Peer Review History
| Original SubmissionJune 9, 2020 |
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PONE-D-20-17563 StationRank: Aggregate dynamics of the Swiss railway PLOS ONE Dear Dr. Anagnostopoulos, 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. Please take careful note of the points indicated by each of the referees as both thought the paper required a number of changes before it could be accepted, although these points/changes varied to some degree from referee to referee. Please submit your revised manuscript by September 13, 2020. 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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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. Our internal editors have looked over your manuscript and determined that it is within the scope of our Cities as Complex Systems Call for Papers. This collection of papers is headed by a team of Guest Editors for PLOS ONE: Marta Gonzalez (University of California, Berkeley) and Diego Rybski (Potsdam Institute for Climate Impact Research). The Collection will encompass a diverse and interdisciplinary set of research articles applying the principles of complex systems and networks to problems in urban science. Additional information can be found on our announcement page: https://collections.plos.org/s/cities. If you would like your manuscript to be considered for this collection, please let us know in your cover letter and we will ensure that your paper is treated as if you were responding to this call. If you would prefer to remove your manuscript from collection consideration, please specify this in the cover letter. 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 ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: 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 ********** 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 ********** 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: The manuscript "StationRank:Aggregate dynamics of the Swiss railway" by Georg Anagnostopoulos and Vahid Moosavi presents a Markov Chain (MC) framework to analyse daily aggregated itineraries of the swiss railway systems. They use their MC framework to asses the congestion, resilience and fragility of the railway network. I think that this framework is interesting. It is simple and does not require much computation power and allows one to draw interesting insights from the data. However, this manuscript is not fit for publication in its current state. My main issues are the following: - The authors do not place this study in context. There are many existing tools for the analysis of public transportation that can be much more detailed (using agent-based model for example, as in [1]). In the introduction, the authors should explain what it is they want to do, summarize previous works, explain why their approach is relevant and what is their contribution. In the conclusion, they could elaborate on the limitations of their approach and on possible improvements. - The methodology is not well explained. Many points are unclear. For example, it is not clear how the transition matrices are computed. The authors make many assumptions in their model but do not explain or justify them. There are also many smaller issues that I list below:: - eq. 1, define S and x - p. 2: How is P_ij computed? How is the daily data aggregated? - p. 2 :Why do you use a 1min discretization? why not 10min or each km for example? - p. 2: define L-space and P-space. - p. 2: Describe the final networks of stop and transits. How many nodes are stations? You could show a sub-network as an example. - p. 3: Explain better Fig. 2. what are the labels? what are the nodes? This is really not clear. - p. 3: have you tried different values of alpha in the teleportation trick? You could discuss this a little bit more. Certainly passengers do not teleport in real life. What kind of artefacts does this create? We could also imagine other approaches to make the network strongly connected. For example, nodes connecting to outside of Switzerland could be all connected together. - p. 4: You should also discuss the fact that all the quantities you uses are evaluated at stationarity, but the system is actually never stationary. What does the stationary distribution represents in this case? - p. 4: About the Kemeny constant, the authors write that it can be described as the "average expected time (steps) from any given state (origin) to any other random state (destination)". This is interesting, but surely, the "expected time from any given state to any other random state" has a very heterogeneous distribution. It would be interesting to also have a measure of the standard deviation of this distribution. - p. 4: "For the Swiss railway network, we calculated that K ≈ 30.5, ±1 minute." How is the error (and average) calculated? - p. 5: "Linear reduction of a station’s activity by multiple perturbations of the transition probability matrix is more suitable for a real-world network than simple node removal." Could you explain why? - Fig. 3: Show the dates for each plot and do not use a diverging colourmap for a continuously increasing quantity. The position of the white colour is arbitrary. (see https://matplotlib.org/3.1.0/tutorials/colors/colormaps.html) - p. 5: "In the first weekend, high probabilities were redistributed in the west part of the country. Furthermore, some of the lowest probabilities were reduced near the end of the month." This is not clear at all on Fig. 3. You could show of the variation of pi in the East and West. - p. 5: "namely the fact that the first weekend of October developed a completely distinct dynamic which might be related to the beginning of the Swiss autumn holidays." We see a clear shift, and this is quite nice, but I would not say that it is "a completely distinct dynamic". It would be nice if you could assess if it is related to the beginning of the Swiss autumn holidays by looking at some other statistics in the data that does not rely on the MC framework. - p. 6: "Known network measures, such as various centrality measures [8, 13, 21], are purely based on network structure and often fail to address dynamic aspects of flow and time which are crucial when evaluating the real behaviour of the system and the related risks." This is not true, most centrality measures are based on an underlying diffusion process. E.g. degree centrality can be seen as the ranking given by the stationary distribution of a random walk. Same of page rank. Moreover, here you assess systems at stationarity, so you are not rely considering the dynamic of the system apart from daily evolution of the stationarity. - p. 6: Explain the Bruess Paradox. - p. 7: Explain the intuition behind the definition of systemic influence and systemic fragility. - p. 7: "This is a striking finding that suggests a link between systemic fragility and network growth, a claim which needs to be verified also for other networks in further research." Interesting, but there is no need to use bold. - Fig. 6: Give the names of a few stations. - Fig. 7. Do not use divergent colourmaps for influence and fragility. - Fig. 8. How many highest and lowest values are you showing? [1] P Manser, H Becker, S Hörl, KW Axhausen, Designing a large-scale public transport network using agent-based microsimulation, Transportation Research Part A: Policy and Practice, 2020 Reviewer #2: The study investigates the application of Markov chain (MC) theory to the analysis of the Swiss railroad network historical data. The analytical approach takes inspiration from Goolge’s PageRank algorithm (Page et al., 1999) and follows closely the mathematical and analytical framework established by Crisostomi et al. (2011) for MC applications to transportation networks. The study uses open access data covering a moth worth of activities for the Swiss railroad network to analyze its aggregate dynamics and sensitivity to perturbation in flow. While the article introduces virtually no new theoretical concepts to the problem, it does present an interesting adaptation of the analytical approach to actual historical data for the Swiss railroad network. The article is well written and easy to follow, however the theoretical treatment of some of the concepts utilized in the study are glossed over rather quickly. I suggest the authors take the following comments/suggestions into consideration to address these shortcomings; please see attachment. ********** 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. 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: Yes: Sinan Salman, PhD [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.
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| Revision 1 |
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StationRank: Aggregate dynamics of the Swiss railway PONE-D-20-17563R1 Dear Dr. Georg Anagnostopoulos, 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, Ben Webb, Ph.D. Academic Editor PLOS ONE There are a few remarks/suggestions the referees have for the authors that should be consider for the final version although no changes are required. 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: (No Response) Reviewer #2: 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 ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 ********** 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 ********** 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: I thank the authors for replying to my remarks. They have addressed all of my issues and the manuscript is now much clearer and its results are robust and interesting. I recommend its publication. I just have a few remarks/suggestions that the authors should consider for the final version. Namely: - p.3 " Then, for each day of operation, we convert all trips to special continuous trajectory objects [13] which we descretize: " ext-link-type="uri" xlink:type="simple">https://bit.ly/3iKLx7A." I suggest to add the linked figure in the manuscript (or use Fig. S1). There is also a typo: descretize - discretize - p.4. You could state the number of dwell states and the number of running states. In general, the figure captions could have more information so that it is possible the understand a figure just by looking at it. - Fig. 2 and 3: why use the cube-root of the values? for Fig. 2 the units should be time units, otherwise this figure is rather meaningless. - Fig. 4 and 5: add colorbars with units to the plots. - Fig. 5 and S5: what are the units? percentage of change? please clarify it in the figures. - Fig. 7: clarify the fact that the min, max, median, ... are taken over the temporal dimension. (If I understood). - Fig. 7: show Olten on one of the panel. - p. 9: "According to Fig 7, the high variation of flows in the west part of the country caused shifts in the first and second eigenvector, as expressed by the stationary distribution and by the weakly connected sub-communities." Please describe exactly to which panels of Fig. 7 you refer to support this argument. - Fig. 8: It could be nice to add the names and ranks of the stations on the plots. Reviewer #2: All comments have been addressed. While I understand the authors' statement in the final sentence of the conclusion: "In contrast to disaggregated...". I believe the authors approach can be extended to the redesign of existing networks through evaluation of different extension scenarios, which can be generated manually or algorithmically. I'll leave it to the authors whether they react to this comment or not in their final manuscript. ********** 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: Yes: Sinan Salman |
| Formally Accepted |
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PONE-D-20-17563R1 StationRank: Aggregate dynamics of the Swiss railway Dear Dr. Anagnostopoulos: 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. Ben Webb Academic Editor PLOS ONE |
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