many discrepancies, but there are a few.

1. What should we do when a stock has previously been assessed, but currently is not classified as such under SIS? There are a few stocks that would previously have met the criteria, but currently they're assigned a low level (1 or 2) in SIS. This seems to have occurred in most cases because it's recently been thought that the input data and/or previous assessment are insufficient. These stocks are currently counted as assessed in our dataset, even though SIS does not currently count them as such. Does anyone want to revisit this classification? The stocks are:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GoMaine winter flounder 2003 Winter flounder - Gulf of Maine 1 nGeBank/GoMaine silver hake 1978 Silver hake - Gulf of Maine / Northern Georges Bank 1 sGeBank/midAtl silver hake 1978 Silver hake - Southern Georges Bank / Mid-Atlantic 1 USNE deep sea red crab 1977 Red deepsea crab - Northwestern Atlantic 1 (one-time assessment) USNE longfin inshore squid 1976 Longfin inshore squid - Georges Bank / Cape Hatteras 1 USNE northern shortfin squid 1986 Northern shortfin squid - Northwestern Atlantic Coast 2 USWC market squid 2001 Opalescent inshore squid - Pacific Coast 2

1. In contrast, there are a couple stocks that we've classified as not assessed ("only relative indices"), but SIS has a "3" assigned. (No mismatches involving a 4 or 5 in SIS). After reviewing the latest stock assessment I think it's appropriate to continue classifying these as unassessed, but here they are for interest:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GOA shortraker rockfish only relative indices Shortraker rockfish - Gulf of Alaska 3 GOA yelloweye rockfish only relative indices Yelloweye rockfish - Gulf of Alaska 3

For reference, these are the SIS categorical definitions:

1. Levels of Stock Assessment Models 0—Although some data may have been collected on this species, these data have not been examined beyond simple time series plots or tabulations of catch. 1—Either: a) time series of a (potentially imprecise) abundance index calculated as raw or standardized CPUE in commercial, recreational, or survey vessel data, or b) onetime estimation of absolute abundance made on the basis of tagging results, a depletion study, or some form of calibrated survey. 2—Simple equilibrium models applied to life history information; for example, yield per recruit or spawner per recruit functions based on mortality, growth, and maturity schedules; catch curve analysis; survival analysis; or length-based cohort analysis. 3—Equilibrium and non-equilibrium production models aggregated both spatially and over age and size; for example, the Schaefer model and the Pella-Tomlinson model. 4—Size, stage, or age structured models such as cohort analysis and untuned and tuned VPA analyses, age-structured production models, CAGEAN, stock synthesis, size or age-structured Bayesian models, modified DeLury methods, and size or age-based mark-recapture models. 5—Assesssment models incorporating ecosystem considerations and spatial and seasonal analyses in addition to Levels 3 or 4. Ecosystem considerations include one or more of the following: a) one or more time-varying parameters, either estimated as constrained series, or driven by environmental variables, b) multiple target species as state variables in the model, or c) living components of the ecosystem other than the target species included as state variables in the model.

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[Philipp-Neubauer]

Same here, I think that as long as we detail the reasoning behind our decision its fine to stick with our definition. Given that the SIS is a 5 level classification, and ours is binary, we are bound to not align perfectly with any one category.

On Sat, Nov 12, 2016 at 2:27 PM, Jim Thorson notifications@github.com wrote:

I'm fine classifying stocks that were previously assessed but have since been downgraded in SIS as "assessed", as we currently do

I also agree with not listing index-only models as "assessed".

So I vote for keeping our database as-is rather than updating to match SIS for these two points.

Mike -- would you be willing to write an appendix listing these detailed decisions in applying our definition of "assessments"?

On Nov 11, 2016 4:08 PM, "Michael Melnychuk" notifications@github.com wrote:

There are not many discrepancies, but there are a few.

1. What should we do when a stock has previously been assessed, but currently is not classified as such under SIS? There are a few stocks that would previously have met the criteria, but currently they're assigned a low level (1 or 2) in SIS. This seems to have occurred in most cases because it's recently been thought that the input data and/or previous assessment are insufficient. These stocks are currently counted as assessed in our dataset, even though SIS does not currently count them as such. Does anyone want to revisit this classification? The stocks are:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GoMaine winter flounder 2003 Winter flounder - Gulf of Maine 1 nGeBank/GoMaine silver hake 1978 Silver hake - Gulf of Maine / Northern Georges Bank 1 sGeBank/midAtl silver hake 1978 Silver hake - Southern Georges Bank / Mid-Atlantic 1 USNE deep sea red crab 1977 Red deepsea crab - Northwestern Atlantic 1 (one-time assessment) USNE longfin inshore squid 1976 Longfin inshore squid - Georges Bank / Cape Hatteras 1 USNE northern shortfin squid 1986 Northern shortfin squid - Northwestern Atlantic Coast 2 USWC market squid 2001 Opalescent inshore squid - Pacific Coast 2

1. In contrast, there are a couple stocks that we've classified as not assessed ("only relative indices"), but SIS has a "3" assigned. (No mismatches involving a 4 or 5 in SIS). After reviewing the latest stock assessment I think it's appropriate to continue classifying these as unassessed, but here they are for interest:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GOA shortraker rockfish only relative indices Shortraker rockfish - Gulf of Alaska 3 GOA yelloweye rockfish only relative indices Yelloweye rockfish - Gulf of Alaska 3

For reference, these are the SIS categorical definitions:

1. Levels of Stock Assessment Models

0—Although some data may have been collected on this species, these data have not been examined beyond simple time series plots or tabulations of catch. 1—Either: a) time series of a (potentially imprecise) abundance index calculated as raw or standardized CPUE in commercial, recreational, or survey vessel data, or b) onetime estimation of absolute abundance made on the basis of tagging results, a depletion study, or some form of calibrated survey. 2—Simple equilibrium models applied to life history information; for example, yield per recruit or spawner per recruit functions based on mortality, growth, and maturity schedules; catch curve analysis; survival analysis; or length-based cohort analysis. 3—Equilibrium and non-equilibrium production models aggregated both spatially and over age and size; for example, the Schaefer model and the Pella-Tomlinson model. 4—Size, stage, or age structured models such as cohort analysis and untuned and tuned VPA analyses, age-structured production models, CAGEAN, stock synthesis, size or age-structured Bayesian models, modified DeLury methods, and size or age-based mark-recapture models. 5—Assesssment models incorporating ecosystem considerations and spatial and seasonal analyses in addition to Levels 3 or 4. Ecosystem considerations include one or more of the following: a) one or more time-varying parameters, either estimated as constrained series, or driven by environmental variables, b) multiple target species as state variables in the model, or c) living components of the ecosystem other than the target species included as state variables in the model.

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Phil

[mcmelnychuk]

Sounds good. In theory our positives SHOULD align with SIS >= 3, but the two lists below cover both types of mismatches that occur.

Yes, I'm happy to write an appendix that summarizes the comparison with SIS. I'm happy to include all the year of first assessment values and release those publicly. Should we list all the taxonomic and habitat assignments in the same big table?

Mike

On 2016-11-11 5:58 PM, Philipp Neubauer wrote:

Same here, I think that as long as we detail the reasoning behind our decision its fine to stick with our definition. Given that the SIS is a 5 level classification, and ours is binary, we are bound to not align perfectly with any one category.

On Sat, Nov 12, 2016 at 2:27 PM, Jim Thorson notifications@github.com wrote:

I'm fine classifying stocks that were previously assessed but have since been downgraded in SIS as "assessed", as we currently do

I also agree with not listing index-only models as "assessed".

So I vote for keeping our database as-is rather than updating to match SIS for these two points.

Mike -- would you be willing to write an appendix listing these detailed decisions in applying our definition of "assessments"?

On Nov 11, 2016 4:08 PM, "Michael Melnychuk" notifications@github.com wrote:

There are not many discrepancies, but there are a few.

1. What should we do when a stock has previously been assessed, but currently is not classified as such under SIS? There are a few stocks that would previously have met the criteria, but currently they're assigned a low level (1 or 2) in SIS. This seems to have occurred in most cases because it's recently been thought that the input data and/or previous assessment are insufficient. These stocks are currently counted as assessed in our dataset, even though SIS does not currently count them as such. Does anyone want to revisit this classification? The stocks are:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GoMaine winter flounder 2003 Winter flounder - Gulf of Maine 1 nGeBank/GoMaine silver hake 1978 Silver hake - Gulf of Maine / Northern Georges Bank 1 sGeBank/midAtl silver hake 1978 Silver hake - Southern Georges Bank / Mid-Atlantic 1 USNE deep sea red crab 1977 Red deepsea crab - Northwestern Atlantic 1 (one-time assessment) USNE longfin inshore squid 1976 Longfin inshore squid - Georges Bank / Cape Hatteras 1 USNE northern shortfin squid 1986 Northern shortfin squid - Northwestern Atlantic Coast 2 USWC market squid 2001 Opalescent inshore squid - Pacific Coast 2

1. In contrast, there are a couple stocks that we've classified as not assessed ("only relative indices"), but SIS has a "3" assigned. (No mismatches involving a 4 or 5 in SIS). After reviewing the latest stock assessment I think it's appropriate to continue classifying these as unassessed, but here they are for interest:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GOA shortraker rockfish only relative indices Shortraker rockfish

• Gulf of Alaska 3 GOA yelloweye rockfish only relative indices Yelloweye rockfish - Gulf of Alaska 3

For reference, these are the SIS categorical definitions:

1. Levels of Stock Assessment Models

0—Although some data may have been collected on this species, these data have not been examined beyond simple time series plots or tabulations of catch. 1—Either: a) time series of a (potentially imprecise) abundance index calculated as raw or standardized CPUE in commercial, recreational, or survey vessel data, or b) onetime estimation of absolute abundance made on the basis of tagging results, a depletion study, or some form of calibrated survey. 2—Simple equilibrium models applied to life history information; for example, yield per recruit or spawner per recruit functions based on mortality, growth, and maturity schedules; catch curve analysis; survival analysis; or length-based cohort analysis. 3—Equilibrium and non-equilibrium production models aggregated both spatially and over age and size; for example, the Schaefer model and the Pella-Tomlinson model. 4—Size, stage, or age structured models such as cohort analysis and untuned and tuned VPA analyses, age-structured production models, CAGEAN, stock synthesis, size or age-structured Bayesian models, modified DeLury methods, and size or age-based mark-recapture models. 5—Assesssment models incorporating ecosystem considerations and spatial and seasonal analyses in addition to Levels 3 or 4. Ecosystem considerations include one or more of the following: a) one or more time-varying parameters, either estimated as constrained series, or driven by environmental variables, b) multiple target species as state variables in the model, or c) living components of the ecosystem other than the target species included as state variables in the model.

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[James-Thorson]

I'm in favor of releasing our "processed" database along with the paper. So yes, ideally all merged attributes of assessed and unassessed species if that's easy to output as a CSV Phil?

On Nov 11, 2016 6:07 PM, "Michael Melnychuk" notifications@github.com wrote:

Sounds good. In theory our positives SHOULD align with SIS >= 3, but the two lists below cover both types of mismatches that occur.

Yes, I'm happy to write an appendix that summarizes the comparison with SIS. I'm happy to include all the year of first assessment values and release those publicly. Should we list all the taxonomic and habitat assignments in the same big table?

Mike

On 2016-11-11 5:58 PM, Philipp Neubauer wrote:

Same here, I think that as long as we detail the reasoning behind our decision its fine to stick with our definition. Given that the SIS is a 5 level classification, and ours is binary, we are bound to not align perfectly with any one category.

On Sat, Nov 12, 2016 at 2:27 PM, Jim Thorson notifications@github.com wrote:

I'm fine classifying stocks that were previously assessed but have since been downgraded in SIS as "assessed", as we currently do

I also agree with not listing index-only models as "assessed".

So I vote for keeping our database as-is rather than updating to match SIS for these two points.

Mike -- would you be willing to write an appendix listing these detailed decisions in applying our definition of "assessments"?

On Nov 11, 2016 4:08 PM, "Michael Melnychuk" <notifications@github.com

wrote:

There are not many discrepancies, but there are a few.

1. What should we do when a stock has previously been assessed, but currently is not classified as such under SIS? There are a few stocks that would previously have met the criteria, but currently they're assigned a low level (1 or 2) in SIS. This seems to have occurred in most cases because it's recently been thought that the input data and/or previous assessment are insufficient. These stocks are currently counted as assessed in our dataset, even though SIS does not currently count them as such. Does anyone want to revisit this classification? The stocks are:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GoMaine winter flounder 2003 Winter flounder - Gulf of Maine 1 nGeBank/GoMaine silver hake 1978 Silver hake - Gulf of Maine / Northern Georges Bank 1 sGeBank/midAtl silver hake 1978 Silver hake - Southern Georges Bank / Mid-Atlantic 1 USNE deep sea red crab 1977 Red deepsea crab - Northwestern Atlantic 1 (one-time assessment) USNE longfin inshore squid 1976 Longfin inshore squid - Georges Bank / Cape Hatteras 1 USNE northern shortfin squid 1986 Northern shortfin squid - Northwestern Atlantic Coast 2 USWC market squid 2001 Opalescent inshore squid - Pacific Coast 2

1. In contrast, there are a couple stocks that we've classified as not assessed ("only relative indices"), but SIS has a "3" assigned. (No mismatches involving a 4 or 5 in SIS). After reviewing the latest stock assessment I think it's appropriate to continue classifying these as unassessed, but here they are for interest:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GOA shortraker rockfish only relative indices Shortraker rockfish

• Gulf of Alaska 3 GOA yelloweye rockfish only relative indices Yelloweye rockfish - Gulf of Alaska 3

For reference, these are the SIS categorical definitions:

1. Levels of Stock Assessment Models

0—Although some data may have been collected on this species, these data have not been examined beyond simple time series plots or tabulations of catch. 1—Either: a) time series of a (potentially imprecise) abundance index calculated as raw or standardized CPUE in commercial, recreational, or survey vessel data, or b) onetime estimation of absolute abundance made on the basis of tagging results, a depletion study, or some form of calibrated survey. 2—Simple equilibrium models applied to life history information; for example, yield per recruit or spawner per recruit functions based on mortality, growth, and maturity schedules; catch curve analysis; survival analysis; or length-based cohort analysis. 3—Equilibrium and non-equilibrium production models aggregated both spatially and over age and size; for example, the Schaefer model and the Pella-Tomlinson model. 4—Size, stage, or age structured models such as cohort analysis and untuned and tuned VPA analyses, age-structured production models, CAGEAN, stock synthesis, size or age-structured Bayesian models, modified DeLury methods, and size or age-based mark-recapture models. 5—Assesssment models incorporating ecosystem considerations and spatial and seasonal analyses in addition to Levels 3 or 4. Ecosystem considerations include one or more of the following: a) one or more time-varying parameters, either estimated as constrained series, or driven by environmental variables, b) multiple target species as state variables in the model, or c) living components of the ecosystem other than the target species included as state variables in the model.

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[Philipp-Neubauer]

Yes, that's easy. I'll add some code to put out all relevant fields.

On Sat, Nov 12, 2016 at 4:58 PM, Jim Thorson notifications@github.com wrote:

I'm in favor of releasing our "processed" database along with the paper. So yes, ideally all merged attributes of assessed and unassessed species if that's easy to output as a CSV Phil?

On Nov 11, 2016 6:07 PM, "Michael Melnychuk" notifications@github.com

wrote:

Sounds good. In theory our positives SHOULD align with SIS >= 3, but the two lists below cover both types of mismatches that occur.

Yes, I'm happy to write an appendix that summarizes the comparison with SIS. I'm happy to include all the year of first assessment values and release those publicly. Should we list all the taxonomic and habitat assignments in the same big table?

Mike

On 2016-11-11 5:58 PM, Philipp Neubauer wrote:

Same here, I think that as long as we detail the reasoning behind our decision its fine to stick with our definition. Given that the SIS is a 5 level classification, and ours is binary, we are bound to not align perfectly with any one category.

On Sat, Nov 12, 2016 at 2:27 PM, Jim Thorson <notifications@github.com

wrote:

I'm fine classifying stocks that were previously assessed but have since been downgraded in SIS as "assessed", as we currently do

I also agree with not listing index-only models as "assessed".

So I vote for keeping our database as-is rather than updating to match SIS for these two points.

Mike -- would you be willing to write an appendix listing these detailed decisions in applying our definition of "assessments"?

On Nov 11, 2016 4:08 PM, "Michael Melnychuk" < notifications@github.com

wrote:

There are not many discrepancies, but there are a few.

1. What should we do when a stock has previously been assessed, but

currently is not classified as such under SIS? There are a few stocks that would previously have met the criteria, but currently they're assigned a low level (1 or 2) in SIS. This seems to have occurred in most cases because it's recently been thought that the input data and/or previous assessment are insufficient. These stocks are currently counted as assessed in our dataset, even though SIS does not currently count them as such. Does anyone want to revisit this classification? The stocks are:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GoMaine winter flounder 2003 Winter flounder - Gulf of Maine 1 nGeBank/GoMaine silver hake 1978 Silver hake - Gulf of Maine / Northern Georges Bank 1 sGeBank/midAtl silver hake 1978 Silver hake - Southern Georges Bank / Mid-Atlantic 1 USNE deep sea red crab 1977 Red deepsea crab - Northwestern Atlantic 1 (one-time assessment) USNE longfin inshore squid 1976 Longfin inshore squid - Georges Bank / Cape Hatteras 1 USNE northern shortfin squid 1986 Northern shortfin squid - Northwestern Atlantic Coast 2 USWC market squid 2001 Opalescent inshore squid - Pacific Coast 2

1. In contrast, there are a couple stocks that we've classified as not assessed ("only relative indices"), but SIS has a "3" assigned. (No mismatches involving a 4 or 5 in SIS). After reviewing the latest stock assessment I think it's appropriate to continue classifying these as unassessed, but here they are for interest:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GOA shortraker rockfish only relative indices Shortraker rockfish

• Gulf of Alaska 3 GOA yelloweye rockfish only relative indices Yelloweye rockfish - Gulf of Alaska 3

For reference, these are the SIS categorical definitions:

1. Levels of Stock Assessment Models

0—Although some data may have been collected on this species, these data have not been examined beyond simple time series plots or tabulations of catch. 1—Either: a) time series of a (potentially imprecise) abundance index calculated as raw or standardized CPUE in commercial, recreational, or survey vessel data, or b) onetime estimation of absolute abundance made on the basis of tagging results, a depletion study, or some form of calibrated survey. 2—Simple equilibrium models applied to life history information; for example, yield per recruit or spawner per recruit functions based on mortality, growth, and maturity schedules; catch curve analysis; survival analysis; or length-based cohort analysis. 3—Equilibrium and non-equilibrium production models aggregated both spatially and over age and size; for example, the Schaefer model and the Pella-Tomlinson model. 4—Size, stage, or age structured models such as cohort analysis and untuned and tuned VPA analyses, age-structured production models, CAGEAN, stock synthesis, size or age-structured Bayesian models, modified DeLury methods, and size or age-based mark-recapture models. 5—Assesssment models incorporating ecosystem considerations and spatial and seasonal analyses in addition to Levels 3 or 4. Ecosystem considerations include one or more of the following: a) one or more time-varying parameters, either estimated as constrained series, or driven by environmental variables, b) multiple target species as state variables in the model, or c) living components of the ecosystem other than the target species included as state variables in the model.

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[mcmelnychuk]

Sounds good, once we've finalized that I'll add on the fields containing the comparison with the SIS database.

Mike

On 2016-11-11 10:22 PM, Philipp Neubauer wrote:

Yes, that's easy. I'll add some code to put out all relevant fields.

On Sat, Nov 12, 2016 at 4:58 PM, Jim Thorson notifications@github.com wrote:

I'm in favor of releasing our "processed" database along with the paper. So yes, ideally all merged attributes of assessed and unassessed species if that's easy to output as a CSV Phil?

On Nov 11, 2016 6:07 PM, "Michael Melnychuk" notifications@github.com

wrote:

Sounds good. In theory our positives SHOULD align with SIS >= 3, but the two lists below cover both types of mismatches that occur.

Yes, I'm happy to write an appendix that summarizes the comparison with SIS. I'm happy to include all the year of first assessment values and release those publicly. Should we list all the taxonomic and habitat assignments in the same big table?

Mike

On 2016-11-11 5:58 PM, Philipp Neubauer wrote:

Same here, I think that as long as we detail the reasoning behind our decision its fine to stick with our definition. Given that the SIS is a 5 level classification, and ours is binary, we are bound to not align perfectly with any one category.

On Sat, Nov 12, 2016 at 2:27 PM, Jim Thorson <notifications@github.com

wrote:

I'm fine classifying stocks that were previously assessed but have since been downgraded in SIS as "assessed", as we currently do

I also agree with not listing index-only models as "assessed".

So I vote for keeping our database as-is rather than updating to match SIS for these two points.

Mike -- would you be willing to write an appendix listing these detailed decisions in applying our definition of "assessments"?

On Nov 11, 2016 4:08 PM, "Michael Melnychuk" < notifications@github.com

wrote:

There are not many discrepancies, but there are a few.

1. What should we do when a stock has previously been assessed, but

currently is not classified as such under SIS? There are a few stocks that would previously have met the criteria, but currently they're assigned a low level (1 or 2) in SIS. This seems to have occurred in most cases because it's recently been thought that the input data and/or previous assessment are insufficient. These stocks are currently counted as assessed in our dataset, even though SIS does not currently count them as such. Does anyone want to revisit this classification? The stocks are:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GoMaine winter flounder 2003 Winter flounder - Gulf of Maine 1 nGeBank/GoMaine silver hake 1978 Silver hake - Gulf of Maine / Northern Georges Bank 1 sGeBank/midAtl silver hake 1978 Silver hake - Southern Georges Bank / Mid-Atlantic 1 USNE deep sea red crab 1977 Red deepsea crab - Northwestern Atlantic 1 (one-time assessment) USNE longfin inshore squid 1976 Longfin inshore squid - Georges Bank / Cape Hatteras 1 USNE northern shortfin squid 1986 Northern shortfin squid - Northwestern Atlantic Coast 2 USWC market squid 2001 Opalescent inshore squid - Pacific Coast 2

1. In contrast, there are a couple stocks that we've classified as not assessed ("only relative indices"), but SIS has a "3" assigned. (No mismatches involving a 4 or 5 in SIS). After reviewing the latest stock assessment I think it's appropriate to continue classifying these as unassessed, but here they are for interest:

Stock name Year of first stock assessment SIS stock name SIS Assessment Level GOA shortraker rockfish only relative indices Shortraker rockfish

• Gulf of Alaska 3 GOA yelloweye rockfish only relative indices Yelloweye rockfish - Gulf of Alaska 3

For reference, these are the SIS categorical definitions:

1. Levels of Stock Assessment Models

0—Although some data may have been collected on this species, these data have not been examined beyond simple time series plots or tabulations of catch. 1—Either: a) time series of a (potentially imprecise) abundance index calculated as raw or standardized CPUE in commercial, recreational, or survey vessel data, or b) onetime estimation of absolute abundance made on the basis of tagging results, a depletion study, or some form of calibrated survey. 2—Simple equilibrium models applied to life history information; for example, yield per recruit or spawner per recruit functions based on mortality, growth, and maturity schedules; catch curve analysis; survival analysis; or length-based cohort analysis. 3—Equilibrium and non-equilibrium production models aggregated both spatially and over age and size; for example, the Schaefer model and the Pella-Tomlinson model. 4—Size, stage, or age structured models such as cohort analysis and untuned and tuned VPA analyses, age-structured production models, CAGEAN, stock synthesis, size or age-structured Bayesian models, modified DeLury methods, and size or age-based mark-recapture models. 5—Assesssment models incorporating ecosystem considerations and spatial and seasonal analyses in addition to Levels 3 or 4. Ecosystem considerations include one or more of the following: a) one or more time-varying parameters, either estimated as constrained series, or driven by environmental variables, b) multiple target species as state variables in the model, or c) living components of the ecosystem other than the target species included as state variables in the model.

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[Philipp-Neubauer]

Is the number in the discussion (7) still right?

[mcmelnychuk]

It looks like my responding to emails is not always getting picked up in the threads, so I apologize if any of my replies haven't gone through properly. I'm going to add a few sent emails to the corresponding threads. Here is one from a few days ago:

That should still be correct. All of the stocks we just added were either not in SIS, or else were a level 4 in SIS, so there are no further discrepancies.

[mcmelnychuk]

looks like there were only 2 emails that didn't get picked up. The second one is redundant now after my post in thread 5 today.

[mcmelnychuk]

I wrote up a short appendix comparing our assessment classifications with those of SIS. I'm unsure of the fomatting and insertion points for an Appendix in Latex, so I'll just attach the text file here; the text can just be copy/pasted wherever it best belongs.

When "dataset.csv" and "dataset_missed.csv" files are finalized, I'll add two columns to each of those files containing the corresponding SIS stock names and assessment level categories.

Appendix - validation with SIS.txt

[Philipp-Neubauer]

Thanks, Mike, the best time to add the SIS appendix would be when we deal with Rick's comments - I think; do it all in one go.

I don't anticipate any more changes to dataset.csv - unless I've missed something, of course...

Happy new year btw!

[Philipp-Neubauer]

woops

[James-Thorson]

@mcmelnychuk

Do you know anything about fishsource.org? Rick's wondering.

Also, any guess why emails to "mikem@zoology.ubc.ca" are bouncing, and what email I should use for you?

Jim

[mcmelnychuk]

hi Jim,

Thanks for letting me know about the bounces. I think I tested that the other day and it was fine, so maybe it's a temporary thing. At any rate, please use "mmel@uw.edu" or "mmel@u.washington.edu".

We coordinate with FishSource and have previously done a QAQC cross-check, but not recently (another is planned for a few months down the road). They also get their information from stock assessments. They build qualitative scores based on assessment data. I don't think they explicitly collect anything about historical changes, like year of first assessment. Did Rick have anything in mind?

Mike

On 2017-01-24 9:55 AM, Jim Thorson wrote:

@mcmelnychuk https://github.com/mcmelnychuk

Do you know anything about fishsource.org? Rick's wondering.

Also, any guess why emails to "mikem@zoology.ubc.ca mailto:mikem@zoology.ubc.ca" are bouncing, and what email I should use for you?

Jim

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[James-Thorson]

Could you email Rick directly and cc me? I'm not sure what he has in mind...

On Tue, Jan 24, 2017 at 10:08 AM, Michael Melnychuk < notifications@github.com> wrote:

hi Jim,

Thanks for letting me know about the bounces. I think I tested that the other day and it was fine, so maybe it's a temporary thing. At any rate, please use "mmel@uw.edu" or "mmel@u.washington.edu".

We coordinate with FishSource and have previously done a QAQC cross-check, but not recently (another is planned for a few months down the road). They also get their information from stock assessments. They build qualitative scores based on assessment data. I don't think they explicitly collect anything about historical changes, like year of first assessment. Did Rick have anything in mind?

Mike

On 2017-01-24 9:55 AM, Jim Thorson wrote:

@mcmelnychuk https://github.com/mcmelnychuk

Do you know anything about fishsource.org? Rick's wondering.

Also, any guess why emails to "mikem@zoology.ubc.ca mailto:mikem@zoology.ubc.ca" are bouncing, and what email I should use for you?

Jim

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