andrew-edwards
commented
3 years ago Way to go Chris, thanks!
Closed andrew-edwards closed 3 years ago
andrew-edwards
commented
3 years ago Way to go Chris, thanks!
kellijohnson-NOAA
commented
3 years ago Regarding 9, are we okay with just adding the citations on the page trevor noted, i don't really see the benefit of citing all the papers or really any paper every single time we mention NUTS. We don't for other methods.
aaronmberger-nwfsc
commented
3 years ago Yes, first time only is fine, or perhaps better yet is the first time only in the executive summary and first time only in the main document should suffice. Good point.
On Wed, Feb 24, 2021 at 10:36 AM Kelli Johnson notifications@github.com wrote:
Regarding 9, are we okay with just adding the citations on the page trevor noted, i don't really see the benefit of citing all the papers or really any paper every single time we mention NUTS. We don't for other methods.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/pacific-hake/hake-assessment/issues/813#issuecomment-785286240, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4T76RHOVD4V73SLULNY33TAVBMJANCNFSM4XVSXNNQ .
-- Aaron Berger, PhD https://www.fisheries.noaa.gov/contact/aaron-m-berger-phd Fisheries Resource and Monitoring Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2032 SE OSU Drive Newport, OR 97365 USA
aaron.berger@noaa.gov aaron.berger@noaa.gov541.867.0562 (office)
541.231.1417 (cell)
kellijohnson-NOAA
commented
3 years ago I didn't do the Executive summary b/c I kind of saw that as an abstract without citations. Was that thought wrong? I guess I can look to see if we have other citations in the executive summary.
aaronmberger-nwfsc
commented
3 years ago sounds good; yea, we don't need it in the executive summary
On Wed, Feb 24, 2021 at 10:49 AM Kelli Johnson notifications@github.com wrote:
I didn't do the Executive summary b/c I kind of saw that as an abstract without citations. Was that thought wrong? I guess I can look to see if we have other citations in the executive summary.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pacific-hake/hake-assessment/issues/813#issuecomment-785294813, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4T76RIY24IPZSIGGF4AH3TAVC4VANCNFSM4XVSXNNQ .
-- Aaron Berger, PhD https://www.fisheries.noaa.gov/contact/aaron-m-berger-phd Fisheries Resource and Monitoring Division Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration 2032 SE OSU Drive Newport, OR 97365 USA
aaron.berger@noaa.gov aaron.berger@noaa.gov541.867.0562 (office)
541.231.1417 (cell)
kellijohnson-NOAA
commented
3 years ago We don't have an answer for point 2, as in there is no way to know what the major driver of observed dynamics is. So, I am not too sure how to answer Trevor. BTW this is the last one we are set to deal with.
aaronmberger-nwfsc
commented
3 years ago I'll do that one; I think we just need to reword it so we don't get in that pickle of a description. I may even remove the sentence. But I'll think about that one.
aaronmberger-nwfsc
commented
3 years ago finished the remaining one (# 2) in commit d21bf14f5929f09fc9d6e7ea5bc698615e76840f, closing...
[x] 1 Figure h & Figure 32: the label “2020” is not closest to the data point for 2020, it is closer to two other data points from earlier years. [Andy: think he means "2021"; could be shifted a little to the right]
[x] 2 p. 16 “While the target fishing mortality (FSPR=40%) and B40% result in different population sizes (see Table f), this difference is not, by far, the major driver of the observed dynamics.” This seems incomplete because the ensuing paragraph does not mention what the main driver is.
[x] 3 p. 17 first para: “until it is has been observed” -> “until it is observed”
[x] 4 p. 25 final line, you could delete “Genetic studies indicate that”.
[x] 5 p. 29 second para: “with an exported value of CA$100 million” needs clarifying whether this is the value of the salaries being exported to workers’ home countries, or the export value of the fish itself, given the first part of this sentence.
[x] 6 p. 33 “Whereas, Canadian shoreside landings” delete “Whereas”
[x] 7 p.35 First line “all three U.S. fleets (Tables 5–7). Whereas the” change to “all three U.S. fleets (Tables 5–7), whereas the”
[ ] 8 p. 40 last para (and p. 46 line 3) “lognormal distribution with a median of -1.61” has a weird value for the median for natural mortality. This should be in the range of 0.2-0.3 as in previous assessments. CJG - We changed this in the tables to be in logspace as it is here. I think we leave this.
[x] 9 p. 44 Second para and elsewhere, when first mentioning NUTS, the Monnahan and other papers should be cited, rather than only citing these later in the assessment.
[x] 10 p. 45 last para “Dirichlet-Multinomial” I think multinomial should probably be lower case whereas Dirichlet is named after a person.
[x] 11 p. 56 line 2 delete “Overall,”
[x] 12 p. 57 line 1 delete “stationary”, since posterior distributions are by definition stationary (if converged).
[x] 13 p. 60 para 2 “These are also shown by phase plot” should be “These are also shown by a phase plot”.
[x] 14 p. 61 para 3 “for inclusion of of the age-1” delete the second “of”.
[x] 15 p. 63 second para “the difference between the 2021 and 2021 medians” should be “the difference between the 2021 and 2022 medians”
[x] 16 p. 66 para 1 “then what the base model otherwise estimates” should be “than the base model”
[x] 17 p. 75 doi for second Malick reference is wrong, should be https://doi.org/10.3389/fmars.2020.578490 (not 10.3390)
[x] 18 p. 76 Methot & Wetzel “biologial” should be “biological”
[x] 19 Table 19 could be simplified by renaming age 6 to 6+ and deleting columns for ages 7-20+ since these are all identical. CJG - NO!
[x] 20 There is a possible mistake in Tables 32 and 33 where under Negative Log likelihoods the final column is identical to the first column in both tables. Perhaps also reference points in Table 32, with the same issue. CJG - This is not a mistake, I noticed this when working on the tables and double-checked
[x] 21 Table 34: negative log likelihoods don’t make sense to include for retrospective analysis since they come from different data in each column.
[x] 22 Figure 2 caption: “Histograms..” -> “Barplots…”
[x] 23 p. 129 caption of Figure 15 “more accurately reflects the timing of when other methods that manually tune data weights occurs.” -> “more accurately reflects the timing used in other methods that manually tune data weights.”