Comparing phonological and orthographic networks: A multiplex analysis

Pablo Lara-Martínez; Bibiana Obregón-Quintana; Cesar F. Reyes-Manzano; Irene López-Rodríguez; Lev Guzmán-Vargas

doi:10.1371/journal.pone.0245263

Peer Review History

Original SubmissionAugust 3, 2020
11 Nov 2020 Decision Letter - Diego Raphael Amancio, Editor PONE-D-20-23977 Comparing phonological and orthographic networks: a multiplex analysis PLOS ONE Dear Dr. Guzmán-Vargas, 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 notice that only comments that are applicable to a Registered Report Protocol should be addressed. You can consider additional suggestions when preparing a Registered Report. Please submit your revised manuscript by Dec 10 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. 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PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ Additional Editor Comments (if provided): The authors should address only the comments that are applicable for a Registered Report Protocol. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions? The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses? The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable? Reviewer #1: Yes Reviewer #2: Yes ****** 4. Have the authors described where all data underlying the findings will be made available when the study is complete? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. 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 and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics. You may also provide optional suggestions and comments to authors that they might find helpful in planning their study. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The study proposed by the authors in this report is interesting and could yield interesting results. The authors do a good job in motivating their project. The manuscript is well written barring some minor typos (see below). The authors may consider adopting some multilayer community detection algorithms like the ones described in [1] for example to find more interesting clusters across layers. Typo on line 79 on page 3 - A & B should be V & W. Reference: [1] De Bacco, Caterina, et al. "Community detection, link prediction, and layer interdependence in multilayer networks." Physical Review E 95.4 (2017): 042317. Reviewer #2: The manuscript ‘Comparing phonological and orthographic networks: a multiplex analysis’ by Pablo Lara-Martinez, et al. presents several graph-theoretic statistics and metrics of networks build from orthographic and phonological corpora of words for four languages (English, German Russian, and Spanish). The authors assign words to nodes and use the Damerau-Levenshtein distance to create edges between nodes depending on their distance. Several networks are created in which the cutoff for the distance is different and the statistics are listed for each network. The authors also propose a timeline to expand the size of the corpora and repeat the experiments, but this part of the analysis is not included in the manuscript. The main issue with this manuscript is that it does not include a discussion or interpretation of the results. Even though the methods are described and results are listed, there are no scientific claims, there is no analysis of the results, there is no real comparison to relevant work, and there is no discussion of the importance of the results or their significance to the field. The manuscript is unsittable for publication as a scientific article in the present form but could be published if a discussion section is included. I also have minor suggestions: • Make the networks created with the different distance cutoffs publicly available. Calculating the DL distance is not necessarily trivial and this dataset would be useful to other researchers, who can use it to compare their work or methods to the current ones. • In the text, define DL as ‘Damerau-Levenshtein’ before using the acronym. • I did not identify any connection in the results listed between the phonological and the orthographic networks other than 1 to 1, so I don’t think this is rigorously speaking multiplex. • The caption of Fig. 1 states that the illustration is for Spanish but the words are in English in the actual figure. • Although it is understandable, V should be defined for completeness before Eq. 3. • M is used in the definition of the degree of a node right before Eq. 3, but M is never defined. From inspection it seems like M is the multiplex layer, but this should be stated clearly to make it easier for the reader. • I did not understand the definition of the modularity (Eq. 6). It says that the partition includes elements C_1, …, C_M. In this case M is subscript. C is defined as the clustering coefficient in Eq. 4. The set S is not really defined. So this needs more work. • The results in Fig. 2 might not be apples to apples because the highest degree depends on the DL distance cutoff. I suggest normalizing the horizontal axis by the highest degree in each network. • I suggest removing Fig. 3 and mentions of specific start dates and due dates. This is not really part of a scientific 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 [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. https://doi.org/10.1371/journal.pone.0245263.r001
Revision 1
25 Nov 2020 Author Response Reviewer #1 “The study proposed by the authors in this report is interesting and could yield interesting results. The authors do a good job in motivating their project. The manuscript is well written barring some minor typos (see below). The authors may consider adopting some multilayer community detection algorithms like the ones described in [1] for example to find more interesting clusters across layers. Typo on line 79 on page 3 - A & B should be V & W. Reference: [1] De Bacco, Caterina, et al. "Community detection, link prediction, and layer interdependence in multilayer networks." Physical Review E 95.4 (2017): 042317.” Response: Thank you for your comments. We have added the application of the suggested multilayer community dectection method to the revised version of our Protocol (Lines 129-131), which will enrich our discussion about potential grouping of nodes (words) in the context of the two-layer network. The typo was corrected. Reviewer #2 1)• Make the networks created with the different distance cutoffs publicly available. Calculating the DL distance is not necessarily trivial and this dataset would be useful to other researchers, who can use it to compare their work or methods to the current ones. Response: Thank you for your suggestion. We have added the corresponding networks (with 10⁴ nodes) for each corpus to our dataset in the Figshare repository. We plan to update the dataset once we have concluded our study. 2) • In the text, define DL as ‘Damerau-Levenshtein’ before using the acronym. Response: Corrected in the revised version (Line 23) 3)• I did not identify any connection in the results listed between the phonological and the orthographic networks other than 1 to 1, so I don’t think this is rigorously speaking multiplex. Response: We plan to address the multiplex features in the extended paper 4)• The caption of Fig. 1 states that the illustration is for Spanish but the words are in English in the actual figure. Response: The error was corrected 5)• Although it is understandable, V should be defined for completeness before Eq. 3. Response: We have clarified the network notation, and the meaning of the letters (see lines 99-121 ) 6)• M is used in the definition of the degree of a node right before Eq. 3, but M is never defined. From inspection it seems like M is the multiplex layer, but this should be stated clearly to make it easier for the reader. Response: We have corrected the description of the network’s notation (see lines 99-121) 7)• I did not understand the definition of the modularity (Eq. 6). It says that the partition includes elements C_1, …, C_M. In this case M is subscript. C is defined as the clustering coefficient in Eq. 4. The set S is not really defined. So this needs more work. Response: Thank you for your comment. In the revised version of the manuscript we have clarified our notation regarding the modularity definition (see Lines 117-121). 8)• The results in Fig. 2 might not be apples to apples because the highest degree depends on the DL distance cutoff. I suggest normalizing the horizontal axis by the highest degree in each network. Response: We have added the suggested normalization of the horizontal axis in the new version of Fig. 2 9)• I suggest removing Fig. 3 and mentions of specific start dates and due dates. This is not really part of a scientific paper. Response: The mentioned fig was removed. The new dates were updated in the main text. Attachments Attachment Submitted filename: ResponseToReviewers.pdf https://doi.org/10.1371/journal.pone.0245263.r002
28 Dec 2020 Decision Letter - Diego Raphael Amancio, Editor Comparing phonological and orthographic networks: a multiplex analysis PONE-D-20-23977R1 Dear Dr. Guzmán-Vargas, 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, Diego Raphael Amancio Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions? The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field. Reviewer #2: Yes ******** 2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses? The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory. Reviewer #2: Yes ****** 3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable? Reviewer #2: Yes ****** 4. Have the authors described where all data underlying the findings will be made available when the study is complete? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. 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 #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 #2: Yes ******** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics. You may also provide optional suggestions and comments to authors that they might find helpful in planning their study. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #2: The authors satisfactorily addressed in their revised manuscript the points raised in the first round of reviews and I recommend publication of the 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 #2: No https://doi.org/10.1371/journal.pone.0245263.r003
Formally Accepted
7 Jan 2021 Acceptance Letter - Diego Raphael Amancio, Editor PONE-D-20-23977R1 Comparing phonological and orthographic networks: a multiplex analysis Dear Dr. Guzmán-Vargas: 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. Diego Raphael Amancio Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0245263.r004

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