Peer Review History
| Original SubmissionJune 15, 2020 |
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PONE-D-20-16520 PeskAAS: A near-real-time, open-source monitoring and analytics system for small-scale fisheries PLOS ONE Dear Dr. Tilley, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. ============================== ACADEMIC EDITOR: I read this MS with interest as it addresses an important gap in small-scale fisheries which require precision and reliability to address sustainable management of the fisheries. I am sure that the reviews it has received will greatly improve its quality. And, so, please address all the queries, especially of data flow as indicated by Reviewer #2. ============================== Please submit your revised manuscript by Aug 29 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Review notes: The manuscript introduces a new tool for small-scale fisheries data collation and analysis using an Rshiny platform. The manuscript is well written and the introduction does a good job of describing the many issues with monitoring small-scale fisheries. The tool itself is sophisticated and is now being used by the Timor-Leste government in monitoring their fisheries. This is a fantastic example of an operational fisheries tool and will make a great addition to the literature. The tool appears to primarily be used in monitoring catch and effort, rather than providing analytical assessments for fisheries managers (i.e. stock assessment). This is of course fine (and much needed in the case of small scale fisheries), but I think perhaps this specific scope of the tool needs to be stated clearly somewhere, perhaps in the abstract. Or perhaps a paragraph in the discussion could envision the next steps for this tool/data in fisheries management? I.e. what comes next after appropriate monitoring? Much of the manuscript focused on describing the tool pipeline, from shore-based observers to the final Rshiny interface. The description of this pipeline was logical and detailed, but I did have a few line-specific comments below that request more information in some sections to help improve potential reproducibility. Particularly, for Ln 171 – 184 this seems to be the biggest analytical component of the tool but the details and results are limited (see broader comment below). Finally, the introduction makes the case for a ‘light touch’ tool for data collection and analytics. While I agree with their logic in the introduction, I don’t quite agree that peskAAS is ‘light touch’. For example, the peskAAS application in Timor-Leste involved observers with tablet computers, gps trackers on boats, sophisticated coding in R, plus multiple software subscription services (e.g. Rshiny and Kobo toolbox). The authors do detail some of the limitations in the discussion, but I think more could be done to address the scalability and ‘light touch’ effectiveness of this tool. Abstract - Would be useful to indicate what type of data is needed to operate peskAAS? - Needs to explain that the peskAAS was developed and implemented for small scale fisheries in Timor-Leste - Growth parameters doesn’t seem like the correct term to me (see comment below). Suggest using ‘length-weight’. Introduction - Ln 41: can you list some other tools that are used in management? E.g. fishpath (https://www.fishpath.org/the-tool), stock synthesis etc. - Ln 41: there is no closing parenthesis - Reference 15 – title is incorrect here. Also, is this peer-reviewed? If not then I suggest not using it as a reference - Ln 52: need a closing parenthesis - peskAAS - Ln 76: more information needed on spline type here - Ln 89: is this the figure caption? More text is needed here to better explain the pipeline, and all the acronyms and terms. E.g. PDS, DB, API, - Ln 91: list tablet model - Ln 92: can you add a sentence describing what Kobotool box is? - Ln 97: what are the gear type options? - Ln 99: what size was measured (fork length, standard length, total length) and what units? - Ln 99: units for trip duration? - Ln 114: I couldn’t find this supp file 2 - Ln 118: I’m not sure if this is an error, or perhaps I don’t have the right supp file. But the VBGF is typically used to get size-at-age, using parameters k, t, and l-infinite. The parameters in table supplementary information 2 are for a and b, and are described as being used to convert length-to-weight. Suggest not using the VBGF term but rather simply saying ‘length-to-weight’ conversion. - Ln 124: does the italics of ‘via’ have special meaning here? It’s not clear what it is - Ln 135: I didn’t know what - Ln 143-144: roughly how many trips to the shore-based data collectors sample? - Ln 145: insert model number of the gps units (as per typical scientific notation) - Ln 146: was it only voluntary boats that had gps installed? Or is this mandated at a local/state/national level? - Ln 147-148: great figure. Is the concentration of effort near ports a function of effort or the range of cellular towers? - Ln 157: wouldn’t it make more sense to divide by the number of fishers? - Ln 167: isn’t cpue kg per hour per fisher? Or is the per fisher component handled in the EPT? Some clarification needed here. - Equation 1: why multiply by 0.001? - Ln 171 – 184: this seems to be the biggest analytical component of the tool but the details and results are sparse. Suggest adding more methods details and a results figure/table of the cross-validation test. Specifically: (1) clarify if this analysis is done as part of the peskAAS pipeline, or if this is a secondary analysis for validation; (2) can you add references to justify that this was an appropriate method to fill in missing attributes?; (3) what temporal spacing did you use? (ln 177); (4) was the 80%/20% cross validation only performed once? If so this is not adequate. Typically, this random split is repeated multiple times (e.g. 10 times) and the performance validated each time. Or you could use k-folds validation. Ln 198-200: this is really great to see it is operational. Reviewer #2: General comments: This manuscript nicely lays out the development of an online or desktop tool to visualize fisheries-dependent data for use in management and decision making. This tool is already being incorporated into fisheries management in Timor-Leste, indicating its utility and need for supporting small scale fisheries. This manuscript is well done but I would encourage the authors to consider a couple aspects to help highlight where this tool could be useful and to clarify how it functions. 1. Framing: I would encourage the authors to consider how they contextualize where this tool would be useful. The abstract highlights the near real-time production data being aggregated through this tool, indicating an ability to use it for adaptative management. However, the introduction highlights its utility in gaining an understanding of food-security (based on production) while the discussion highlights utility in marine spatial planning. This tool could help in all three of these contexts and they rightly deserve to be highlighted. However, I would encourage the authors to provide more connection on these points being made between sections. For instance: fish as a base for food security requires effective management for lasting security. Small scale fisheries afford the opportunity to provide food security but are difficult to manage because of a lack of data collection and dispersed nature of the fishery. And in order to sustain food security through development it is necessary to understand where fishing effort predominately takes place. 2. Data collection and flow: I had trouble understanding the data flow for this tool. It is not very clear if the spatial and temporal aspects of the data are because of the VMS data or if the shore side sampling provides a spatial component depending on which port the data were collected, it seems only the VMS data provide the spatial component. The VMS data appear to be a critical aspect of the functioning and ultimate use of this tool. However, this feature is called an “optional extra” on line 204. The authors do point out how this would change the function of the tool, however, the abstract and discussion highlight the data gaps around spatial fisheries data. Therefore, it seems that the VMS component is critical for the use of this tool. I understand it will function without the VMS data, so it is important to understand all the data incorporated and how it fits the potential uses outlined in point 1 above. I would note that the description of data collection and flow is highlighted in the Figure 2 caption (lines 90 – 101 after the references). This information should be in the main text as well. Additionally, Figure 2 doesn’t appear to be referenced in the manuscript. Specific Comments Line 27: Missing citation for “small scale fisheries are responsible for half of the global fish catch” Line 69: Where do the landings records come from? Lines 73-74. The resolution for Figure 1 is too low to be able to read the screen shot of what the app can do. As a side note about the app: upon taking a look at the shinyapp, I wonder if it would be more intuitive to have none of the satellite boxes checked upon opening the app and allowing the user to specify which data they want to see instead of having to deselect everything and then select. Lines 75-78: There is not enough detail about the smoothing spline or how a user should decide whether to use this function. Equation 1 at line 163 does not include the smoothing spline either, therefore it is not possible to decipher how this aspect of the tool functions. Line 114: It looks like supplementary information 2 is a species list with growth parameters, am I missing supplementary file 2 to support ‘peskaPARSE.R’? Line 143: Are shore-based data collectors how catch data are normally collected for these fisheries? The information provided under the Figure 2 Caption titled Catch document at landing sites is very helpful context. I would recommend this being added to the methods to help readers understand data collection a little more clearly. I also am not seeing Figure 2 (or Figure 3) referenced in the text, I see Figure 1 at line 73 and then Figure 4 at line 148. Line 146: were the GPS/VMS units that were placed on the 5-15 boats per landing site placed on both power and canoe vessels? L ine 147: Is it costly to the harvesters to upload VMS data via cell phone? For people interested in implementing this system it could be helpful to get an idea of the overall cost to harvesters. Is there also a logbook on the cellphone that harvesters can record catch that then gets associated with the location data or that only comes from the shore side data? Line 154: what does relative fishing success mean? I would recommend rephrasing this for clarity. Line 188: are there a minimum number of observations that are needed to be able to use the data? For instance, US federal fisheries require a minimum of 3 observations to be able to aggregate data otherwise it can’t be shown. This would mean some data are left out, is this the case for Timor-Leste? It would be good to know if not all data are shown. Lines 198 – 200: I personally would like to have a bit more detail about how this tool is being utilized by the Timorese government than what is provided. Line 204: the spatial data from VMS seems critical, unless the port samples are also considered to be part of the spatial data (doesn’t seem like it). Are there area closures or other types of management that make this spatial data critical to adaptive management. Lines 205-207 indicate the fishery footprint data are most useful for coastal zone planning, are they not used in the current fisheries management practices? Figures 2 and 3 are not cited in the text from what I can tell. It is not clear what Supplementary Information 2 is supporting Reviewer #3: Dear Authors, Thank you very much for an interesting paper describing this new system for an open-source monitoring and analytics system. I agree that especially for small-scale fisheries it is a great problem to have reliable landings and catch data as a very important first step to establish some kind of fisheries management. I think your system well developed and you present the results in an appropriate fashion supported by the data. The results show that this could be a very useful tool for collecting data for fisheries managers. I have, however, some doubts how this system could be established in practice in low income countries. For the development of your system and to show how it works you have selected Timor-Leste as an example. For this trial you have organised the data collection by hiring data collectors (at least that how it is described) and I am asking myself how this should work in the long run. Should the fishers report the data themselves (what I assume from your descriptions)? What will be the incentives of the fishers to participate in such a system? Misreporting is a problem in all fisheries management systems around the world. Therefore, could you describe a bit better how you foresee that this system will be used afterwards, who need to participate in the system and what the authorities can do with this information. As I am not a fisheries biologist, I am also not sure about the fishbase database. Is the catch weight (average of all fishes in the catch, the single fish weights?) really the only parameter you need to judge the conditions of the fish stocks in mixed fisheries? I have a few additional more detailed comments regarding your paper: Line 36 ff.: I agree that it is a problem in low income countries to collect data on catch/landings but the question is if those data alone would help to overcome the malnutrition in many countries due to the ability to establish a management system. I think we are still far away from introducing a fisheries management system with catch and/or landings data alone. Especially for mixed fisheries I believe that another approach could work. Many coastal communities have established some kind of management strategies as they have usually a substantial knowledge about the resources and have established some kind of self-management (e.g. in a community-based-management system). Is there information on self-management in the fishing communities in Timor-Leste? Lines 154 ff.: How does e.g. the number of fishers on a vessel influence the input data (fisher-hours)? The CPUE is very much depending on vessels size, fishing gear employed, number of fishers on board, etc. In small-scale fisheries often the owner alone is fishing or only a small number of fishers fish together. Lines 166 ff.: I cannot judge how good those estimated numbers are. My guess is, however, that there are so many factors influencing catch levels that this may squeeze everything too much into a certain routine calculation. However, I am aware that this may be the best methodology available in this case. Lines 183-185: Looks good but still I have doubts about the overall effort necessary to get all this detailed information and if there are no other possibilities. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. 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| Revision 1 |
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PeskAAS: A near-real-time, open-source monitoring and analytics system for small-scale fisheries PONE-D-20-16520R1 Dear Dr. Tilley, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Ismael Aaron Kimirei, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: (No Response) Reviewer #3: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: (No Response) Reviewer #2: I would like to thank the authors for their responsiveness and extensive effort in addressing reviewer comments. The data flow is much clearer now and the authors response to Reviewer 2 regarding the different spatial scales of the data collected was extremely helpful, although not necessary the authors could consider adding this explicit description to the abstract or overview. I particularly like the last sentence of the abstract and think it highlights nicely how information from this tool could be useful. I recommend publishing this article as a nice description of the authors analytical tool to collate fisheries data. I would also like to encourage the authors to consider another publication highlighting lessons learned from the full process they undertook in Timor-Leste. For instance, the development of the fisheries form sounds like it took an extensive collaborative effort with the Timorese government and fishers that could be beneficial to share with those interested in utilizing this approach in other countries and circumstances. Below are a few grammatical edits to consider before publication. Line 13: insert ‘the’ before world’s fish catch Line 40: remove the ‘s’ from nutrients Line 100: should be ‘catering to humanitarian organizations’ instead of ‘for’ Line 130: could consider expanding on what these various feedback mechanisms are Line 153: the dash (-) is noted needed between interface and that Line 222: function nn2 and package RANN are in a different font, the R package on line 156 is not in a different font Line 223: is 0.20 km, there isn’t a unit of distance here Line 224: should read available as of July (change the at to of) Line 240: I would recommend changing sustainability to sustainable fishing Line 244: add (PDS) after Pelagic Data Systems Line 280: envisage should be envision Reviewer #3: Dear Authors, Thank you for your revised manuscript. I have no further comments although I would still like to know if in Timor fishers implemented something like community-based-management systems to limit fishing effort outside of governmental intervention. However, I am aware that this goes to far for the paper. ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No Reviewer #3: No |
| Formally Accepted |
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PONE-D-20-16520R1 PeskAAS: A near-real-time, open-source monitoring and analytics system for small-scale fisheries Dear Dr. Tilley: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Ismael Aaron Kimirei Academic Editor PLOS ONE |
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