Cutoff at 11:30?

[allanhicks]

I think that we are getting to a good place when we are having merge conflicts over backslashes. Do you think that a cutoff at 11:30 so that we can build the document and distribute it by noon is a good idea?

[cgrandin]

I think so. At this point I am just looking for things to do, I believe we are in a good place as well.

[andrew-edwards]

All these changes to automate the fish name are doing my head in!! Why bother doing them now - they could have waited until after we submit! Anyway, see my comment on Chris's commit - you've left Whiting out of the Agreement's name I think, which is presumably incorrect.

[aaronmberger-nwfsc]

11:30 good for me, just committed some table caption changes

[andrew-edwards]

Yes, agree to cut-off at 11:30 to stop people making minor un-needed edits ;)

[cgrandin]

I'm done committing, I'll just merge any new changes in and build the document.

[allan-hicks]

i have one more important commit to the one-pager, so please hold on.

On Fri, Feb 12, 2016 at 11:09 AM, cgrandin notifications@github.com wrote:

I'm done committing, I'll just merge any new changes in and build the document.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183453394 .

[allan-hicks]

Thanks. I'm done with commits unless something is glaringly obvious. I would say let's merge, quick check, then submit.

On Fri, Feb 12, 2016 at 11:11 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

i have one more important commit to the one-pager, so please hold on.

On Fri, Feb 12, 2016 at 11:09 AM, cgrandin notifications@github.com wrote:

I'm done committing, I'll just merge any new changes in and build the document.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183453394 .

[allan-hicks]

Do we want to reflect that this is an updated draft? Or is the date on the title page sufficient?

On Fri, Feb 12, 2016 at 11:16 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

Thanks. I'm done with commits unless something is glaringly obvious. I would say let's merge, quick check, then submit.

On Fri, Feb 12, 2016 at 11:11 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

i have one more important commit to the one-pager, so please hold on.

On Fri, Feb 12, 2016 at 11:09 AM, cgrandin notifications@github.com wrote:

I'm done committing, I'll just merge any new changes in and build the document.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183453394 .

[aaronmberger-nwfsc]

I'm done.

On Fri, Feb 12, 2016 at 11:17 AM, Allan C Hicks notifications@github.com wrote:

Do we want to reflect that this is an updated draft? Or is the date on the title page sufficient?

On Fri, Feb 12, 2016 at 11:16 AM, Allan Hicks - NOAA Federal <

allan.hicks@noaa.gov> wrote:

Thanks. I'm done with commits unless something is glaringly obvious. I would say let's merge, quick check, then submit.

On Fri, Feb 12, 2016 at 11:11 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

i have one more important commit to the one-pager, so please hold on.

On Fri, Feb 12, 2016 at 11:09 AM, cgrandin notifications@github.com wrote:

I'm done committing, I'll just merge any new changes in and build the document.

— Reply to this email directly or view it on GitHub < https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183453394

.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183455391 .

Aaron M. Berger, Ph.D. Research Mathematical Statistician Fishery Resource Analysis and Monitoring Division Northwest Fisheries Science Center 2032 SE OSU Dr. Bldg. 955 Newport, OR 97365-5275

aaron.berger@noaa.gov aaron.berger@noaa.gov541.867.0562

[allan-hicks]

Shoudl the date be in the footer? Sorry to be worried about this, but I am concerned that with multiple drafts floating around, some people may be looking at the incorrect version.

On Fri, Feb 12, 2016 at 11:16 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

Do we want to reflect that this is an updated draft? Or is the date on the title page sufficient?

On Fri, Feb 12, 2016 at 11:16 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

Thanks. I'm done with commits unless something is glaringly obvious. I would say let's merge, quick check, then submit.

On Fri, Feb 12, 2016 at 11:11 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

i have one more important commit to the one-pager, so please hold on.

On Fri, Feb 12, 2016 at 11:09 AM, cgrandin notifications@github.com wrote:

I'm done committing, I'll just merge any new changes in and build the document.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183453394 .

[cgrandin]

I think so. I will attempt it now

[cgrandin]

I have the date in footer working, just need to get a short form so it doesn't overlap page numbers. Stand by

[andrew-edwards]

I wouldn't mind spending 20 minutes or so checking it. Feels like we've wasted some time with all the \fishname stuff, which may have messed things up a little (I never got to finish reading the Exec Summary) - I'm guessing people weren't really re-latex'ing and checking it was all okay ;) But looks like we've all caught up almost - so let's merge when Chris does the commit. Redo source("all.r"), delete knitr-cache and redo, and then take a look through. I may print the whole thing out. Expect we can submit by, say, 12:15?

[allan-hicks]

What about "Pacific Hake stock assessment 2/12/2016" in the footer?

On Fri, Feb 12, 2016 at 11:28 AM, cgrandin notifications@github.com wrote:

I have the date in footer working, just need to get a short form so it doesn't overlap page numbers. Stand by

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183458237 .

[allan-hicks]

I'll check with Miako to see if she is going to lunch before then. I would like the JMC to have at least 2 hours to look at this.

On Fri, Feb 12, 2016 at 11:33 AM, andrew-edwards notifications@github.com wrote:

I wouldn't mind spending 20 minutes or so checking it. Feels like we've wasted some time with all the \fishname stuff, which may have messed things up a little (I never got to finish reading the Exec Summary) - I'm guessing people weren't really re-latex'ing and checking it was all okay ;) But looks like we've all caught up almost - so let's merge when Chris does the commit. Redo source("all.r"), delete knitr-cache and redo, and then take a look through. I may print the whole thing out. Expect we can submit by, say, 12:15?

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183459541 .

[aaronmberger-nwfsc]

ok by me. I'll source all.r, but no need to enter any 'y', correct?

On Fri, Feb 12, 2016 at 11:33 AM, andrew-edwards notifications@github.com wrote:

I wouldn't mind spending 20 minutes or so checking it. Feels like we've wasted some time with all the \fishname stuff, which may have messed things up a little (I never got to finish reading the Exec Summary) - I'm guessing people weren't really re-latex'ing and checking it was all okay ;) But looks like we've all caught up almost - so let's merge when Chris does the commit. Redo source("all.r"), delete knitr-cache and redo, and then take a look through. I may print the whole thing out. Expect we can submit by, say, 12:15?

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183459541 .

Aaron M. Berger, Ph.D. Research Mathematical Statistician Fishery Resource Analysis and Monitoring Division Northwest Fisheries Science Center 2032 SE OSU Dr. Bldg. 955 Newport, OR 97365-5275

aaron.berger@noaa.gov aaron.berger@noaa.gov541.867.0562

[cgrandin]

I'd need to figure that out. Right now its "Pacific Hake February 12, 2016". Is there time?

[allan-hicks]

Woudl something like this work?

\usepackage{datetime}\newdateformat{specialdate}{\THEYEAR-\twodigit{\THEMONTH}-\twodigit{\THEDAY}}\date{\specialdate\today}

On Fri, Feb 12, 2016 at 11:35 AM, cgrandin notifications@github.com wrote:

I'd need to figure that out. Right now its "Pacific Hake February 12, 2016". Is there time?

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183460146 .

[allan-hicks]

Miako will be able to distribute it at 12:15. So let's make 12pm time to build.

On Fri, Feb 12, 2016 at 11:37 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

Woudl something like this work?

\usepackage{datetime}\newdateformat{specialdate}{\THEYEAR-\twodigit{\THEMONTH}-\twodigit{\THEDAY}}\date{\specialdate\today}

On Fri, Feb 12, 2016 at 11:35 AM, cgrandin notifications@github.com wrote:

I'd need to figure that out. Right now its "Pacific Hake February 12, 2016". Is there time?

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183460146 .

[cgrandin]

Maybe, it's not the figuring it out that takes the time, its the building. I'm on it.. look for a commit in awhile for this

[cgrandin]

Ok, should be good. I am going to build from scratch now.

[allan-hicks]

Do we want to resolve our issue regarding the one-page summary and rounding percentages?

On Fri, Feb 12, 2016 at 11:55 AM, cgrandin notifications@github.com wrote:

Ok, should be good. I am going to build from scratch now.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183466468 .

[cgrandin]

It's easy to do. What do you want to change?

[allan-hicks]

Any thoughts Andy?

On Fri, Feb 12, 2016 at 11:56 AM, cgrandin notifications@github.com wrote:

It's easy to do. What do you want to change?

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183467235 .

[cgrandin]

The ones in the last bullet are rounded to zero digits where the others are all 1 digit. Is that the issue? If so, I can change that

[allan-hicks]

Can you have a look at my commit to see if you like this?

show the estimated median relative spawning biomass increasing from 76\% in \Sexpr{end.yr} to 80\% in \Sexpr{end.yr+1} and beginning to stabilize in \Sexpr{end.yr+2}.

On Fri, Feb 12, 2016 at 11:57 AM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

Any thoughts Andy?

On Fri, Feb 12, 2016 at 11:56 AM, cgrandin notifications@github.com wrote:

It's easy to do. What do you want to change?

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183467235 .

[andrew-edwards]

Or just:

to 80\% in \Sexpr{end.yr+1} and \Sexpr{end.yr+2}.

Loses the word stabilise though. Kind of obvious though?

[andrew-edwards]

Footer - you could take out 'stock' just to shorten it and keep it away from page numbers.

[cgrandin]

I managed to get everything in the footer now. I think we should do final merges, build, and submit..

[allan-hicks]

Given my experience with this crowd, I think that it is useful to keep the word stabilize. We have been talking a lot about when the stock will stabilize and begin to decline. I like to let them know what I want them to know rather than have them infer it. Does that make sense?

On Fri, Feb 12, 2016 at 12:06 PM, andrew-edwards notifications@github.com wrote:

Or just:

to 80\% in \Sexpr{end.yr+1} and \Sexpr{end.yr+2}.

Loses the word stabilise though. Kind of obvious though?

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183470099 .

[andrew-edwards]

Allan - 'beginning to stabilize' isn't quite right. Implies it's going to stay constant, but it could decline the year after (as you said earlier). Okay - how about just 'stabilize':

...and stabilizing in \Sexpr{end.yr+2}.

[allan-hicks]

I am building. Here is my tex file (trying attach from the email, not sure if it will work).

On Fri, Feb 12, 2016 at 12:07 PM, cgrandin notifications@github.com wrote:

I managed to get everything in the footer now. I think we should do final merges, build, and submit..

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183470640 .

[aaronmberger-nwfsc]

Chris, let me know when to do final merge

[allan-hicks]

or "remaining stable in 2018" which removes any context of what may happen after 2018?

On Fri, Feb 12, 2016 at 12:10 PM, andrew-edwards notifications@github.com wrote:

Allan - 'beginning to stabilize' isn't quite right. Implies it's going to stay constant, but it could decline the year after (as you said earlier). Okay - how about just 'stabilize':

...and stabilizing in \Sexpr{end.yr+2}.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183471643 .

[cgrandin]

Go ahead Aaron, I think we're done And Allan I didn't get a tex file. Just send to our emails

[allan-hicks]

I think the "stable" is unstable. Can we resolve this issue. I think that it is very important and is something that we will focus on a lot in the JMC meeting.

On Fri, Feb 12, 2016 at 12:13 PM, cgrandin notifications@github.com wrote:

Go ahead Aaron, I think we're done And Allan I didn't get a tex file. Just send to our emails

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183472440 .

[allan-hicks]

I just committed to "staying stable in 2018" What do you think?

On Fri, Feb 12, 2016 at 12:14 PM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

I think the "stable" is unstable. Can we resolve this issue. I think that it is very important and is something that we will focus on a lot in the JMC meeting.

On Fri, Feb 12, 2016 at 12:13 PM, cgrandin notifications@github.com wrote:

Go ahead Aaron, I think we're done And Allan I didn't get a tex file. Just send to our emails

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183472440 .

[andrew-edwards]

Okay - I'm good with "remaining stable in 2018" as it doesn't imply what happens after.

[andrew-edwards]

Good. I'm going to shorten the footer also and commit. Less clutter at the bottom.

[aaronmberger-nwfsc]

Fine by me.

On Fri, Feb 12, 2016 at 12:16 PM, andrew-edwards notifications@github.com wrote:

Good. I'm going to shorten the footer also and commit. Less clutter at the bottom.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183473230 .

Aaron M. Berger, Ph.D. Research Mathematical Statistician Fishery Resource Analysis and Monitoring Division Northwest Fisheries Science Center 2032 SE OSU Dr. Bldg. 955 Newport, OR 97365-5275

aaron.berger@noaa.gov aaron.berger@noaa.gov541.867.0562

[andrew-edwards]

Okay. I'm done committing! Will email Chris a .tex so he can compare. I'll build a .pdf and print it, and take a very quick look through.

[allan-hicks]

OK. Let's merge, build, and Chris mark this as the point of the updated draft document

On Fri, Feb 12, 2016 at 12:17 PM, aaronmberger notifications@github.com wrote:

Fine by me.

On Fri, Feb 12, 2016 at 12:16 PM, andrew-edwards <notifications@github.com

wrote:

Good. I'm going to shorten the footer also and commit. Less clutter at the bottom.

— Reply to this email directly or view it on GitHub < https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183473230

.

Aaron M. Berger, Ph.D. Research Mathematical Statistician Fishery Resource Analysis and Monitoring Division Northwest Fisheries Science Center 2032 SE OSU Dr. Bldg. 955 Newport, OR 97365-5275

aaron.berger@noaa.gov aaron.berger@noaa.gov541.867.0562

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183473364 .

[cgrandin]

Ok, I am building now using commit 7fe34c

[andrew-edwards]

I can build the submittable .pdf again. Filename? hake-assessment-preSRG-revised.pdf
or hake-assessment-preSRG-2016-02-12.pdf

[allan-hicks]

I prefer the date in there

On Fri, Feb 12, 2016 at 12:22 PM, andrew-edwards notifications@github.com wrote:

I can build the submittable .pdf again. Filename? hake-assessment-preSRG-revised.pdf

or hake-assessment-preSRG-2016-02-12.pdf

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183475384 .

[allan-hicks]

Can you send it to all of us, then I'll send it to Miako?

On Fri, Feb 12, 2016 at 12:23 PM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

I prefer the date in there

On Fri, Feb 12, 2016 at 12:22 PM, andrew-edwards <notifications@github.com

wrote:

I can build the submittable .pdf again. Filename? hake-assessment-preSRG-revised.pdf

or hake-assessment-preSRG-2016-02-12.pdf

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183475384 .

[allan-hicks]

Did we ever update Figure 2?

On Fri, Feb 12, 2016 at 12:24 PM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

Can you send it to all of us, then I'll send it to Miako?

On Fri, Feb 12, 2016 at 12:23 PM, Allan Hicks - NOAA Federal < allan.hicks@noaa.gov> wrote:

I prefer the date in there

On Fri, Feb 12, 2016 at 12:22 PM, andrew-edwards < notifications@github.com> wrote:

I can build the submittable .pdf again. Filename? hake-assessment-preSRG-revised.pdf

or hake-assessment-preSRG-2016-02-12.pdf

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183475384 .

[cgrandin]

Not that I'm aware of Allan.

[aaronmberger-nwfsc]

Right, i bet not

On Fri, Feb 12, 2016 at 12:26 PM, cgrandin notifications@github.com wrote:

Not that I'm aware of Allan.

— Reply to this email directly or view it on GitHub https://github.com/cgrandin/hake-assessment/issues/125#issuecomment-183476170 .

Aaron M. Berger, Ph.D. Research Mathematical Statistician Fishery Resource Analysis and Monitoring Division Northwest Fisheries Science Center 2032 SE OSU Dr. Bldg. 955 Newport, OR 97365-5275

aaron.berger@noaa.gov aaron.berger@noaa.gov541.867.0562

[cgrandin]

But the figure is just backscatter, not biomass - it should be the same no matter what estimation technique is used. It's raw data