Manuscript text

[James-Thorson]

I just added a few more paragraphs to the introduction (Rnw file), but still can't compile to the PDF (see other issue for next bug).

This intro is basically a standard 5-paragraph style intro giving:

1. context for fisheries management
2. defining stock assessment
3. explaining rate of assessment
4. justifying why studying rate-of-assessment would be useful
5. outlining our paper's goals.

I'm happy to heavily modify it, but think its a decent place to start

[Philipp-Neubauer]

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

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Phil

[Philipp-Neubauer]

To add to this:

I tried the 'un-assessed post 1996' effect, and it comes out negative. I'm not sure if that alone is worth including, as it doesn't say much about price effects in different decades, etc. Just FYI right now, mean price and max landings that go into the model are taken before the assessment year for assessed stocks.

On Mon, Nov 21, 2016 at 11:35 AM, Philipp Neubauer neubauer.phil@gmail.com wrote:

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

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Phil

Phil

[Philipp-Neubauer]

Also, Mike - do you have the citations you added in your ref manager? If so, could you export them as bibtex and copy-paste them into the FirstAssessment.bib? I can add the refs in, but that would save me having to get them all individually...

My apologies for not having managed to get involved much with the discussion - been battling all those grooming rules and little glitches; and lately even the models didn't spit out anything coherent anymore (got that back to normal, at least.)

On Wed, Nov 23, 2016 at 10:25 PM, Philipp Neubauer neubauer.phil@gmail.com wrote:

To add to this:

I tried the 'un-assessed post 1996' effect, and it comes out negative. I'm not sure if that alone is worth including, as it doesn't say much about price effects in different decades, etc. Just FYI right now, mean price and max landings that go into the model are taken before the assessment year for assessed stocks.

On Mon, Nov 21, 2016 at 11:35 AM, Philipp Neubauer < neubauer.phil@gmail.com> wrote:

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-261154300, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_ oVez2nUr0jjGMFAnd21NbMT20dqEPks5q-9vXgaJpZM4KgiJj.

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Phil

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Phil

Phil

Phil

[mcmelnychuk]

Sounds good, and seems we have plenty going on already.

We might have to revise a sentence in the methods, I think I incorrectly mentioned somewhere that the dependency on price was evaluated annually rather that it being the mean of the pre-assessment portion. In the figures, we could label price as "Mean ex-vessel price", which would put it on par with "Maximum landings".

Mike

On 2016-11-23 1:25 AM, Philipp Neubauer wrote:

To add to this:

I tried the 'un-assessed post 1996' effect, and it comes out negative. I'm not sure if that alone is worth including, as it doesn't say much about price effects in different decades, etc. Just FYI right now, mean price and max landings that go into the model are taken before the assessment year for assessed stocks.

On Mon, Nov 21, 2016 at 11:35 AM, Philipp Neubauer neubauer.phil@gmail.com wrote:

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-261154300, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_ oVez2nUr0jjGMFAnd21NbMT20dqEPks5q-9vXgaJpZM4KgiJj.

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Phil

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[mcmelnychuk]

pasted.

No apologies at all needed - thanks instead to you for doing all of the hard work!

Mike

On 2016-11-23 1:31 AM, Philipp Neubauer wrote:

Also, Mike - do you have the citations you added in your ref manager? If so, could you export them as bibtex and copy-paste them into the FirstAssessment.bib? I can add the refs in, but that would save me having to get them all individually...

My apologies for not having managed to get involved much with the discussion - been battling all those grooming rules and little glitches; and lately even the models didn't spit out anything coherent anymore (got that back to normal, at least.)

On Wed, Nov 23, 2016 at 10:25 PM, Philipp Neubauer neubauer.phil@gmail.com wrote:

To add to this:

I tried the 'un-assessed post 1996' effect, and it comes out negative. I'm not sure if that alone is worth including, as it doesn't say much about price effects in different decades, etc. Just FYI right now, mean price and max landings that go into the model are taken before the assessment year for assessed stocks.

On Mon, Nov 21, 2016 at 11:35 AM, Philipp Neubauer < neubauer.phil@gmail.com> wrote:

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-261154300, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_ oVez2nUr0jjGMFAnd21NbMT20dqEPks5q-9vXgaJpZM4KgiJj.

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Phil

Phil

Phil

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[Philipp-Neubauer]

Have done some editing in the methods to more accurately reflect what we're doing with time-to-assessment, and covariates. I've also updated the results to reflect updated model outputs. Did a little bit of editing in the discussion, mainly in the propensity score paragraph - tried to clarify a couple of sentences, hope it worked...

3 possible points to add:

1. In the updated model, the interaction of price and landings is negative. So it seems its more a case of Price OR Landings rather than price AND landings. We should probably edit the discussion to reflect this
2. right?
3. Max length now comes through as significant - a generalisation of the charismatic mega-fauna effect beyond conservation to fisheries management? Would make for an amusing paragraph, perhaps ;) But more seriously, it seems like an argument against the fishing down the food chain hypothesis (at least for US waters) - if large fish are preferentially assessed, they are probably also managed better, preventing fishing-down patterns from occurring in US waters...
4. With some more though, it seems as though the addition of a post-1996 effect could be good to support our statements about the projections: right now we don't really show any evidence that the rate is actually lower - and the model suggests increasing rates. So we could either estimate a separate tau parameter for all stocks that were un-assessed as of 1996 OR jsut add the effect. Then we can point to that effect as confirmation that rates of new assessmment are lower more recently.

On Thu, Nov 24, 2016 at 6:48 AM, Michael Melnychuk <notifications@github.com

wrote:

pasted.

No apologies at all needed - thanks instead to you for doing all of the hard work!

Mike

On 2016-11-23 1:31 AM, Philipp Neubauer wrote:

Also, Mike - do you have the citations you added in your ref manager? If so, could you export them as bibtex and copy-paste them into the FirstAssessment.bib? I can add the refs in, but that would save me having to get them all individually...

My apologies for not having managed to get involved much with the discussion - been battling all those grooming rules and little glitches; and lately even the models didn't spit out anything coherent anymore (got that back to normal, at least.)

On Wed, Nov 23, 2016 at 10:25 PM, Philipp Neubauer neubauer.phil@gmail.com wrote:

To add to this:

I tried the 'un-assessed post 1996' effect, and it comes out negative. I'm not sure if that alone is worth including, as it doesn't say much about price effects in different decades, etc. Just FYI right now, mean price and max landings that go into the model are taken before the assessment year for assessed stocks.

On Mon, Nov 21, 2016 at 11:35 AM, Philipp Neubauer < neubauer.phil@gmail.com> wrote:

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

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Phil

Phil

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[James-Thorson]

Phil,

I'm not sure how a regression model like my understanding of ours could use a variable derived from the response as a predictor --it seems like that would violate the statistical assumption that the predictor is fixed exogenously. But if you think it's possible and you have time, then I agree it's worth exploring.

Another way would be to take the finite population prediction of assessment proportion during retrospective and forecast periods (historical might have a variance of zero if it's fully observed, I forget if species use different censoring years). Then taking the 1st difference and plotting that, it would show by eye if the assessment rate has sped up or slowed down.

On Nov 23, 2016 2:42 PM, "Philipp Neubauer" notifications@github.com wrote:

Have done some editing in the methods to more accurately reflect what we're doing with time-to-assessment, and covariates. I've also updated the results to reflect updated model outputs. Did a little bit of editing in the discussion, mainly in the propensity score paragraph - tried to clarify a couple of sentences, hope it worked...

3 possible points to add:

1. In the updated model, the interaction of price and landings is negative. So it seems its more a case of Price OR Landings rather than price AND landings. We should probably edit the discussion to reflect this
   • right?
2. Max length now comes through as significant - a generalisation of the charismatic mega-fauna effect beyond conservation to fisheries management? Would make for an amusing paragraph, perhaps ;) But more seriously, it seems like an argument against the fishing down the food chain hypothesis (at least for US waters) - if large fish are preferentially assessed, they are probably also managed better, preventing fishing-down patterns from occurring in US waters...
3. With some more though, it seems as though the addition of a post-1996 effect could be good to support our statements about the projections: right now we don't really show any evidence that the rate is actually lower - and the model suggests increasing rates. So we could either estimate a separate tau parameter for all stocks that were un-assessed as of 1996 OR jsut add the effect. Then we can point to that effect as confirmation that rates of new assessmment are lower more recently.

On Thu, Nov 24, 2016 at 6:48 AM, Michael Melnychuk < notifications@github.com

wrote:

pasted.

No apologies at all needed - thanks instead to you for doing all of the hard work!

Mike

On 2016-11-23 1:31 AM, Philipp Neubauer wrote:

Also, Mike - do you have the citations you added in your ref manager? If so, could you export them as bibtex and copy-paste them into the FirstAssessment.bib? I can add the refs in, but that would save me having to get them all individually...

My apologies for not having managed to get involved much with the discussion - been battling all those grooming rules and little glitches; and lately even the models didn't spit out anything coherent anymore (got that back to normal, at least.)

On Wed, Nov 23, 2016 at 10:25 PM, Philipp Neubauer neubauer.phil@gmail.com wrote:

To add to this:

I tried the 'un-assessed post 1996' effect, and it comes out negative. I'm not sure if that alone is worth including, as it doesn't say much about price effects in different decades, etc. Just FYI right now, mean price and max landings that go into the model are taken before the assessment year for assessed stocks.

On Mon, Nov 21, 2016 at 11:35 AM, Philipp Neubauer < neubauer.phil@gmail.com> wrote:

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

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[Philipp-Neubauer]

Jim - I don't think that this is a problem here - we use time to assessment, not any aspect of absolute time (i.e., Julian date) as response. A short time-to-assessment can mean 1960-1970 or 2001-2011. The reponse is the same, but the decade is different. In many medical studies, the interest is in effects of policy on public health, and they do just this; either have some temporal aspect as a predictor OR model tau using an auto-regressive formulation or separate categories. Ultimately, they tend to have a LOT more data, and I think there's limits to how far we can push our model with 600odd data points.But in principle, there shouldn't be an issue...

On Thu, Nov 24, 2016 at 12:25 PM, Jim Thorson notifications@github.com wrote:

Phil,

I'm not sure how a regression model like my understanding of ours could use a variable derived from the response as a predictor --it seems like that would violate the statistical assumption that the predictor is fixed exogenously. But if you think it's possible and you have time, then I agree it's worth exploring.

Another way would be to take the finite population prediction of assessment proportion during retrospective and forecast periods (historical might have a variance of zero if it's fully observed, I forget if species use different censoring years). Then taking the 1st difference and plotting that, it would show by eye if the assessment rate has sped up or slowed down.

On Nov 23, 2016 2:42 PM, "Philipp Neubauer" notifications@github.com wrote:

Have done some editing in the methods to more accurately reflect what we're doing with time-to-assessment, and covariates. I've also updated the results to reflect updated model outputs. Did a little bit of editing in the discussion, mainly in the propensity score paragraph - tried to clarify a couple of sentences, hope it worked...

3 possible points to add:

1. In the updated model, the interaction of price and landings is negative. So it seems its more a case of Price OR Landings rather than price AND landings. We should probably edit the discussion to reflect this
   • right?
2. Max length now comes through as significant - a generalisation of the charismatic mega-fauna effect beyond conservation to fisheries management? Would make for an amusing paragraph, perhaps ;) But more seriously, it seems like an argument against the fishing down the food chain hypothesis (at least for US waters) - if large fish are preferentially assessed, they are probably also managed better, preventing fishing-down patterns from occurring in US waters...
3. With some more though, it seems as though the addition of a post-1996 effect could be good to support our statements about the projections: right now we don't really show any evidence that the rate is actually lower - and the model suggests increasing rates. So we could either estimate a separate tau parameter for all stocks that were un-assessed as of 1996 OR jsut add the effect. Then we can point to that effect as confirmation that rates of new assessmment are lower more recently.

On Thu, Nov 24, 2016 at 6:48 AM, Michael Melnychuk < notifications@github.com

wrote:

pasted.

No apologies at all needed - thanks instead to you for doing all of the hard work!

Mike

On 2016-11-23 1:31 AM, Philipp Neubauer wrote:

Also, Mike - do you have the citations you added in your ref manager? If so, could you export them as bibtex and copy-paste them into the FirstAssessment.bib? I can add the refs in, but that would save me having to get them all individually...

My apologies for not having managed to get involved much with the discussion - been battling all those grooming rules and little glitches; and lately even the models didn't spit out anything coherent anymore (got that back to normal, at least.)

On Wed, Nov 23, 2016 at 10:25 PM, Philipp Neubauer neubauer.phil@gmail.com wrote:

To add to this:

I tried the 'un-assessed post 1996' effect, and it comes out negative. I'm not sure if that alone is worth including, as it doesn't say much about price effects in different decades, etc. Just FYI right now, mean price and max landings that go into the model are taken before the assessment year for assessed stocks.

On Mon, Nov 21, 2016 at 11:35 AM, Philipp Neubauer < neubauer.phil@gmail.com> wrote:

In theory, one could vary the tau parameter to have independent assessment trends in different periods BUT the way the model is set up, it has no specific reference to the actual time; i.e., right now, all the model knows is time from first (recorded) landings to first assessment. We could possibly put in effect for 'un-assessed post 1996' to see if those stocks have a higher probability of being assessed if they were still un-assessed at the time of the fisheries act. I think.

On Mon, Nov 21, 2016 at 11:28 AM, Michael Melnychuk < notifications@github.com> wrote:

Sorry, I forgot about this suggestion in your second paragraph when adding to the Discussion yesterday. I agree that those ideas would be good to add. We could mention in the discussion that perceived abundance/status may be a factor affecting when an assessment is first conducted, but that (obviously) abundance is not actually known before that assessment is done.

I can't remember what we decided, but was there any possibility (or advantage) to allowing model parameters to vary pre- and post-1996? Would that allow us to indirectly get at such questions of whether price matters more earlier on or later on in their exploitation history?

Mike

On 2016-11-17 4:20 PM, Philipp Neubauer wrote:

Hi there;

have just read through the discussion - lots of good points, Jim. I've also added the citations/bib into the manuscript. To make the citations work, in Rstudio you'll need to go to the "Build" menu -> Configure build tools -> choose "Makefile" and select the project directory. From there on, when you want to build after adding writing etc, do "build all" (Shift-Ctrl-B). Outside of Rstudio, open a command window, cd to the first assessment directory and type 'make'....hope this works.

I agree that we need a bit more about Rockfish and Groundsharks. I think the interesting angle here is conservation vs economics: We could asdd something more general: we can only capture the conservation status driver in the taxonomic component since it would be hard to define some kind of surrogate for that for stocks without an assessment. This points to a problem in prioritizing assessments: the conservation status only really factors once we have some evidence that things are probably going badly for a stock. Thus, valuable stocks are potentially well managed early on in their exploitation history, whereas small stocks probably only get that level of attention when there is an indication that things are heading for disaster. This could have unforeseen ecological consequences if the importance of such species is high relative to the economic value from fishing (e.g., bycatch of benthic inverts in trawl fisheries.)

Also, other bycatch species are probably assessed/managed quantitatively, but won't figure in our DB (Turtles, Mammals) since they would probably have a risk- rather than a stock assessment....

Happy to add something about this if you guys feel it makes sense...

Phil

On Thu, Nov 17, 2016 at 6:28 PM, Michael Melnychuk <notifications@github.com

wrote:

no problem, I can look into those in the next couple days.

Mike

On 2016-11-16 8:45 PM, Jim Thorson wrote:

OK, makes sense. I've gone ahead and added a sentence and references explaining Scorpaenids. I don't have any special knowledge of groundsharks or flatfishes, so those might require a bit more sleuthing if anyone is willing to take the lead?

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[Philipp-Neubauer]

As expected, running a model with differing rates gives a lower rate post-1996. Since we lose interpretability of coefficients (the rate enters into the calculation for the acceleration factor), I wouldn't suggest that we use this model for anything other than to discuss post-1996 and future assessment rates. This backs up the model that includes a psot-1996 effect, which is negative.

Ultimately, what this means is that our interpretation wasn't quite right; since we control for price, landings etc, the interpretation is that rates a lower at a given co-variate combination. So either there is something about post-1996 stocks that the model doesn't capture, or rates at which new stocks are assessed have declined despite the fisheries act (e.g., because there is a fixed budget that allows for a limited set to be assessed, such that beyond that set, it becomes increasingly unlikely to have new assessments.).

[James-Thorson]

Phil and Mike,

I've lost track a bit on where things stand. Should we make a timeline to push writing over the finish line? or are we still waiting on some updated QAQC or analysis?

please tell me how I can help!

[mcmelnychuk]

hi Jim and Phil,

Our assistant Nicole has found several US stock assessments that were not originally on our list. She is still going through the list of species:state landing entities and searching for an assessment for each entity for which we don't already have an assessment linked. She was delayed in this for a couple weeks having to work on a different project for Ray, but she's been on this full time for a week or so and will likely finish by tomorrow. Because she's found a few others, the results will change, but probably only slightly. I'll update the input files as soon as she is done and post them. Until then, we may want to hold off on adding too much more taxon-specific detail to the results & discussion, in case the taxonomic effects change somewhat.

Mike

On 2016-11-28 11:16 AM, Jim Thorson wrote:

Phil and Mike,

I've lost track a bit on where things stand. Should we make a timeline to push writing over the finish line? or are we still waiting on some updated QAQC or analysis?

please tell me how I can help!

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[Philipp-Neubauer]

Sounds good, Mike. I'll re-run the grooming and model once I see the files updated in the dropbox.

Any comment on the post-1996 effect? Is this interesting and do we want to keep this in? See my last comment in this issue...

On Tue, Nov 29, 2016 at 8:32 AM, Michael Melnychuk <notifications@github.com

wrote:

hi Jim and Phil,

Our assistant Nicole has found several US stock assessments that were not originally on our list. She is still going through the list of species:state landing entities and searching for an assessment for each entity for which we don't already have an assessment linked. She was delayed in this for a couple weeks having to work on a different project for Ray, but she's been on this full time for a week or so and will likely finish by tomorrow. Because she's found a few others, the results will change, but probably only slightly. I'll update the input files as soon as she is done and post them. Until then, we may want to hold off on adding too much more taxon-specific detail to the results & discussion, in case the taxonomic effects change somewhat.

Mike

On 2016-11-28 11:16 AM, Jim Thorson wrote:

Phil and Mike,

I've lost track a bit on where things stand. Should we make a timeline to push writing over the finish line? or are we still waiting on some updated QAQC or analysis?

please tell me how I can help!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-263365767, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_ oVYaXykQGVqeIu7mNIB6Km28r2Ft3ks5rCyidgaJpZM4KgiJj.

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-- Phil

[mcmelnychuk]

I took a quick look at the species:state landings database to see if the rate of when landings time series were first recorded may have something to do with the post-1996 effect observed. I predicted that with the act in 1996, there would be a big increase in the number of stocks with recorded landings (which are a precursor to whether they may be assessed some time after that). What I found was actually the opposite: there was a buildup in the number of species:state entities with landings data first being recorded from about 1970-1995, but then a steep decline in the number of new entities with landings first recorded after 1996.

Year of first recorded landings data and median landings of the first recorded year for species:state entities:

year range count median (t) <=1950 1052 40.9 1951-1955 234 0.85 1956-1960 120 1.3 1961-1965 113 4.7 1966-1970 66 4.2 1971-1975 123 3.5 1976-1980 267 2.8 1981-1985 325 2.3 1986-1990 368 1.45 1991-1995 375 0.9 1996-1990 200 0.6 2001-2005 210 1.05 2006-2010 170 1.1 2011-2015 68 0.55

This may reflect saturation of species available to be recorded. The requirements for building up comprehensive records of landings data may have been in place well before the act in 1996, so that post-1996 there just weren't that many species left for which to record landings for the first time. I think all this means is that the drop in assessment rate post-1996 cannot be explained by a big increase in the stocks available-but-not-yet-assessed.

Mike

On 2016-11-28 11:49 AM, Philipp Neubauer wrote:

Sounds good, Mike. I'll re-run the grooming and model once I see the files updated in the dropbox.

Any comment on the post-1996 effect? Is this interesting and do we want to keep this in? See my last comment in this issue...

On Tue, Nov 29, 2016 at 8:32 AM, Michael Melnychuk <notifications@github.com

wrote:

hi Jim and Phil,

Our assistant Nicole has found several US stock assessments that were not originally on our list. She is still going through the list of species:state landing entities and searching for an assessment for each entity for which we don't already have an assessment linked. She was delayed in this for a couple weeks having to work on a different project for Ray, but she's been on this full time for a week or so and will likely finish by tomorrow. Because she's found a few others, the results will change, but probably only slightly. I'll update the input files as soon as she is done and post them. Until then, we may want to hold off on adding too much more taxon-specific detail to the results & discussion, in case the taxonomic effects change somewhat.

Mike

On 2016-11-28 11:16 AM, Jim Thorson wrote:

Phil and Mike,

I've lost track a bit on where things stand. Should we make a timeline to push writing over the finish line? or are we still waiting on some updated QAQC or analysis?

please tell me how I can help!

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[Philipp-Neubauer]

Cool - the effect I coded was "assessment year > 1996", so basically, stocks could have been first recorded pre or post-1996, but their "event" is post 1996. So essentially this boils down to a comparison of time-to-assessment of stocks assessed pre and post 1996. The big caveat here is that I took 1960 as the first year, because there were no assessments prior to that. So the effect could well be an artefact of the cutoff since taht limits the time to assessment for stocks assessed pre-1996 more so than for stocks post 1996...so perhaps too flawed to consider?

On Tue, Nov 29, 2016 at 8:59 AM, Michael Melnychuk <notifications@github.com

wrote:

I took a quick look at the species:state landings database to see if the rate of when landings time series were first recorded may have something to do with the post-1996 effect observed. I predicted that with the act in 1996, there would be a big increase in the number of stocks with recorded landings (which are a precursor to whether they may be assessed some time after that). What I found was actually the opposite: there was a buildup in the number of species:state entities with landings data first being recorded from about 1970-1995, but then a steep decline in the number of new entities with landings first recorded after 1996.

Year of first recorded landings data and median landings of the first recorded year for species:state entities:

year range count median (t) <=1950 1052 40.9 1951-1955 234 0.85 1956-1960 120 1.3 1961-1965 113 4.7 1966-1970 66 4.2 1971-1975 123 3.5 1976-1980 267 2.8 1981-1985 325 2.3 1986-1990 368 1.45 1991-1995 375 0.9 1996-1990 200 0.6 2001-2005 210 1.05 2006-2010 170 1.1 2011-2015 68 0.55

This may reflect saturation of species available to be recorded. The requirements for building up comprehensive records of landings data may have been in place well before the act in 1996, so that post-1996 there just weren't that many species left for which to record landings for the first time. I think all this means is that the drop in assessment rate post-1996 cannot be explained by a big increase in the stocks available-but-not-yet-assessed.

Mike

On 2016-11-28 11:49 AM, Philipp Neubauer wrote:

Sounds good, Mike. I'll re-run the grooming and model once I see the files updated in the dropbox.

Any comment on the post-1996 effect? Is this interesting and do we want to keep this in? See my last comment in this issue...

On Tue, Nov 29, 2016 at 8:32 AM, Michael Melnychuk <notifications@github.com

wrote:

hi Jim and Phil,

Our assistant Nicole has found several US stock assessments that were not originally on our list. She is still going through the list of species:state landing entities and searching for an assessment for each entity for which we don't already have an assessment linked. She was delayed in this for a couple weeks having to work on a different project for Ray, but she's been on this full time for a week or so and will likely finish by tomorrow. Because she's found a few others, the results will change, but probably only slightly. I'll update the input files as soon as she is done and post them. Until then, we may want to hold off on adding too much more taxon-specific detail to the results & discussion, in case the taxonomic effects change somewhat.

Mike

On 2016-11-28 11:16 AM, Jim Thorson wrote:

Phil and Mike,

I've lost track a bit on where things stand. Should we make a timeline to push writing over the finish line? or are we still waiting on some updated QAQC or analysis?

please tell me how I can help!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-263365767, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_ oVYaXykQGVqeIu7mNIB6Km28r2Ft3ks5rCyidgaJpZM4KgiJj.

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-- Phil

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-- Phil

[mcmelnychuk]

It might not make that big of a difference, but a different cutoff could be 1950 instead of 1960, aligning with the availability of landings data. That would give an extra 10 years for time-to-assessment for the pre-1996 stocks. (But this might not make sense; you have your head wrapped around the implementation much better than I do.)

Mike

On 2016-11-28 12:17 PM, Philipp Neubauer wrote:

Cool - the effect I coded was "assessment year > 1996", so basically, stocks could have been first recorded pre or post-1996, but their "event" is post 1996. So essentially this boils down to a comparison of time-to-assessment of stocks assessed pre and post 1996. The big caveat here is that I took 1960 as the first year, because there were no assessments prior to that. So the effect could well be an artefact of the cutoff since taht limits the time to assessment for stocks assessed pre-1996 more so than for stocks post 1996...so perhaps too flawed to consider?

On Tue, Nov 29, 2016 at 8:59 AM, Michael Melnychuk <notifications@github.com

wrote:

I took a quick look at the species:state landings database to see if the rate of when landings time series were first recorded may have something to do with the post-1996 effect observed. I predicted that with the act in 1996, there would be a big increase in the number of stocks with recorded landings (which are a precursor to whether they may be assessed some time after that). What I found was actually the opposite: there was a buildup in the number of species:state entities with landings data first being recorded from about 1970-1995, but then a steep decline in the number of new entities with landings first recorded after 1996.

Year of first recorded landings data and median landings of the first recorded year for species:state entities:

year range count median (t) <=1950 1052 40.9 1951-1955 234 0.85 1956-1960 120 1.3 1961-1965 113 4.7 1966-1970 66 4.2 1971-1975 123 3.5 1976-1980 267 2.8 1981-1985 325 2.3 1986-1990 368 1.45 1991-1995 375 0.9 1996-1990 200 0.6 2001-2005 210 1.05 2006-2010 170 1.1 2011-2015 68 0.55

This may reflect saturation of species available to be recorded. The requirements for building up comprehensive records of landings data may have been in place well before the act in 1996, so that post-1996 there just weren't that many species left for which to record landings for the first time. I think all this means is that the drop in assessment rate post-1996 cannot be explained by a big increase in the stocks available-but-not-yet-assessed.

Mike

On 2016-11-28 11:49 AM, Philipp Neubauer wrote:

Sounds good, Mike. I'll re-run the grooming and model once I see the files updated in the dropbox.

Any comment on the post-1996 effect? Is this interesting and do we want to keep this in? See my last comment in this issue...

On Tue, Nov 29, 2016 at 8:32 AM, Michael Melnychuk <notifications@github.com

wrote:

hi Jim and Phil,

Our assistant Nicole has found several US stock assessments that were not originally on our list. She is still going through the list of species:state landing entities and searching for an assessment for each entity for which we don't already have an assessment linked. She was delayed in this for a couple weeks having to work on a different project for Ray, but she's been on this full time for a week or so and will likely finish by tomorrow. Because she's found a few others, the results will change, but probably only slightly. I'll update the input files as soon as she is done and post them. Until then, we may want to hold off on adding too much more taxon-specific detail to the results & discussion, in case the taxonomic effects change somewhat.

Mike

On 2016-11-28 11:16 AM, Jim Thorson wrote:

Phil and Mike,

I've lost track a bit on where things stand. Should we make a timeline to push writing over the finish line? or are we still waiting on some updated QAQC or analysis?

please tell me how I can help!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-263365767, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_ oVYaXykQGVqeIu7mNIB6Km28r2Ft3ks5rCyidgaJpZM4KgiJj.

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-- Phil

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-- Phil

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[Philipp-Neubauer]

Given the thorough QAQC and checking of assessments by @mcmelnychuk and Nicole, are we ready to draw a line in the sand and finalise the MS? I'm happy to help resolve remaining issues (can fill in some ?s in the text etc)...

I will add some tasks to the issues list, hopefully we can tick them off reasonably quickly...though the first task should probably be to QAQC the final dataset.csv for errors and omissions.

Phil

[James-Thorson]

yeah, let's call this the final one! Definitely done a good and thorough QAQC from my perspective, given our use of both SIS and careful quality checks.

[James-Thorson]

sorry, I think I mistook which issue this was... Are we ready to return to writing, or is there more updating to do for the analysis given this final dataset?

[mcmelnychuk]

A couple comparisons today:

1) I've gone through the dataset.csv and dataset_missed.csv files and compared them to the initial dataset. All species, assessment years, and habitats match up. However, there are two stocks (among the just-added ones) that should have their region manually assigned as USEC-NE instead of USEC-SE. It's the North Carolina issue again. They are: USEC smooth dogfish shark USNE midAtl red drum

2) I took an older FishBase dataset and linked by species to the "migration" variable, for the non-assessed stocks. Three stocks (2 species) came out that I didn't previously identify as "freshwater". I've just added these to the "exclude" column in "SpeciesCrossReference.csv" in the Dropbox folder. They are: USEC-NE SNAPPER, DOG Lutjanus jocu USEC-SE PINFISH Lagodon rhomboides USEC-SE SNAPPER, DOG Lutjanus jocu

In this latter comparison, there were still ~200 stocks that didn't have a corresponding FishBase entry (mostly invertebrates, or else alternative Latin names). There is a chance that some of these are freshwater species. Do either of you have a SeaLifeBase dataset on hand, and could link some kind of marine/brackish/freshwater designation to Latin names, to check if there are other freshwater species still on the list (attached)?

Mike

On 2016-12-08 9:52 AM, Jim Thorson wrote:

sorry, I think I mistook which issue this was... Are we ready to return to writing, or is there more updating to do for the analysis given this final dataset?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/issues/5#issuecomment-265806936, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_oVY6PovZ2uBx1LNVScvo5XqRH7so-ks5rGEPZgaJpZM4KgiJj.

[mcmelnychuk]

to check for freshwater species.xlsx

[Philipp-Neubauer]

Hi Mike - I can fix the region issue;

For the freshwater, both of those species are Marine fish with no diadromous behaviour as far as I can find. Dog Snapper use estuaries as nurseries, so are occasionally found in freshwater tributaries, but not because of migratory behaviour...

Jim; yes I think we can start writing again - I fixed a few missing values in the text already, would be good to add in some missing references and final edits to have a full V1 manuscript.

Phil

On Fri, Dec 9, 2016 at 7:32 AM, Michael Melnychuk notifications@github.com wrote:

A couple comparisons today:

1) I've gone through the dataset.csv and dataset_missed.csv files and compared them to the initial dataset. All species, assessment years, and habitats match up. However, there are two stocks (among the just-added ones) that should have their region manually assigned as USEC-NE instead of USEC-SE. It's the North Carolina issue again. They are: USEC smooth dogfish shark USNE midAtl red drum

2) I took an older FishBase dataset and linked by species to the "migration" variable, for the non-assessed stocks. Three stocks (2 species) came out that I didn't previously identify as "freshwater". I've just added these to the "exclude" column in "SpeciesCrossReference.csv" in the Dropbox folder. They are: USEC-NE SNAPPER, DOG Lutjanus jocu USEC-SE PINFISH Lagodon rhomboides USEC-SE SNAPPER, DOG Lutjanus jocu

In this latter comparison, there were still ~200 stocks that didn't have a corresponding FishBase entry (mostly invertebrates, or else alternative Latin names). There is a chance that some of these are freshwater species. Do either of you have a SeaLifeBase dataset on hand, and could link some kind of marine/brackish/freshwater designation to Latin names, to check if there are other freshwater species still on the list (attached)?

Mike

On 2016-12-08 9:52 AM, Jim Thorson wrote:

sorry, I think I mistook which issue this was... Are we ready to return to writing, or is there more updating to do for the analysis given this final dataset?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-265806936, or mute the thread https://github.com/notifications/unsubscribe-auth/AV_ oVY6PovZ2uBx1LNVScvo5XqRH7so-ks5rGEPZgaJpZM4KgiJj.

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-- Phil

[mcmelnychuk]

Thank you for double-checking that, and sorry - you're right. The old FishBase extract I used clearly had some errors in it. I've removed the "freshwater" designation for those species from the "exclude" column in "SpeciesCrossReference.csv".

Mike

[mcmelnychuk]

hi Phil,

Thank you for double-checking that, and sorry - you're right. The old FishBase extract I used clearly had some errors in it. I've removed the "freshwater" designation for those species from the "exclude" column in "SpeciesCrossReference.csv".

Mike

[James-Thorson]

Phil and Mike,

I've just committed some edits, and added some references in-text and citations to the "FirstAssessment.bib" file. Its not really compiling right on my machine, but the warning isn't useful to debug, so I can't really confirm whether the references are working right or not.

At this point, I think that its probably important for a single person to try and edit extensively to get the tone right (currently, it reads poorly perhaps because there's "too many cooks in the kitchen" for proper editing)

Phil -- would you be willing to do a last sweep for edits? I would offer, but I can't get the Rstudio to compile right, so I probably can't get it very polished.

And if you're willing, just tell me when you think its in a good place and I'll start doing my internal review -- I'm planning to ask Rick Methot given his ongoing interest in the topic.

cheers, jim

On Thu, Dec 8, 2016 at 12:36 PM, Michael Melnychuk <notifications@github.com

wrote:

hi Phil,

Thank you for double-checking that, and sorry - you're right. The old FishBase extract I used clearly had some errors in it. I've removed the "freshwater" designation for those species from the "exclude" column in "SpeciesCrossReference.csv".

Mike

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[Philipp-Neubauer]

Great, thanks Jim.

yes, happy to go through for a final, thorough edit. I'll try and do so early on Mon morning, so you should have it back on Mon your time.

cheers

On Fri, Dec 9, 2016 at 10:24 AM, Jim Thorson notifications@github.com wrote:

Phil and Mike,

I've just committed some edits, and added some references in-text and citations to the "FirstAssessment.bib" file. Its not really compiling right on my machine, but the warning isn't useful to debug, so I can't really confirm whether the references are working right or not.

At this point, I think that its probably important for a single person to try and edit extensively to get the tone right (currently, it reads poorly perhaps because there's "too many cooks in the kitchen" for proper editing)

Phil -- would you be willing to do a last sweep for edits? I would offer, but I can't get the Rstudio to compile right, so I probably can't get it very polished.

And if you're willing, just tell me when you think its in a good place and I'll start doing my internal review -- I'm planning to ask Rick Methot given his ongoing interest in the topic.

cheers, jim

On Thu, Dec 8, 2016 at 12:36 PM, Michael Melnychuk < notifications@github.com

wrote:

hi Phil,

Thank you for double-checking that, and sorry - you're right. The old FishBase extract I used clearly had some errors in it. I've removed the "freshwater" designation for those species from the "exclude" column in "SpeciesCrossReference.csv".

Mike

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/Philipp-Neubauer/FirstAssessment/ issues/5#issuecomment-265848104, or mute the thread https://github.com/notifications/unsubscribe-auth/ AHnqTWsvhRbi14XCkBXK0kgKIwrC1Xuqks5rGGo5gaJpZM4KgiJj .

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-- Phil

[mcmelnychuk]

Sounds good, thanks, guys. I won't be able to give this a careful look until after the 18th - I'm swamped getting ready for a NCEAS workshop next week.

I will try to put together an acknowledgments paragraph before then (especially since Rick Methot will be in it!)

Mike

[mcmelnychuk]

happy new year to you both. Just checking in on where things are. I haven't pulled this out for nearly a month - is it a good time for me to take a look at now, or is it in the middle of some edits or internal review? I updated the acknowledgments just now, but that's all I've done.

[James-Thorson]

Its on Rick's desk for internal review -- I'll email him now to check up

On Tue, Jan 3, 2017 at 2:07 PM, Michael Melnychuk notifications@github.com wrote:

happy new year to you both. Just checking in on where things are. I haven't pulled this out for nearly a month - is it a good time for me to take a look at now, or is it in the middle of some edits or internal review? I updated the acknowledgments just now, but that's all I've done.

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