[REVIEW]: discourseGT: An R package to analyze discourse networks in educational contexts

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@q1cui@marcosvital<!--end-editor-- Reviewers: @schochastics, @zoometh Archive: 10.5281/zenodo.8164950

Status

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Markdown: [![status](https://joss.theoj.org/papers/a314249ea3e4590c441d425462201db6/status.svg)](https://joss.theoj.org/papers/a314249ea3e4590c441d425462201db6)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@schochastics & @zoometh & @lebebr01, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @marcosvital know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @schochastics

📝 Checklist for @zoometh

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (891.8 files/s, 120868.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               14            173            475            714
TeX                              1             66              0            676
Markdown                         2             48              0            152
-------------------------------------------------------------------------------
SUM:                            17            287            475           1542
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1104

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

marcosvital commented 1 year ago

Dear @schochastics, @zoometh and @lebebr01, thank you again for accepting review this submission for JOSS. The reviewing process is checklist based, and instructions were already posted above by the editorial bot - but let me know if you need any assistance, ok? Also, you can tag @q1cui if you have specific questions about the manuscript.

@q1cui, you can tag any of your co-authors GitHub accounts if you want, so they will be able to follow this issue.

marcosvital commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1073/pnas.1319030111 is OK
- 10.1119/1.17117 is OK
- 10.3102/00346543052003421 is OK
- 10.21061/jte.v7i1.a.2 is OK
- 10.3102/00028312031002369 is OK
- 10.1007/s11409-006-6893-0 is OK
- 10.1007/s11409-009-9053-5 is OK
- 10.1037/0022-0663.85.4.571 is OK
- 10.1080/00221546.2016.1243942 is OK
- 10.1187/cbe.18-11-0222 is OK
- 10.1371/journal.pone.0173851 is OK
- 10.1073/pnas.1605554113 is OK
- 10.3102/00346543071003449 is OK
- 10.1073/pnas.122653799 is OK
- 10.1002/spe.4380211102 is OK
- 10.1039/D0RP00031K is OK
- 10.3102/0013189X18777741 is OK
- 10.3102/00028312031002338 is OK
- 10.3102/00028312037004911 is OK
- 10.1023/A:1014097416157 is OK
- 10.1177/1046496416689710 is OK
- 10.1016/j.cedpsych.2008.05.001 is OK
- 10.1080/10508400802224830 is OK
- 10.1016/j.ijer.2009.01.001 is OK
- 10.1207/s15327809jls1503_3 is OK
- 10.1187/cbe.17-08-0176 is OK
- 10.1207/S15326950DP3502_3 is OK
- 10.1598/RT.60.7.5 is OK
- 10.1016/j.obhdp.2005.03.002 is OK
- 10.1016/j.learninstruc.2016.05.002 is OK
- 10.5951/jresematheduc.43.1.0034 is OK
- 10.5951/jresematheduc.44.5.0775 is OK
- 10.3102/00346543071003449 is OK

MISSING DOIs

- 10.2307/2959965 may be a valid DOI for title: Classrooms as Communities: Exploring the Educational Character of Student Persistence
- 10.1002/9781119008989.ch8 may be a valid DOI for title: Algebraic Graph Theory
- 10.1109/tse.1981.234519 may be a valid DOI for title: Tidier Drawings of Trees
- 10.1101/gr.1239303 may be a valid DOI for title: Cytoscape: a software environment for integrated models of biomolecular interaction networks
- 10.3998/mpub.7106945 may be a valid DOI for title: Undertaking Discourse Analysis for Social Research
- 10.1177/0170840603024006005 may be a valid DOI for title: The professional partnership: Relic or exemplary form of governance?
- 10.1037/e648122011-001 may be a valid DOI for title: Productive Helping in Cooperative Groups

INVALID DOIs

- 10.1207/s1532690xci2104\_2 URL is INVALID
- 10.1207/S15326985EP3502\_4 URL is INVALID
- https://doi.org/10.1016/0020-0190(89)90102-6 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/j.1538-7305.1948.tb01338.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0022-5193(66)90013-0 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/tea.20003 is INVALID because of 'https://doi.org/' prefix
- 10.1207/s15327809jls1501\_8 URL is INVALID
- 10.1207/S1532690XCI1901\_1 URL is INVALID
- https://doi.org/10.1016/S0732-3123(03)00003-8 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1073/pnas.1319030111 is OK
- 10.1119/1.17117 is OK
- 10.3102/00346543052003421 is OK
- 10.21061/jte.v7i1.a.2 is OK
- 10.3102/00028312031002369 is OK
- 10.1007/s11409-006-6893-0 is OK
- 10.1007/s11409-009-9053-5 is OK
- 10.1037/0022-0663.85.4.571 is OK
- 10.1080/00221546.2016.1243942 is OK
- 10.1187/cbe.18-11-0222 is OK
- 10.1371/journal.pone.0173851 is OK
- 10.1073/pnas.1605554113 is OK
- 10.3102/00346543071003449 is OK
- 10.1073/pnas.122653799 is OK
- 10.1002/spe.4380211102 is OK
- 10.1039/D0RP00031K is OK
- 10.3102/0013189X18777741 is OK
- 10.3102/00028312031002338 is OK
- 10.3102/00028312037004911 is OK
- 10.1023/A:1014097416157 is OK
- 10.1177/1046496416689710 is OK
- 10.1016/j.cedpsych.2008.05.001 is OK
- 10.1080/10508400802224830 is OK
- 10.1016/j.ijer.2009.01.001 is OK
- 10.1207/s15327809jls1503_3 is OK
- 10.1187/cbe.17-08-0176 is OK
- 10.1207/S15326950DP3502_3 is OK
- 10.1598/RT.60.7.5 is OK
- 10.1016/j.obhdp.2005.03.002 is OK
- 10.1016/j.learninstruc.2016.05.002 is OK
- 10.5951/jresematheduc.43.1.0034 is OK
- 10.5951/jresematheduc.44.5.0775 is OK
- 10.3102/00346543071003449 is OK

MISSING DOIs

- 10.2307/2959965 may be a valid DOI for title: Classrooms as Communities: Exploring the Educational Character of Student Persistence
- 10.1002/9781119008989.ch8 may be a valid DOI for title: Algebraic Graph Theory
- 10.1109/tse.1981.234519 may be a valid DOI for title: Tidier Drawings of Trees
- 10.1101/gr.1239303 may be a valid DOI for title: Cytoscape: a software environment for integrated models of biomolecular interaction networks
- 10.3998/mpub.7106945 may be a valid DOI for title: Undertaking Discourse Analysis for Social Research
- 10.1177/0170840603024006005 may be a valid DOI for title: The professional partnership: Relic or exemplary form of governance?
- 10.1037/e648122011-001 may be a valid DOI for title: Productive Helping in Cooperative Groups

INVALID DOIs

- 10.1207/s1532690xci2104\_2 URL is INVALID
- 10.1207/S15326985EP3502\_4 URL is INVALID
- https://doi.org/10.1016/0020-0190(89)90102-6 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/j.1538-7305.1948.tb01338.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0022-5193(66)90013-0 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/tea.20003 is INVALID because of 'https://doi.org/' prefix
- 10.1207/s15327809jls1501\_8 URL is INVALID
- 10.1207/S1532690XCI1901\_1 URL is INVALID
- https://doi.org/10.1016/S0732-3123(03)00003-8 is INVALID because of 'https://doi.org/' prefix

marcosvital commented 1 year ago

@q1cui, please check the missing and invalid DOIs above when you can, and let me know if you need any assistance, ok?

schochastics commented 1 year ago

Review checklist for @schochastics

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/q1cui/discourseGT?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license? Please add a LICENSE.md file for the MIT license e.g. as described here
[x] Contribution and authorship: Has the submitting author (@q1cui) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item. (see https://github.com/q1cui/discourseGT/issues/1)
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution. (see https://github.com/q1cui/discourseGT/issues/1)
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)? (see https://github.com/q1cui/discourseGT/issues/5)
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified? (see https://github.com/q1cui/discourseGT/issues/3)
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support (see https://github.com/q1cui/discourseGT/issues/4)

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

zoometh commented 1 year ago

Review checklist for @zoometh

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/q1cui/discourseGT?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@q1cui) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

schochastics commented 1 year ago

I have added a few issues to the repository which I would like to authors to address. Especially the test part is crucial to me. Please take some time and effort to add some tests to the package.

Overall this is a very nice package which just lacks a bit of good practice but that should be fixable. I am happy with the submission once my issues are addressed adequately. (cc @q1cui)

zoometh commented 1 year ago

Sorry for the delay, I will start my review at the end of the week.

q1cui commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1073/pnas.1319030111 is OK
- 10.1119/1.17117 is OK
- 10.3102/00346543052003421 is OK
- 10.21061/jte.v7i1.a.2 is OK
- 10.3102/00028312031002369 is OK
- 10.1207/s1532690xci2104_2 is OK
- 10.1007/s11409-006-6893-0 is OK
- 10.1007/s11409-009-9053-5 is OK
- 10.1037/0022-0663.85.4.571 is OK
- 10.1207/S15326985EP3502_4 is OK
- 10.1080/00221546.1997.11779003 is OK
- 10.1080/00221546.2016.1243942 is OK
- 10.1187/cbe.18-11-0222 is OK
- 10.1371/journal.pone.0173851 is OK
- 10.1073/pnas.1605554113 is OK
- 10.3102/00346543071003449 is OK
- 10.1007/978-1-4613-0163-9 is OK
- 10.1073/pnas.122653799 is OK
- 10.1002/spe.4380211102 is OK
- 10.1016/0020-0190(89)90102-6 is OK
- 10.1109/TSE.1981.234519 is OK
- 10.1101/gr.1239303 is OK
- 10.3998/mpub.7106945 is OK
- 10.1039/D0RP00031K is OK
- 10.3102/0013189X18777741 is OK
- 10.1002/j.1538-7305.1948.tb01338.x is OK
- 10.1016/0022-5193(66)90013-0 is OK
- 10.3102/00028312031002338 is OK
- 10.3102/00028312037004911 is OK
- 10.1023/A:1014097416157 is OK
- 10.1002/tea.20003 is OK
- 10.1207/s15327809jls1501_8 is OK
- 10.1177/1046496416689710 is OK
- 10.1016/j.cedpsych.2008.05.001 is OK
- 10.1080/10508400802224830 is OK
- 10.1016/j.ijer.2009.01.001 is OK
- 10.1177/0170840603024006005 is OK
- 10.1207/s15430421tip4101_3 is OK
- 10.1207/s15327809jls1503_3 is OK
- 10.1187/cbe.17-08-0176 is OK
- 10.1207/S15326950DP3502_3 is OK
- 10.1598/RT.60.7.5 is OK
- 10.1016/j.obhdp.2005.03.002 is OK
- 10.1016/j.learninstruc.2016.05.002 is OK
- 10.1207/S1532690XCI1901_1 is OK
- 10.1016/S0732-3123(03)00003-8 is OK
- 10.5951/jresematheduc.43.1.0034 is OK
- 10.5951/jresematheduc.44.5.0775 is OK
- 10.3102/00346543071003449 is OK

MISSING DOIs

- None

INVALID DOIs

- None

zoometh commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

zoometh commented 1 year ago

👋 @q1cui

License: change https://github.com/q1cui/discourseGT/blob/main/LICENSE to something like https://github.com/eamena-project/eamenaR/blob/main/LICENSE.md

Some minor errors:

missing ORCID | typos:

one missing reference:

change null to uppercase (NULL) since R is case sensitive:

No clear Community guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support. Please add them in GH

q1cui commented 1 year ago

Thanks a lot @schochastics @zoometh for your thorough review! We appreciate the valuable feedback you have provided, and we have carefully considered all of your comments and suggestions. Your comments will definitely help improve the quality of this package. Students and I will fix everything you mentioned within the next week. We really appreciate your effort! Thank you again for your time and consideration.

q1cui commented 1 year ago

Thank you again @schochastics @zoometh for taking the time to review our manuscript and package. We have carefully considered all of your comments and have made revisions to the manuscript accordingly. We believe that these changes have addressed the concerns raised by both reviewers, and have significantly improved the overall quality of the manuscript. Here is the detailed response to each of your comments and suggestions. We hope that you find our responses satisfactory and that they address all of your concerns. If you have any further comments or suggestions, please do not hesitate to let us know.

We have changed data to SampleData1 to make our paper reproducible.
We have fixed plotNGTData(), it is free of warnings now in Github. We will update CRAN later this week accordingly.
We have added key function descriptions and examples to guide users, they are documented in README.
We have updated the License file.
We have added community guidelines to README.
We have checked the format of the reference and ORCID. For undergraduate students who don’t have ORCID, we cannot include ORCID in this manuscript.

schochastics commented 1 year ago

@q1cui Thanks for your revision. However, there are still some open issues which i would like you to address. Especially adding some tests would be crucial for accepting the package

oliviaguest commented 1 year ago

@schochastics maybe it's time to email as I think they have missed this?

schochastics commented 1 year ago

@oliviaguest you might be right. Should I do that, or do you do that?

oliviaguest commented 1 year ago

Sorry, I meant to tag @marcosvital. It's certainly the editor's call to make, not the reviewer's, my apologies.

marcosvital commented 1 year ago

@schochastics and @zoometh: thank you for all the effort so far on reviewing this submission. I'm trying to reach the author so we can move on. I'll let you know if we have any news about that.

q1cui commented 1 year ago

@schochastics and @zoometh: thank you for all the effort so far on reviewing this submission. I'm trying to reach the author so we can move on. I'll let you know if we have any news about that.

Thanks @oliviaguest @marcosvital Currently, I am working on the second round of revisions, which I expect to complete by the end of this week. Once finished, I will promptly submit the revised manuscript for review.

I would like to kindly request your assistance in reminding the third reviewer to provide their feedback, as I am still awaiting their comments. Additionally, I have yet to receive feedback from Reviewer 2 regarding the first round of revisions. If possible, please remind them as well. I am committed to addressing their comments in a timely manner to further improve the manuscript.

Thank you for your time and consideration!

marcosvital commented 1 year ago

Glad to know that you are working in a new version, @q1cui. Let us know when you finish this version, and we'll contact the reviewers again.

q1cui commented 1 year ago

I greatly appreciate the constructive feedback @schochastics provided on my manuscript. Your insights are valuable, and they have given me a broader perspective on how to improve the manuscript. Here are the responses to each of your comments:

The use of iscsvfile = TRUE to interpret the first parameter as a path might be a bit redundant. The parameter iscsvfile = TRUE is used to help differentiate the two possible input types for input_file as you mentioned: path to CSV file(character) or a loaded R data frame. It is used as a protection to ensure that users are aware of the input being passed into the function. However, taking your suggestion into consideration, I understand that checking the input type within the function itself might be a more efficient and good practice. If there is any misinterpretation of your suggestion, please correct me. Here is a sample modification: edgelist_raw <- function(input_file) {

check input type, read external input file into data.frame

if (is.data.frame(input_file)) { df <- input_file } else if (is.character(input_file)) { df <- read.csv(input_file) } else { warning("Invalid input type. Please input file path as character or input data.frame directly.") } # rest of the code}
It was noted that the ?discourseGT is too short and could benefit from a description of the key functions. Thank you for pointing this out. To address this, we have expanded the ?discourseGT section to include descriptions of the key functions. These updates can be found in this file: discourseGT/R/discourseGT.R.
The reviewer identified issues with plotNGTData() and summaryNet() functions. We have addressed these concerns and ensured that plotNGTData() is free of warnings on Github. Additionally, we have corrected summaryNet() so that the ----DISCLAIMER AND WARRANTY OF PROVIDED RESULTS AND CODE---- is no longer included in the output.
It was suggested that the addition of some unit tests would be beneficial. In response to this suggestion, we have introduced a few unit tests that can be found in the tests folder. We appreciate this suggestion and will continue to develop and expand these tests in the future.

I hope these revisions and clarifications are in line with your expectations. Once again, I appreciate your constructive feedback and look forward to your continued guidance.

schochastics commented 1 year ago

@q1cui tanks for your hard work. I left comments as issues again.

q1cui commented 1 year ago

@schochastics We would like to extend our gratitude to you for taking the time to review our manuscript and for your valuable feedback which has helped us improve the package. Herein, we would like to provide a detailed response to your concerns. Unit Tests: We appreciate your suggestion to incorporate unit tests into our package. Based on your feedback, we added several tests which we found to be crucial for assessing the package’s functionality and reliability. However, we acknowledge that there were some issues initially causing a few tests to fail. After a thorough investigation, we have addressed these issues and made sure that all tests are passing. Generic Functions: Your suggestion to include generic functions was insightful and has indeed improved the design of our package. We have now incorporated a series of generic functions. Vignette Errors: We are thankful for your observation about the errors occurring during the building of the vignette. Upon your suggestion, we revisited our vignette build process and rectified the issues causing the errors. We have now ensured that the vignette builds successfully without any errors.

marcosvital commented 1 year ago

Thank you for your new feedback, @schochastics!

@zoometh, are you still able to look on the new revised version of this submission?

zoometh commented 1 year ago

@marcosvital Yes. I'll do it now

zoometh commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

zoometh commented 1 year ago

@marcosvital and @q1cui

I suggest to change the chapter named "Run Graph Theory Analysis" to "Run Graph Analysis" or "Run Network Analysis" since graphs are mathematical structures, whereas networks are the objects of study.

For the rest, I agree with @schochastics

q1cui commented 1 year ago

@zoometh In response to your suggestion regarding the chapter "Run Graph Theory Analysis", we have revised the title to "Run Graph Analysis". Thank you for your insightful suggestions. We look forward to any further feedback you may have.

schochastics commented 1 year ago

@q1cui thanks for your great work on fixing the package. You are almost there. There is one issue remaining that I just opened. Once this is fixed, I think I am happy

marcosvital commented 1 year ago

Thank you for all your effort put into this submission so far, @schochastics and @zoometh!

As we move on with our last steps, please don't forget to finish the review checklist, as it should be all checked for the submission to be accepted.

zoometh commented 1 year ago

Done. Congrats @q1cui !

marcosvital commented 1 year ago

@editorialbot remove @lebebr01 from reviewers

editorialbot commented 1 year ago

@lebebr01 removed from the reviewers list!

schochastics commented 1 year ago

I have checked everything but the last issue should be fixed before acceptance

q1cui commented 1 year ago

Thank you @schochastics for your detailed feedback and suggestions on our manuscript. We have carefully considered your comments and have made the following corrections: We have removed the directory 'discourseGT/Meta' as per your suggestion. We have addressed the issue of no visible binding for global variables in the 'plotNGTData.data.frame' function. Lastly, we have created a '.Rbuildignore' file and added 'LICENSE.md', 'doc', and 'paper' directories. We believe that these corrections have improved the quality of our work and have addressed your concerns.

schochastics commented 1 year ago

@q1cui Thank you! @marcosvital I am happy now to accept it

q1cui commented 1 year ago

Dear Editor @marcosvital @oliviaguest and Reviewers @schochastics @zoometh, I am writing to express my deepest gratitude for your time, expertise, and invaluable feedback during the review process of our paper. Your detailed comments and suggestions were instrumental in improving the quality of this package. I sincerely appreciate your time, expertise, and support throughout this process.

q1cui commented 1 year ago

@marcosvital I am grateful that the paper has been accepted by two reviewers. However, I have noticed that the status of the paper has not changed on the submission portal, and I would like to confirm if there are any further steps that I need to undertake at my end. I understand that the administrative process may take some time, and I do not mean to rush. I only wish to ensure that no further actions are required from my side that could potentially delay the process. I look forward to hearing from you at your earliest convenience. Thanks!

q1cui commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

q1cui commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

openjournals / joss-reviews