{"action":"created","issue":{"url":"https://api.github.com/repos/quantifish/TagGrowth/issues/29","labels_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/29/labels{/name}","comments_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/29/comments","events_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/29/events","html_url":"https://github.com/quantifish/TagGrowth/issues/29","id":74178968,"number":29,"title":"Reviewer #2","user":{"login":"quantifish","id":5566375,"avatar_url":"https://avatars.githubusercontent.com/u/5566375?v=3","gravatar_id":"","url":"https://api.github.com/users/quantifish","html_url":"https://github.com/quantifish","followers_url":"https://api.github.com/users/quantifish/followers","following_url":"https://api.github.com/users/quantifish/following{/other_user}","gists_url":"https://api.github.com/users/quantifish/gists{/gist_id}","starred_url":"https://api.github.com/users/quantifish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/quantifish/subscriptions","organizations_url":"https://api.github.com/users/quantifish/orgs","repos_url":"https://api.github.com/users/quantifish/repos","events_url":"https://api.github.com/users/quantifish/events{/privacy}","received_events_url":"https://api.github.com/users/quantifish/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"quantifish","id":5566375,"avatar_url":"https://avatars.githubusercontent.com/u/5566375?v=3","gravatar_id":"","url":"https://api.github.com/users/quantifish","html_url":"https://github.com/quantifish","followers_url":"https://api.github.com/users/quantifish/followers","following_url":"https://api.github.com/users/quantifish/following{/other_user}","gists_url":"https://api.github.com/users/quantifish/gists{/gist_id}","starred_url":"https://api.github.com/users/quantifish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/quantifish/subscriptions","organizations_url":"https://api.github.com/users/quantifish/orgs","repos_url":"https://api.github.com/users/quantifish/repos","events_url":"https://api.github.com/users/quantifish/events{/privacy}","received_events_url":"https://api.github.com/users/quantifish/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/quantifish/TagGrowth/milestones/1","html_url":"https://github.com/quantifish/TagGrowth/milestones/Fisheries%20Research%20Manuscript%20Due","labels_url":"https://api.github.com/repos/quantifish/TagGrowth/milestones/1/labels","id":1101194,"number":1,"title":"Fisheries Research Manuscript Due","description":"I can now inform you that the Editorial Board has evaluated the manuscript FISH5958: Variation in growth among individuals and over time: a case study and simulation experiment involving tagged Antarctic toothfish.\r\n\r\nThe Editor has advised that the manuscript will be acceptable subject to satisfactory moderate revision.\r\n\r\nThe comments below should be taken into account when revising the manuscript. Along with your revised manuscript, you will need to supply revision notes in which you list all the changes you have made to the manuscript, and in which you detail your responses to all the comments passed by the reviewer(s) and the Editor. Should you disagree with any comment(s), please explain why.\r\n\r\nTo submit a revision, please visit http://ees.elsevier.com/fish/ and log in as an Author. You will see a menu item called Submission Needing Revision. The revised manuscript and the revision notes can be submitted there.\r\n\r\n When submitting your revised manuscript, please ensure that you upload the source files (e.g. Word). Uploading a PDF file at this stage will create delays should your manuscript be finally accepted for publication. If your revised submission does not include the source files, we will contact you to request them.\r\n\r\nYou are kindly requested to submit your revised manuscript within 4 weeks. If your revision is received after that deadline, it may be treated as a new submission.","creator":{"login":"quantifish","id":5566375,"avatar_url":"https://avatars.githubusercontent.com/u/5566375?v=3","gravatar_id":"","url":"https://api.github.com/users/quantifish","html_url":"https://github.com/quantifish","followers_url":"https://api.github.com/users/quantifish/followers","following_url":"https://api.github.com/users/quantifish/following{/other_user}","gists_url":"https://api.github.com/users/quantifish/gists{/gist_id}","starred_url":"https://api.github.com/users/quantifish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/quantifish/subscriptions","organizations_url":"https://api.github.com/users/quantifish/orgs","repos_url":"https://api.github.com/users/quantifish/repos","events_url":"https://api.github.com/users/quantifish/events{/privacy}","received_events_url":"https://api.github.com/users/quantifish/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":0,"state":"open","created_at":"2015-05-08T00:41:29Z","updated_at":"2015-05-08T00:47:45Z","due_on":"2015-06-02T12:00:00Z","closed_at":null},"comments":6,"created_at":"2015-05-08T00:47:22Z","updated_at":"2015-05-13T20:47:08Z","closed_at":null,"body":"Major comments\r\n- [ ] 1. The introduction is generally difficult to read. To help the reader, I suggest you introduce the general concept of persistent and transient growth e.g. in line 56 before describing these aspects in details. \r\nThe sentences in lines 53-55 (\"Similarly …\") and lines 60-63 ('For example…\") do not link with the previous sentences. Also, you have to more specific with 'size-specific harvest' (line 61), as a fishery may target small rather than large fish which could lead to a dominance of fast-growing animals in the fish population. \r\nThe introduction mentions mixed-effect and hierarchical models, but leaves the reader to ponder why they were describe here (e.g. were they used in this study?). \r\n- [ ] 2. Please present the model fits from all four growth models and combine them to one figure (not separately as in current Figures 1 and 3) so that the reader can easily compare the impact of the different model structures. \r\nMy main points of concerns are about the simulation: \r\n- [x] 3. The logic and flow of this paper would be much helped if the evaluation of the method through simulation was reported before the actual application of the method.\r\n- [ ] 4. The description of the simulation is unclear and insufficient to exactly understand the logic of the simulations and how they were performed. Please describe in detail what the general approach was and what it tests? I could also not understand some details, such as in lines 240-243: do you mean that for each sample, you randomly selected two out of the three parameters age at release, age at recapture and time at liberty, then randomly select estimates for those two parameters and finally calculate the parameter value for the third parameter?\r\n- [ ] 5. I remain unconvinced that the simulation fully tests the proposed method in the intended way. As far as I understood, you may have tested some statistical properties of the growth model, but not whether the model does correctly and unambiguously describe the actual processes of growth. \t\r\nBy deriving samples from the real data set as it was done in this study, the underlying processes that have led to the structure of these real data remain unknown. To conduct an simulation evaluation correctly, you need to fully simulate all processes when creating simulation data. This must be done to avoid false-positive conclusions about growth processes, where e.g. the preferred model includes variation in k and z, but the data was only created with variation in k. I suggest you conduct four simulation scenarios where data are created with (1) nor variation, (2) with variation in k, (3) variation in z, and (4) variation in k and z. Each of these scenarios is then evaluated with all four model structures. The same approach could also be used if you want to further expand the evaluation and investigate e.g. the impact of annual/spatial variation in growth between animals as touched on in the Discussion. These simulations can be conditioned with toothfish-like parameters,\r\nbut of course proof of generality of the method would be beneficial. \r\n- [ ] 6. What is the consequence of fixing <PSI> to values other than 0 (line 167)? Are the conclusions the same?\r\n\r\nMinor comments: \r\n- [x] 7. Please provide all parameter values that you use for the simulation in a table, especially from non-publicly available working group papers such as Dunn et al. (2006). \r\n- [x] 8. Lines 137-138 is repeated in lines 146-149. Be more specific on what other time intervals you tested. \r\n- [x] 9. Avoid judgemental descriptions (e.g. 'reasonable' in line 216), and replace with e.g. 'to evaluate potential bias and precision of the models'. \r\n- [x] 10. I don't consider that papers in review should be cited in a publication, but leave this issue to the editor of this journal to decide. \r\n- [x] 11. There are also a number of grammatical and word errors in the text which should be easily picked up in the editorial process. "},"comment":{"url":"https://api.github.com/repos/quantifish/TagGrowth/issues/comments/101811532","html_url":"https://github.com/quantifish/TagGrowth/issues/29#issuecomment-101811532","issue_url":"https://api.github.com/repos/quantifish/TagGrowth/issues/29","id":101811532,"user":{"login":"James-Thorson","id":7989837,"avatar_url":"https://avatars.githubusercontent.com/u/7989837?v=3","gravatar_id":"","url":"https://api.github.com/users/James-Thorson","html_url":"https://github.com/James-Thorson","followers_url":"https://api.github.com/users/James-Thorson/followers","following_url":"https://api.github.com/users/James-Thorson/following{/other_user}","gists_url":"https://api.github.com/users/James-Thorson/gists{/gist_id}","starred_url":"https://api.github.com/users/James-Thorson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/James-Thorson/subscriptions","organizations_url":"https://api.github.com/users/James-Thorson/orgs","repos_url":"https://api.github.com/users/James-Thorson/repos","events_url":"https://api.github.com/users/James-Thorson/events{/privacy}","received_events_url":"https://api.github.com/users/James-Thorson/received_events","type":"User","site_admin":false},"created_at":"2015-05-13T20:47:08Z","updated_at":"2015-05-13T20:47:08Z","body":"Personally, I would still use a proposed data-generating process, rather\nthan the bootstrap.  I see your point that time-at-liberty has a more\npeaked distribution that an exponential (and maybe also some seasonal\nsinuosity).  But that just affects how much contrast we get in estimating\ngrowth increments.  The main reason I'd use an explicit DGP is because hte\nreviewer asked, and I don't like rolling dice during hte review process.\nIt also seems like one of the easier requests, given that machine time is\ncheaper than human (editing) time.\n\nbut as I said, if you want to argue against it in the response, I have no\nobjection.\n\njim\n\nOn Wed, May 13, 2015 at 1:09 PM, Darcy Webber <notifications@github.com>\nwrote:\n\n> Hey again Jim.\n>\n> Sorry about this Jim, I know you're busy, but it's been on my mind a\n> little.\n>\n> I'm gonna bring up the Age1, Age2, time at liberty thing again. So I've\n> done that bootstrap thing that you don't really like. The alternative is to\n> simulate Age1, Age2 and time at liberty from distributions (that are fitted\n> to the data, you mention this above).\n>\n> You may or may not remember that I looked into this a little bit. I dug up\n> the plots that I created while looking in to this (I couldn't find the code\n> though, it'll be somewhere). But the plots below shows the distributions of\n> observed (in the true toothfish data) Age1, Age2 and time at liberty in\n> black and what happens if we simulate from lognormal distributions for each\n> independently:\n>\n> [image: sim-age-liberty-2]\n> <https://cloud.githubusercontent.com/assets/5566375/7619812/454ecd40-fa0f-11e4-9797-8c9afef9f25f.png>\n>\n> This next plot shows the distributions of observed (in the true toothfish\n> data) Age1, Age2 and time at liberty in black again and what happens if I\n> use my clunky bootsrap method:\n>\n> [image: sim-age-liberty-1]\n> <https://cloud.githubusercontent.com/assets/5566375/7619793/2f40887c-fa0f-11e4-9836-be125c71cc51.png>\n>\n> You can see that each method has its pros and cons, but the bottom right\n> panel in each plot is what worries me the most.\n>\n> So, am I overthinking this and should I just not worry about this and use\n> the fitted distributions? Just keen to get your opinion on this once more.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/quantifish/TagGrowth/issues/29#issuecomment-101799406>\n> .\n>\n"}}