Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: WORKLOAD ASSESSMENT FOR MENTAL ARITHMETIC TASKS USING THE TASK-EVOKED PUPILLARY RESPONSE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is very clearly, if rather densely written. The use of acronyms does require a certain mental agility from the reader but I am not sure there is a way round this and the authors do reiterate the basic terms in the Results section.

There is a good introduction to motivate the work, primarily a replication of the previous work of Ahern and Klingner with better temporal resolution and only visual stimuli. It is not entirely clear from the way the paper is written that the NASA TLX is a new measure added to this study. See for instance the abstract. From reading Klingner's thesis, I see that the workload measures are an introduction for this study but this should be addressed with more clear phrasing in the paper itself. I think there might be room to go more into the details of exactly what Ahern and Klingner did so that the contrast with the current work is clearer. In particular, many measures are used: MPD, MPDC, MPDCR. Is there a reason for this? I would have thought only MPDC was needed. Unless of course this is part of the replication (I can't see Ahern so can't be sure). So some clarity there would help.

I also felt that the Results section could be more coherently organised. Understandably there are lots of results and anything that helps the reader navigate them would be useful. For instance, MPDC effect sizes are reported several paragraphs after the MPDC is analysed. It makes logical sense (and is also analytically appropriate) to put these together. Similarly, NASA TLX analysis is separated from correlations with the NASA TLX measures. I found myself skipping around between tables, figures and sections of the Results and I think some of the skipping could have been removed.
Experimental design: The experimental design seems to be very appropriate and the experiment seems to have been conducted very well.
Validity of the findings: The findings seem good to me though I would query a couple of points. I was not aware that Tukey's HSD was appropriate for repeated measures ANOVA. I finally tracked down an online resource by Howell, of statistical textbook fame so a decent source if not an authoritative outlet. He reckons that such follow ups are not sensitive to violations of assumption and recommends Bonferroni corrected t-tests. The authors may have a more authoritative reason for their approach but I feel it should be referenced as this is not common practice (unlike most of the other aspects of the statistical testing). At the same time, the use of Bonferroni corrections can be very conservative. There is room to discuss this.

I am very happy that this is replication work with the added in NASA TLX measures. Equipment does change and provides new opportunities. And of course any measurement instrument operationalises the measures in new ways. It is good to have up to date support for commonly accepted historical results.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: WORKLOAD ASSESSMENT FOR MENTAL ARITHMETIC TASKS USING THE TASK-EVOKED PUPILLARY RESPONSE
Review round: 1
Reviewer: 2

Output:
Basic reporting: No Comments
Experimental design: The Design of the experiment was fine for a repeated measures study - counterbalancing was in place.

I would have liked more details about lighting levels in the testing room.  How could the authors be sure that lighting was consistent across all testing conditions?  Was lighting level measured?
Validity of the findings: The results of the experiment are rigorously reported and conclusions are accurate and clearly stated.
- Given that the authors measured 3 different aspects of pupil (MPD, MPDC, MPDCR), I would prefer to see some clear recommendations about strengths and weaknesses of each variable, especially for HCI evaluation.  Is one measure less sensitive than others to fluctuations in naturalistic light.
- It is good that MPDC is as sensitive to subjective workload but could authors spell out advantage of physiological monitoring for the naive reader in the conclusions?
- The presentation of the eye blink data in Fig 10 was hard to understand, more text required to explain this aspect
- the task used by the authors had minimal visual demand but high cognitive demand, could they please speculate in the discussion section about how their results may generalise to other types of tasks, especially ones where visual workload may be manipulated, e.g. locating information on different screen designs or web pages.
Additional comments: I appreciate the thorough reporting of data, but I felt that Figure 5 was not really necessary


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A SURVEY OF CHINESE INTERPRETING STUDIES: WHO INFLUENCES WHO …AND WHY?
Review round: 1
Reviewer: 1

Output:
Basic reporting: The aim of this paper it to perform a deep bibliometric analysis of the Chinese Interpreting Studies using social network analysis techniques.

In general, the paper is well written and organized. Although, the main drawback is that the paper is biased to the bibliometric Chinese literature. I miss a lot of important reference to co-word, co-citation, co-author, etc. In fact, the map of a research field is also known as Science Mapping analysis.

Moreover, the paper is somewhat large and some parts of it are repeated constantly along the paper.
Experimental design: The data acquisition is not well explained. Authors should make an effort, an explian the procedure and query used.
Validity of the findings: The findings are correct.
Additional comments: In what follows, some suggestions are comments are listed:

Line 77. Includes reference to social network analysis and citation analysis

Line 201. How data acquisition has been performed? Authors should describe the procedure and the query used to retrieve the data.

Line 295. “Cited one another’s research” is also known as co-author citation.

Line 317. Why the authors not use h-index to measure the most influential scholars?

Line 343. The authors used a non-common similarity measure. According to van Eck 2009, the Association strength should be used to normalize co-occurrence network. Also, the equivalence index has been traditionally used in co-word network.

Line 367. Under my point of view, 40% of authors not-matched is too much.

Line 394. Authors may refer to Zipf’s law: “Zipf's law states that while only a few words are used very often, many or most are used rarely”.

Line 462. The software used to perform the analysis and visualization should me mentioned. There are a great variety of software tool to perform a science mapping analysis (e.g. VOSViewer, SciMAT, Sci2 Tool, VantagePoint, etc.), and also a great variety of software to visualize network (e.g. Gephi, Pajek, etc.)

Line 512. Figure 3 should be enlarged and better laid out. Authors should draw the network avoiding use circular layout. Now, it is very difficult to see the relation between nodes of the same cluster.

Line 606. H-Classics should be used to highlight the mots influent works.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A SURVEY OF CHINESE INTERPRETING STUDIES: WHO INFLUENCES WHO …AND WHY?
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper carries out a scientometric survey on Chinese Interpreting studies (CIS) to obtain a description of the ways in which CIS scholars interact and which are the most influential studies. They use both traditional technique of citation analysis and Social Network Analysis.

The paper describes correctly their purpose and a considerable number of works are included. Moreover, different metrics are considered in the study. However, some points should be improved related to disscussion of the results obtained.
Experimental design: It would be necessary that authors detail the software and methods used to obtain results. Concretely,

+ In section 6.1, it is not mentioned a software to carry out the work. How authors have obtained the different networks and their different metrics?

+ In section 6.3, the specification of the software and the methods used to carry out this study neither they are mentioned.

Also, it would be convenient that authors specify the number of years considered in the study.
Validity of the findings: It is appropriate
Additional comments: Authors should improve the next points:

-  Figure 3 it is very complicated to visualize. It would be convenient that authors try to simply or divide it to be able to understand better the results.

- In general, the section 6.3 would be reviewed. Some times it is very difficult to understand appropriately the results obtained. Definitions, descriptions and discussions are mixed and sometimes information is duplicated. It would be interesting that authors try following the same steps in the discussion of all results. First, it would be necessary to comment the specific numerical results of each table (in some tables, it is not specified the metrics shown neither in this section neither in section 5). Second, it would be necessary to show specific examples and detail the general conclusions. Normally, all information is available, but they should be restructured.

- Finally, some times authors use an acronym, but this is specified later. For example:
  - - Line 51 the acronym “BCE” it is not specified previously.
  - - Line 260 the acronym “PRA” it is not specified previously.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: A SURVEY OF CHINESE INTERPRETING STUDIES: WHO INFLUENCES WHO …AND WHY?
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have addressed the majority of the changes suggested. Therefore, I recommend to accept the paper.
Experimental design: Ok
Validity of the findings: Ok
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MLITB: MACHINE LEARNING IN THE BROWSER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The research issue is well presented and is a challenging one. The structure of the paper is also sound and easy to follow, although several sub-sections should be combined into larger ones.
The main contribution of the paper regards the proposed architecture for having ML capabilities in the browser. The main drawback of the presentation regards clear presentation of client and server side. It was somehow difficult to figure out exactly which parts are on the server side and which are on the client side.
For example:
- The Boss is a data worker and/or a web worker?
- Both Master Server and Data Server are on the same server machine?
- Is Hadoop used in this project? Where? On Master Server and/or Data Server?
- The paper looks more or less like a development guide for a software application. Many technical details are provided (e.g., JavaScript, MapReduce, Hadoop) although a clear indication of how exactly MapReduce is used is not provided. Did authors use an already existing implementation of MapReduce, like Hadoop? ... and if yes, how does it integrates with JavaScript?
Experimental design: The experiments are fine although more accuracy and performance metrics may be required.
Validity of the findings: Yes, the findings are valid but may be a little preliminary. More structured experimental results may be needed.
Additional comments: The paper needs two improvements:
- refine the presentation of the architectural decisions for a better understanding
- more structured experimental results (accuracy metrics and performance assessment) may be needed.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MLITB: MACHINE LEARNING IN THE BROWSER
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is clear and readable. The idea is interesting, and I really enjoyed reading the manuscript.

In the introduction, the authors should clearly clarify the three objectives that are later mentioned in Section 2. Additionally, it is important to clearly state the motivation and justification of the paper. In this sense, research questions are missing. The paper should be more focused on the scientific side, but it mostly covers technological aspects.

Please describe the organisation of the paper uniformly. For example, Section 3.2 is described but section 3.1 is not even mentioned. Mentioning the main sections is more than enough.

Please, avoid including explanatory text in captions (Fig. 1 to 3). Such pieces of text should be incorporated to the section.

All the acronyms should be explained (e.g. SGD, etc.)
Experimental design: The paper is not properly motivated and the experimental framework presented is weak. For example, how did the authors reach this approach? Which design choices were made? Which limitations have their solution and how were they neutralised? Are other solutions (e.g. using services) viable in this case?

The technological contribution is notorious and technically sound, but the scientific side should be conducted more precisely. Additionally, technological choices should be plenty justified as well, e.g., why node.js?

A more detailed comparative framework with both other design alternatives and other previous solutions would be required.

All the implementation and contribution seems to be focused on a given problem domain. What if the library should be scaled, integrated within other system or just a single module would be reused? How is it done? I am afraid that it would be not that simple, and most of the current modules should be adapted or reimplemented, e.g. to add preprocessing capabilities, data and result handlers, new algorithms, etc. Who is in charge of extending the library? Can an external developer to add new features or should we depend on the releases provided by a development team? If it is considered extendable, then please include evidences (case studies, a further discussion, etc.) All these aspects should be explained in detailed so the real contribution is clearer.

The experimental framework should be clearly defined. Important information is missing to support the scalability of this approach. Which is the largest amount of data supported? Which technical/performance limitations have the authors found in their approach? Any limitation regarding data (type, size, etc.)?
Validity of the findings: The paper makes some strong assumptions without any substantial and precise scientific support. For example, in Section 2.1, the authors mention that “to make ML truly ubiquitous requires ML writing models and algorithms with web programming languages and using the browser as the engine”. This should be supported by references.

In fact, a major issue is that the authors often make use of subjective references to endorse their work and assumptions. It is clearly lacking of rigour. References to particular blog entries or subjective articles should be avoided. Please cite instead peer-reviewed works and other precise sources of information. If assertions are not properly founded, they become speculation.

Another strong issue is that the paper is not clear about what is really done and what is to be. For example, the abstract seems to indicate that GPU capabilities are already provided (“MlitB offers [..] including: development of distributed learning algorithms, advancement of web GPU algorithms [..]”. Until Section 2 we do not know whether it is really implemented or not. In fact, the last paragraph of Section 2.2 should be moved to Future Work.

Please, clearly differentiate the current contribution from future work.
It also happens with Objective 2 and 3, described in Section 2, which are not properly developed later.

Section 2.3 explains how important is to provide mechanisms to make reproducibility easier. I totally agree. However, it seems to be an item in our wish list, because how to make it with the library is not properly explained in the paper. In this sense, it is likely that the contribution of Dr. Antonio Ruiz and Dr. Jose Antonio Parejo (University of Seville, Spain) about reproducibility in the field of ML (they are building some sort of framework in this context) would be of interest.

A performance analysis is required so that we can really compare this approach and know whether it would be a viable choice. Citing other external works about the language performance is not enough. Please, design and include a comparative performance study of your own proposal. This becomes especially important in the field of ML because of its increasing computational requirements.

In a real environment, how many users could it support? How would the increase of users affect the performance?
Additional comments: In general, my view on this work is very positive. The idea is really interesting and the work, promising and challenging. However, I regret to say that, according to the criteria given to the reviewers by PeerJ, the manuscript seems to be immature yet and requires an important rewriting effort. The experimental framework and its validation from a scientific perspective are weak.

Web workers and web sockets should be explained. Discuss why they are the best choice would be interesting (limitations, characteristics, etc.)

In Fig. 5, what does “Probability” means? It is not a precise measure.

Figure 6 is unreadable.

I cannot see Section 5.3 as an opportunity. It should be presented as future work, right?

Section 7.2 does not provide a significant contribution. Please extend to a better clarification.

How are new developments incorporated to the server?

What would happen if the browser is suddenly closed?

Is there any domain/s to which this library is especially well-suited?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MLITB: MACHINE LEARNING IN THE BROWSER
Review round: 2
Reviewer: 1

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: The authors have addressed the majority of my concerns, so the paper could be accepted.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PYLOGENY: AN OPEN-SOURCE PYTHON FRAMEWORK FOR PHYLOGENETIC TREE RECONSTRUCTION AND SEARCH SPACE HEURISTICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No Comments
Experimental design: No Comments
Validity of the findings: No Comments
Additional comments: Overall, this is a well-written manuscript describing a new python library for phylogenetic tree reconstruction and tree space heuristics.  As the authors note at the end of the manuscript, there is a gap in available python libraries to explore tree space and manipulate tree structures.  I believe this new resource will be well received by the greater phylogenetics community and is a significant contribution.

The API is documented on the github site and I successfully installed the program and tested some functions.  One thing that could be improved in the future is the examples on the github repository.  As it stands now there is one example on the repo site; however, there are a few examples in the manuscript.  It would be nice if the authors could develop a few simple examples of executed commands and output on the github repository so researchers can test your software and get a feel for the commands.  Otherwise, I think the library is currently documented well enough for developers to begin using.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PYLOGENY: AN OPEN-SOURCE PYTHON FRAMEWORK FOR PHYLOGENETIC TREE RECONSTRUCTION AND SEARCH SPACE HEURISTICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: (1) The authors list the dependencies of the package clearly, and this is welcome.
However, as many of these dependencies are independent projects on their own trajectories of development, it is important that the authors include in their documentation (a) the mininum versions of the dependencies required, and (b) the latest version of the dependencies that they have tested. They do the latter with [libpll](http://libpll.org), but it would be useful if the authors did the same for other libraries as well.

(2) I recommend that the authors reference the [libpll](http://libpll.org) library in the abstract, and, perhaps more importantly, very prominantly (i.e., up front in the first few lines) of the README and other documentation. This is important to let users looking for Python bindings that leverage the libpll library quickly and easy locate Pylogeny through basic searches through GitHub or Google (the text describing the libpll usage shows up in the search teaser description).
Experimental design: ### Installation

-   I recommend that the authors explicitly mention in the program documentation that access to build tools (`gcc` etc.) are required. This may seem very obvious to most of us, but because, sadly, many OS's do install developer tools by default, some new users may be unaware of this, and a simple line in the documentation will save them a lot of frustration.

-   I suggest that the author explicitly mention in the program documentation that `setuptools` or `pip` are required for installation, and perhaps provide links in the program documentation for their downloads or commands (e.g., "`sudo apt-get install pip setuptools -y`"). Again, this may seem obvious to anyone who has been doing any Python development work for more than an hour, but it does not do any harm to be as clear and thorough as possible in the documentation (if nothing to reduce the noise the authors will get in terms of spurious bug reports and support requests!).

-   I suggest that the authors explicitly mention in the program documentation that access to Python development header include files are required. In Debian/Ubuntu-derived distributions, this can be installed by `sudo apt-get install python-dev -y` (things may be more complicated in OSX). This one, I think, is more tricky for naive users to figure out (the only error is an indication that `Python.h` is missing, and users may not understand that the problem is with their development environment and not Pylogeny). Similarly with `mysqldb`: it is not sufficient for just the package, but developmental headers also seem required.

-   For this sort of package, where, the dependency stack is deep and complex, while, at the same time, running on an HPC is a reasonable expectation, it would be immensely useful if the authors could provide instructions on installing Pylogeny in clean environments (i.e., with no assumption of any third-party libraries available) with *no* administrative privileges. I suggest the authors create a clean virtual machine using Vagrant, and attempt to install their library there from scratch without administrative privileges, and present the steps that they take as installation instructions in the README. I recognize that it is impossible to cater to every possible environment, but it should be possible to install in at least one clean environment following the instructions given in the documentation. If the authors can do this, because these instruction are targeted at the most constrained case (clean environment + no administrative privileges), users can easily extrapolate to their own cases.
Validity of the findings: ## Major Issues

-   The example codes are given, without any explanation of what they really do. In fact, even though the code "works" in the sense that it runs without error, from reading the article text and reading the program documentation alone, it is impossible to understand what the code is supposed to do.

    For example, the first example code (page 3) is described as "constructing a landscape from an alignment file, and finding trees in the space". Given the description of the code, I would have expected a collection of tree objects. But instead the return value is a boolean (`True`). Inspecting the `exploreTree` method, that is all that it returns. The documentation for the method claims that it should "Get all neighbors to a tree named i in the landscape using a respective rearrangement operator as defined in the rearrangement module." So, if the method is supposed to return `True`, and something else is meant by "get all neighbors" rather than the tree is to be returned, how do we know what that means? How would users understand how to access those tree returned? The same goes for the second example. `h.explore()` returns `None`. Are the trees loaded in the `h` object? How do we access/view/print those trees? With sufficient experimentation, one can figure it out. But given that the examples are part of a formal publication and stand as canonical reference examples of the library usage, I think they need to be made more complete.

    As it happens, the `lscape` object gets populated with the trees in the landscape, and the users need to call `lscape.toTreeSet()`. This may seem obvious to the developers, or even adequately document, but I would argue that this is not the case.
    In principle, one could claim that there is sufficient documentation to figure this out (as evidenced, for example, by the fact that I figured it out), but I think this is very poor practice both as a software developer as well as a member of a research community.

    Given all this, I think that authors need to expand the working examples to provide end-to-end steps, i.e., going from an alignment file right back out to newick strings. Otherwise the examples are useless (or worse than useless, in that the suggest a full-functional self-contained recipe for a procedure but are sadly incomplete), especially given that the API documentation is similarly lacking. I suggest that the authors create a "cookbook"/"recipe" web page, with *FULL* examples that will run unmodified (i.e., without steps commented out like "#ali = open an alignment file"), and make sure the example demonstrated how to access trees explored. If one of the main features of the library is access to the tree arrangements, then it is not unreasonable to expect that the documentation, article, and examples show at least one complete workflow recovering these tree arrangements.

    Note that even if this cookbook/recipe page is done, the examples in the article should still be fleshed out to be more complete (i.e., going end-to-end from alignment to trees).

-   I think the major methods should be documented as to what they do, what parameters they take, and what values are returned. I can see that the authors have put in quite a bit of work in this regard, and I really congratulate them on this! However, I think that the documentation needs to be improved before the library can be used by the community. I understand that some perspectives might find documentation such as this as an optional extra, not part of the primary software project. But I feel if the authors have gone to the trouble of writing an article to publish their library (as opposed to simply releasing the library on GitHub), it is an indication that the library is meant to be shared and used by the academic research community. I think documentation of methods in the way I describe would is a mandatory pre-requisite for this. Documentation of the method "contract" ensures that researchers understand exactly how the method is supposed to behave, what inputs it takes, and what they can expect in return. This is, I feel, the difference between a open source project shared with the community and a project that is housed in a publication. These standards are adhered to in, e.g. all R projects. There is no reason Python projects should be allowed to have any sloppier standards of documentation. The authors may wish to adopt the documentation standards of one of their dependencies as an example, and follow the [NumPy standards](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt).

    Examples of documentation that needs to be improved:

        1.
        ~~~
        __init__(self, dir=None)
            x.__init__(...) initializes x; see help(type(x)) for signature Overrides: object.__init__ extit(inherited documentation)
        ~~~

        2.
        ~~~
        addTree(self, tr, score=True, check=True, newick=None, struct=None)
        Add a tree to the landscape. Will return its index. Overrides: pylogeny.tree.treeSet.addTree
        ~~~

        3.
        ~~~
        exploreTree(self, i)
        Get all neighbors to a tree named i in the landscape using a respective rearrangement operator as defined in the rearrangement module. Rearrangement type is provided as a rearrangement module type definition of form, for example, TYPE_SPR, TYPE_NNI, etc. By default, this is TYPE_SPR.
        ~~~

    The first is simply noise. It should be removed from the public documentation.

    The second actually is quite encouraging. But unfortunately fails to describe the remaining parameters.

    The third is also almost there: it documents the parameters, but not the return value. Worse, its wording of "Get all neighbors" implied that the "neighbors" are what is returned. Ideally, it should describe itself (for example) as populating the internal set of trees with all neighbors, and that these set of trees can be accessed through such-and-such method, and the that return value is True.

-   It is crucial that there is documentation or evidence that the library is functioning as advertised. The library ships with tests, but there is no documentation as to what the tests actually test. The authors do not need to go into great detail about the tests, but the article should reference which aspects of the library have been tested or are covered by unittests (e.g., tree rearrangements, likelihood scoring, etc. etc.).

-   The authors mention that Pylogeny supports translating its tree structure to DendroPy. I found no support for this either in the code or the documentation. I personally would find this feature very useful (full disclosure: I am one of the authors of DendroPy), and if the authors are having trouble doing this, I urge them to contact me for assistance. If they have decided not to support this feature, then reference to it being supported should be removed from the article.
Additional comments: -   While not critical, unless there is a good reason to do so, why would the authors not follow the standard coding conventions recommended for Python in [PEP-8](https://www.python.org/dev/peps/pep-0008/)? This convention is by no means universally adhered to, and, indeed, even some packages in Python standard library do not follow them. However, the majority of Python packages do, and it is generally recommended.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PYLOGENY: AN OPEN-SOURCE PYTHON FRAMEWORK FOR PHYLOGENETIC TREE RECONSTRUCTION AND SEARCH SPACE HEURISTICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No Comments
Experimental design: No Comments
Validity of the findings: No Comments
Additional comments: I want to thank the authors for considering most reviewer comments and suggestions.  I specifically want to thank the authors for addressing my comments and adding a working example to the code repository, in addition to contributing more detail to the submodule documentation.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PYLOGENY: AN OPEN-SOURCE PYTHON FRAMEWORK FOR PHYLOGENETIC TREE RECONSTRUCTION AND SEARCH SPACE HEURISTICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: -  There are still some errors in the canonical example code (noted below) that should be fixed prior to release/publication. However, despite this, I am still recommending the paper for acceptance, taking it on good faith that the authors will fix these at their earliest convenience in the interests both of the usability of their software as well as benefit to the community.

     -   First example on the GitHub page (under "Code Example") does not work for me with error:

            Traceback (most recent call last):
            File "t.py", line 8, in <module>
                heu.explore()
            File "/home/vagrant/Pylogeny/pylogeny/heuristic.py", line 86, in explore
                landscape.exploreTree(cursor['index'])
            TypeError: 'NoneType' object has no attribute '__getitem__'

    -   Example "Rearrangements" has typos (e.g. missing opening quote).

    -   Example "Heuristics" fails with:

            Traceback (most recent call last):
            File "t5.py", line 13, in <module>
                h.explore()
            File "/home/vagrant/Pylogeny/pylogeny/heuristic.py", line 86, in explore
                landscape.exploreTree(cursor['index'])
            TypeError: 'NoneType' object has no attribute '__getitem__'

    -   DendroPy conversion: this works by serializing the a Pylogeny tree instance to a Newick string and then re-reading the tree using DendroPy. For most purposes, this should be sufficient (though the current implementation does not support control of, e.g., edge lengths, rooting state etc.). Helpful hint: ``Tree.read_from_string()`` is no longer supported as of DendroPy 4.xx onwards. Instead of:

            t = dendropyTree()
            t.read_from_string(self.toNewick(),'newick')

        use:

            t = dendropyTree.get_from_string(
                self.toNewick(),
                schema='newick')

        or, using the more modern:

            t = dendropyTree.get(
                data=self.toNewick(),
                schema='newick')

-   With respect to recommendations made in the original review, the authors have indeed revised the documentation and examples, as well as installation instructions. In particular, the detailed annotatations accompanying the code exampels in the main paper itself, as well as the table describing the structure and outline of the library, is very welcome! Kudos!

-   The primary author states in the rebuttal letter that: "I have chosen to, for the time being, dismiss the suggestion to follow the standard coding conventions recommended for Python as this is something planned for a future milestone and would take a considerable amount of time for relatively small reward. So, while the authors promise this will be done in a future release, upon resubmission this has not been done yet". I think it is fine not (though regrettable) not to follow the Python coding conventions. However, I think once the software is released, the API should not be changed just to conform to coding conventions.
Experimental design: (All remarks are in the "Basic Reporting" field)
Validity of the findings: (All remarks are in the "Basic Reporting" field)
Additional comments: (All remarks are in the "Basic Reporting" field)


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: WHAT SHOULD WE KNOW TO DEVELOP AN INFORMATION ROBOT?
Review round: 1
Reviewer: 1

Output:
Basic reporting: No Comments
Experimental design: No Comments
Validity of the findings: No Comments
Additional comments: This article reported a new interesting study on how to make information robots be more intelligent, and the obtained results may be helpful to other researchers. I think it may be more valuable if this study could contain the experimental results on users' satisfaction when they interact with an information robot.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: WHAT SHOULD WE KNOW TO DEVELOP AN INFORMATION ROBOT?
Review round: 1
Reviewer: 2

Output:
Basic reporting: 'information' (with quotations) indicates that the authors used the word in a special meaning, but it was used as in the range of the general meaning, such as direction-giving. So, I would like to suggest you get rid of the quotations. Also, in the title, it would be grammatically appropriate if it was "What should we know to develop 'information' robots?" or "What should we know to develop a 'information' robot?"

I found grammatical errors and typos in writing. I would like you to revise those error. The authors should use native check for the paper.
Experimental design: The study designs and analysis methods are appropriate.
Validity of the findings: The findings are offered with statistics, and the interpretations are appropriately stated.
Additional comments: The paper reports an development of a direction-giving robot (knowledge and algorithms) and field studies exploring the effects of self-introduction in direction-giving interaction.

The study was interesting. I believe the contributions described in the paper were sufficient for publishing.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: AN INTERACTIVE AUDIO-VISUAL INSTALLATION USING UBIQUITOUS HARDWARE AND WEB-BASED SOFTWARE DEPLOYMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper presents an interactive audio-visual musical installation, MOTUS, developed with low-cost hardware and software and experienced by a possible large audience, e.g., at home.
The topic is interesting and quite original. Analysis of background is based on a few papers and should be extended. For example, I think that a search in journals such as Computer Music Journal or Journal on New Music Research or in the proceedings of conferences such as NIME, SMC, and ICMC would provide useful references for a deeper analysis of the state of the art.
The paper is overall well written, even if some minor language fixes would be needed. It does not comply with the standard sections PeerJ requires, but I think this is acceptable given the peculiarity of the topic, i.e., an interactive audio-visual musical installation rather than a scientific experiment. Figures are relevant, but limited to block diagrams of the system. One or more figures showing the visual output of the installation would be interesting and useful as well. A short video showing the installation at work could be supplied as additional material.
Experimental design: I think the submission is within the scope of the journal: even if this is not a scientific experiment, it can be included in the framework of Sound and Music Computing, which ACM recognized as a specific field of Computer Science. The work is quite original and the techniques used for developing the installation are appropriately described. Nevertheless, I think the approach is quite naïf, grounding on very basic computer vision algorithms and on very basic mappings between movement qualities and sound. While keeping things simple, so that everything can still run on low-cost devices, I think that something more sophisticated and more interesting than basic direct mapping could be achieved.
Whereas, on the one hand, this submission cannot be evaluated using the classical standards as if it were a scientific experiment, on the other hand I think that a deeper evaluation would be worth pursuing. Given the possibly large number of people experiencing the installation, questionnaires for evaluating audience experience with it (e.g., in terms of engagement, pleasantness, interest, and so on) could be administered and a statistical analysis could be performed on them. Such an evaluation would make the paper stronger.
Validity of the findings: See my comments above: given the peculiarity of this submission, it cannot be evaluated with the usual standards for scientific experiments. Nevertheless, a more formal and quantitative evaluation of the installation with the audience would be needed and would provide interesting information about how the installation is perceived.
Additional comments: In conclusion, I think this paper addresses an interesting topic, i.e., making audio-visual musical installations that can be experienced by a large and possibly distributed audience, being the installation grounded on simple techniques running on low-cost devices. However, as it is, the paper is quite weak for journal publication: the approach seems quite naïve and does not sufficiently explore the possibilities that novel technologies open in this field. For example, several different computer vision techniques could be exploited and several different mapping could be applied. Such different versions/installations could be tested (quantitatively) with the audience in order assess e.g., the extent to which they are interesting, engaging, of artistic value.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: AN INTERACTIVE AUDIO-VISUAL INSTALLATION USING UBIQUITOUS HARDWARE AND WEB-BASED SOFTWARE DEPLOYMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper describes Motus, a low-cost interactive musical installation. I enjoyed reading about this work. The author’s merit is to have evidenced a very important gap in related work. Most of the existing interactive systems for music creation indeed require expensive hardware and software. A very well formulated research objective follows: to develop a musical installation that can be used using a common laptop.

The paper describes in details the algorithms for motion capture and music generation. Despite none of them are particularly innovative for the community, they allow for tracking audience movements and generating the musical output with an acceptable computational burden. With respect to the musical model, I am confused about the decision of the author to "avoid inducing the audience to perform known popular dance moves” and "preventing the induction of expectations on the audience”. Both dancing and fulfilment of expectations are typical conditions of engagement, so it is not clear why they should be avoided. Also, I believe that piano music is not easier to understand than, say, classical music with richer orchestration. A reference to confirm author’s claim is missing.
Experimental design: I found a relevant experimental design flaw. Unexplainably, the set-up of the live audience condition comprises "a big screen for video feedback and an amplifier for audio playback”. This set-up is not aligned with the initial objectives of the work about having all the hardware embedded in a single laptop.
Validity of the findings: Given the objective of the paper, providing an extensive evaluation of the audience experience is necessary to assess the quality of the system. The key contribution of this work would indeed be to provide the audience with an experience that could be comparable, in terms of engagement, to that usually achieved with more expensive installations. Unfortunately, the evaluation methodology is weak, and that’s the biggest limitation of this work. There is no information about the evaluation techniques and about how data were analysed and processed. The author makes use of vague statements such as “it was found that”, missing to reference how these findings came to light. Missing this, the scientific contribution of the paper is highly affected.
Additional comments: The paper should be better ground on the literature. To this end, I suggest the author to improve the related work section given the numerous musical installations about music and movements (Camurri 2013; Morreale 2014) - as well as algorithmic music creation (e.g. the works of Cope, Miranda, Legaspi, ecc).

Finally, pictures of the visual interface and the user interaction would be appreciated.

I like the idea behind Motus and I really encourage the author to keep working with this project, which is very promising. Also, the research objective of opening the access to this form of art to a broader audience is definitely a interesting topic that worth much more investigation. However, the evaluation shortcomings highly impact the quality of the contribution.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: AN INTERACTIVE AUDIO-VISUAL INSTALLATION USING UBIQUITOUS HARDWARE AND WEB-BASED SOFTWARE DEPLOYMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: The structure of the article seems acceptable. The sequence focus the installation, the movement detection, the video rendering, the music logical models, the audio rendering, the audience feedback and the conclusions. So the structure seems to belong only to a technical communication. My suggestion is to focus better, in the beginning, the cultural field where this experiment was born and the character of the used music, by discovering  references as  ancient architecture buildings, i.e. Battistero di Pisa.
Experimental design: The search question is clarified and focuses the "easy" way to perform the interactive experiment by using simple devices. The management of the sound output seems to be well performed. The character of the generated music is defined through technical references, parameters and only some cultural references. It's better if the author will try in deep to  identify some of  these characters also by discovering them inside his own music references.
It's interesting that the generative system is performed with four different voices whose generations are independent each one from the others, by performing a different music logical model. But it's not clarified how they are different and which character will identify each voice, apart from the range of notes.
Validity of the findings: The search is well focused in the technical field and in the musical field. The results are well described. Also if it should be necessary to hear MOTUS for a global evaluation.
My suggestion is to identify the word MOTUS with a peculiar character, being the Latin word used a lot from all the world
So the article seems to be of interest and my suggestion is to publish it with only some revisions, focused in primis on the music culture references.
Additional comments: The author focuses the search of character in the output of sound, clarifying several different parallel events. I suggest to identify better the different characters and the music vision at the base of the different voices and of the ensamble, focusing better the type of control of random factors. So the possibility to increase the peculiar cultural references should be interesting for increasing the quality of the article


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NAVIGATING THE MASSIVE WORLD OF REDDIT: USING BACKBONE NETWORKS TO MAP USER INTERESTS IN SOCIAL MEDIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: The paper employs methods from network science to understand the structure of the Reddit interest network. Using a backbone extraction method to subset the raw network data into important links at different significance levels, the analyses find evidence of scale-free, small-world, and modular network structure often found in other online social networks. In addition to these empirical findings, the paper provides some network visualization maps to encourage navigation of online information communities. This large-scale network analysis of Reddit data demonstrates that this online social network exhibits features found in many other OSNs and also importantly shares anonymized data for future research. However, the paper would benefit from a clearer motivation for why network visualization in this context is appropriate, revised data analysis to address concerns about distribution fitting, and re-focusing away or towards the dynamics of users' interests over time. These lead me to recommend the authors undertake major revisions before accepting the manuscript.

"Maps" are a central metaphor that motivates the present study including the introductory research question "Is it possible to build a map to aid users in the discovery of relevant interests on social networks?" Drawing on the information visualization literature [1-3], especially around knowledge mapping [4,5], I would have liked to see the paper make a stronger case for why spatialization is a relevant metaphor for information relevance and relatedness (see [6] for alternatives). I don't think this is a bad metaphor, but the question of whether it's "possible" has a trivial answer --- instead, I would encourage the authors to reflect more thoughtfully on the potential and limitations of network visualizations [7-10] for supporting their suggestion that "the integration of such interest maps into popular social media platforms will assist users in organizing themselves". Ideally the paper would have conducted some sort of usability study to assess lay users' ability to interpet these maps, but as an empirical analysis of visualizing relational data, the paper misses some important limitations and considerations.

The paper finds evidence of the inter-subreddit network having scale-free, small-world, and modular community structure, and attributes the scale-free property to a preferential attachment process (pg. 2). I find attribution to a preferential attachment process unconvincing given the multitude of distinct mechanisms that generate such distributions [11-13], the absence of any curve-fitting estimation to differentiate among distinct classes of long-tailed distributions [14,15], and lack of an empirical comparison between a preferential attachment model and the observed data in the paper. Indeed, linear (naive) preferential attachment models are unable to generate the modularity and clustering seen in these data, which would imply that preferential attachment alone is not an appropriate model for the observed results [16,17].

I appreciated the inclusion of a sensitivity analysis (Fig 3) for different cut-off values in the backbone extraction, but these charts would benefit from indicating where the 0.05 cutoff value is as well as sub-figure labels (3a, 3b, etc.) for reference. The specification of the ER null model also lacks details on how it was parameterized in the context of a weighted network. There's a broken reference to a table on pg. 4. Related to my concerns about the exponent for the powerlaw fit, there are no details on the estimation procedure and the reference to a R^2 value indicates that least-squares procedure was inappropriately used instead of MLE [14, 15]. Some statistical test producing a p-value was conducted, but there are again no details about it, which is important given that the skewed nature of the data suggests the need for using non-parametric tests [18].

The backbone extraction method, while valuable for data visualization purposes, systematically throws away information about weak ties in the graph. Similarly, the choice to project into a one-mode network rather than preserve the two-mode relationships also produces a loss of information despite the availability of bipartite metrics [19]. Was there a motivating rationale for using this method as opposed to other graph sparsification or backbone extraction methods [20-22]? The methods indicate that the backbone extraction methods was applied after an initial global thresholding step of excluding users with fewer than 10 posts, which is the kind of approach the Serrano, et al. paper criticizes. Wouldn't other methods for thresholding ties based on more meaningful features like posts within a date range (to capture changing rather than aggregated user interests), posts since account creation (to weed out throw-aways), etc. produce more meaningful sub-community linkages?

The discussion claims the map allows users to explore related interests by providing a "*dynamic* view of interests on the social network." This statement is surprising as there was no discussion of time in the previous analyses, so the maps are actually very much cross-sectional samples and do *not* reflect evolving interests or trajectories [8]. I think the question of user dynamics over time on the site could be fascinating from the theoretical perspectives like socialization, recruitment, and persistence, but the analyses in the paper only provide cross-sectional evidence of large-scale structural patterns. The paper references previous Reddit research, but excludes some more recent examples [23, 24]. Did this large-scale collection of user data follow relevant policies from Reddit's terms of service and privacy policies and MSU's human subjects research protections?

[1] Shneiderman, B. (1996). The eyes have it: A task by data type taxonomy for information visualizations. In Visual Languages, 1996. Proceedings., IEEE Symposium on (pp. 336-343). IEEE.
[2] Keim, D. A. (2002). Information visualization and visual data mining. Visualization and Computer Graphics, IEEE Transactions on, 8(1), 1-8.
[3] Healy, K., & Moody, J. (2014). Data visualization in sociology. Annual review of sociology, 40, 105-128.
[4] Börner, K., Chen, C., & Boyack, K. W. (2003). Visualizing knowledge domains. Annual review of information science and technology, 37(1), 179-255.
[5] Borner, K. (2010). Atlas of science: Visualizing what we know. The MIT Press.
[6] Hecht, B., Carton, S. H., Quaderi, M., Schöning, J., Raubal, M., Gergle, D., & Downey, D. (2012, August). Explanatory semantic relatedness and explicit spatialization for exploratory search. In Proc SIGIR (pp. 415-424). ACM.
[7] Welles, B. F., & Meirelles, I. (2014). Visualizing Computational Social Science The Multiple Lives of a Complex Image. Science Communication, 1075547014556540.
[8] Bender-deMoll, S., & McFarland, D. A. (2006). The art and science of dynamic network visualization. Journal of Social Structure, 7(2), 1-38.
[9] Freeman, L. C. (2000). Visualizing social networks. Journal of social structure, 1(1), 4.
[10] McGrath, C., Blythe, J., & Krackhardt, D. (1997). The effect of spatial arrangement on judgments and errors in interpreting graphs. Social Networks, 19(3), 223-242.
[11] Mitzenmacher, M. (2004). A Brief History of Generative Models for Power Law and Lognormal Distributions. Internet Mathematics, 1(2), 226–251.
[12] Andriani, P., & McKelvey, B. (2009). Perspective—From Gaussian to Paretian Thinking: Causes and Implications of Power Laws in Organizations. Organization Science, 20(6), 1053–1071.
[13] Newman, M. E. (2005). Power laws, Pareto distributions and Zipf's law. Contemporary physics, 46(5), 323-351.
[14] Clauset, A., Shalizi, C. R., & Newman, M. E. (2009). Power-law distributions in empirical data. SIAM review, 51(4), 661-703.
[15] Alstott, J., Bullmore, E., & Plenz, D. (2014). powerlaw: a Python package for analysis of heavy-tailed distributions. PLoS One, 9(1), e85777.
[16] Vázquez, A. (2003). Growing network with local rules: Preferential attachment, clustering hierarchy, and degree correlations. Physical Review E, 67(5), 056104.
[17] Leskovec, J., Kleinberg, J., & Faloutsos, C. (2007). Graph evolution: Densification and shrinking diameters. ACM Transactions on Knowledge Discovery from Data (TKDD), 1(1), 2.
[18] Corder, G. W., & Foreman, D. I. (2009). Nonparametric statistics for non-statisticians: a step-by-step approach. John Wiley & Sons.
[19] Latapy, M., Magnien, C., & Del Vecchio, N. (2008). Basic notions for the analysis of large two-mode networks. Social Networks, 30(1), 31-48.
[20] Foti, N.J., Hughes, J.M., and Rockmore, D.N. Nonparametric Sparsification of Complex Multiscale Networks. PLoS ONE 6, 2 (2011), e16431.
[21] Mathioudakis, M., Bonchi, F., Castillo, C., Gionis, A., and Ukkonen, A. Sparsification of Influence Networks. Proc. KDD, ACM (2011), 529–537.
[22] Macdonald, P.J., Almaas, E., and Barabási, A.-L. Minimum spanning trees of weighted scale-free networks. EPL (Europhysics Letters) 72, 2 (2005), 308.
[23] Buntain, C., & Golbeck, J. (2014). Identifying social roles in reddit using network structure. In Proc. WWW (pp. 615-620).
[24] Leavitt, A., & Clark, J. A. (2014). Upvoting Hurricane Sandy: event-based news production processes on a social news site. In Proc. CHI (pp. 1495-1504). ACM.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NAVIGATING THE MASSIVE WORLD OF REDDIT: USING BACKBONE NETWORKS TO MAP USER INTERESTS IN SOCIAL MEDIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: No Comments
Experimental design: No comments
Validity of the findings: No  comments
Additional comments: The article meets the PeerJ criteria and should be accepted.
There are few typos to be corrected:
Page 4, line 8 from bottom:  Table ??
Page 8, second paragraph, line 3: if larger ... should be: is larger


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ZBROWSE: AN INTERACTIVE GWAS RESULTS BROWSER
Review round: 1
Reviewer: 1

Output:
Basic reporting: No Comment
Experimental design: Overall a great tool with an intuitive interface that facilitates analysis of SNP data over multiple traits.

More attention should be given to the type of input data / formats / columns.     When evaluating the utility, I think it would be helpful to know how the data must be wrangled to use your tool.   The difficulty becomes more apparent when you talk about adding additional organisms.   This should be documented and/or explained as it is often the most difficult part of preparing for analysis and I think will help with additional adoption of your toolchain.

I think using R as a starting point is great and makes it instantly accessible to scientists.   I think that using the web-browser as an interface makes a lot of sense.   I think that longer-term it might make more sense to allow it be run out of a more global server (e.g., tomcat, jetty) to better facilitate data sharing.

In you limitations, you mention limiting the genotype data and getting around that by trimming the data.  I think that a better solution (architecture allowing) would be to calculate an intermediate view for the denser traits, or automatically apply an adjustable filter.

I wholeheartedly agree with database support so long as you can keep the simplicity of your current setup for individual users.

Fig. 1 Interface:  Would it be possible to show the NSP's in their own column instead of including redundant information in the name (e.g., chromosome, BP)?  Would prefer just to see G/A instead (even if the name is stored the same internally).
Validity of the findings: No comments.
Additional comments: Is Z in ZBrowse for Ziegler?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ZBROWSE: AN INTERACTIVE GWAS RESULTS BROWSER
Review round: 1
Reviewer: 2

Output:
Basic reporting: No Commnts
Experimental design: Ok
Validity of the findings: Ok
Additional comments: In this paper, the authors have developed an R package for displaying GWAS results, along with genomic annotations of several plant genomes, including arabidopsis thaliana,maize, soybean, and sorghum. The results can also be viewed by using a browser locally.

Comparing to some existing tools, an important feature from this tool is that it can show results from multiple traits. However, the current input format requires all p-values from different traits in one column and the program cannot accept other type of formats, such as p-values of one trait in one column, which might be more common in practice.

Some other limitations:

- It can only plot about 5000 points per trait due to memory, time and plotting constraints. Given that many SNP arrays normally have hundreds of thousands SNPs, it requires users first to perform filtering to only keep small p-values.

- User interface can be further improved. For example, it is better to have an indication (i.e. waiting mouse cursor) for tasks requiring long time.

Overall, this is a simple, but potentially useful tool for some plant biologists.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MORE TIES THAN WE THOUGHT
Review round: 1
Reviewer: 1

Output:
Basic reporting: Fink and Mao described a formalism to enumerate usual tie knots (four-in-hand or Windsor for instance). One contribution of this paper is to simplify the original formalism.

One of the characters in the movie "The Matrix Reloaded" used a tie knot of a distinctively different style, wrapping the thinner blade around the other. This leads to tie knots whose "facade" is not plain, since it shows more of the internal structure of the knot. The natural question is then to enumerate tie knots following this new pattern, which is the main realization of this paper. This result has already received a lot of attention in mainstream media.

The enumeration relies on a presentation through formal languages, and qualifies that language (regular, context sensitive) in the different subcases considered.
Experimental design: No comment.
Validity of the findings: The results are valid, and the conclusions are clearly stated. The paper includes (long) tables of knots satisfying different constraints and a printout of the code used to produce these tables. This code has been put on Figshare, to ensure complete transparency. I do not know if PeerJ has a policy on the topic, but it would seem to me desirable to keep both code and paper tied for archival purposes.
Additional comments: This paper looks like a worthwhile opportunity to include a closeup picture of a real knot. This would dramatically increase its accessibility.

p. 1 l. 18: The story presented here comes with no context. Who are those people, where did this take place? Knorr tells the story on his blog, but it is not clear where the original conversation took place.
p. 3, l. 95-96 "No region/direction shall repeat": unclear phrasing
p.3 l. 96: It would be helpful to have a reminder somewhere, maybe here, of which symbol is inwards, which is outwards.
p.4 l. 123: As far as I can tell, theorem 1 does not exclude tucks that would be simultaneously k-fold or k'-fold (from just reading the sequence of windings). Is this correct? If so, does your enumeration distinguish this? Please clarify. In the cases where there are multiple tucks, you should probably say why it is not a concern that a tuck makes later tucks spanning more windings impossible (if I have two overlapping bows, and tuck under the top one, it makes it impossible later to tuck under the bottom one).
p. 5 The rules after line 156 and line 157 are contradictory (in presentation only)
p. 6 l. 171: I think this automaton is wrong. It allows for the following sequence "TTTUTTTUTTTU", which should not be allowed according to 4.1
p. 7 line 206: finish the sentence with "... k-2 W and T symbols with proper counts".

I have labeled the article "Major revision" because I want to make sure the language used to make the corrections is clear enough (i.e. that this goes through me again). The changes asked are not actually major.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MORE TIES THAN WE THOUGHT
Review round: 1
Reviewer: 2

Output:
Basic reporting: The problem is novel, and the authors touch on several interesting aspects. There should be more useful figures.
Experimental design: The authors describe a novel formal language which models "necktie configurations". They propose a modification of classic work, which eliminates and ending configuration. The language is given explicitly a as an attribute grammar.
Validity of the findings: The formulas appear to be correct.
Additional comments: As a matter of form, I would add that the first page is dominated by a verbatim history of the problem. It is unusual to me to see such a large amount of "fact" text copied from another source. Not all of this information is necessary, and I recommend the authors edit this section considerably.

The proofs of theorems 3 and 4 are adhoc combinatorial arguments, but could be harmonized if more sophisticated enumeration tools were used. There are several formalisms which translate grammars into enumerative generating functions, and it seems like these should be a good candidate for such a process. Hence, from an enumeration point of view, it is lacking as the state of the art is more sophisticated. At the very least, they should offer an asymptotic comparison.

From a language theoretic point of view it is interesting that it is a context-sensitive language. Is there a similar argument for the Fink and Mao case?

If the intended goal is to make new, usable patterns for ties, then the authors should add some focus on this-- can they highlight some new knots that one could actually wear, (for which they provided have criteria).
The full tables at the back seem unnecessary given that they describe how to generate them.
The authors definitely succeed on the whimsy front, and it was enjoyable to read. From a combinatorics point of view, it is a relatively minor adaptation from the existing case and as such could benefit from a tighter presentation, or a closer investigation into modern enumeration techniques.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MORE TIES THAN WE THOUGHT
Review round: 2
Reviewer: 1

Output:
Basic reporting: The article was substantially improved from the first version. However I still have a few suggestions to improve its readability.

something went wrong on page 5,  line 140: "For intermediate tucks, and to avoid..." the symbols for Tie3 are wrong.

The labels used in the various grammars are inconsistent. While this does not invalidate the results, it makes it substantially more difficult to understand the role of each rule. For instance, I do not understand the logic in introducing <last_> in the first grammar on page 6, while this was not present in the first grammar in Section 4.1. (I think it is more clear with "last" present)

In the grammar given in 4.2, <label> can refer to either information at the current position (for instance <tw2>: "A this stage the surrounding context has two more T than W mod 3") or information about the content (for instance <wstart>: this is a tuck starting with W). This is very annoying and I think unneccessarily complicates the grammar and misses the opportunity of fully using the power of Theorem 1. I suggest:
<wstart> ---> <wtuck2> (the 2 hints that #W-#T = 2 mod 3 inside)
<tstart> ---> <ttuck1> (the 1 hints that #W-#T= 1 mod 3 inside)
<tw?> and <wt?> both to <wX>, which indicates that #W - #T mod 3 = X.

In this way, with minor adjustments, one needs only 3 rules <wX> instead of 6 <tw?> or <wt?>, one only ever considers #W-#T (not #T-#W, which only complicates things), and the grammar of 4.2 only ever uses labels that refer to their content, not the position (which is a legacy from the original tie problem, which Theorem 1 dispenses us of). Simplifying the grammar in this way might also be helpful for the generating function that memory-bombed later in the paper.

When defining the grammars, particularly in 4.2, a reminder on the precedence of | would be useful. More spacing would also be helpful.

Theorem 1 should be rephrased: "if the position is preceded by..." "If the subsequence of the last 2k W or T symbols is such that"

The automaton on page 7 and its description don't match: "Execution starts in the middle node" ???

Page 7, line 179 "At most context-free" -> "At worst context-free". This introduces a value judgement (more properties == better), but what does it really mean if left as is?

Page 10, line 249: Unclear to me what U'UU is.
Experimental design: N/A
Validity of the findings: The counts are now dependent on the correct implementation of a Maple package, and the correct entering by the authors of the grammar they described.

I didn't check either.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MORE TIES THAN WE THOUGHT
Review round: 2
Reviewer: 2

Output:
Basic reporting: A nice report, with a clear narrative
Experimental design: The grammar describes well the problem, and the generating function resolution is elegant.
Validity of the findings: The mathematics appears to be correct.
Additional comments: Kudos on the generating functions. It is a much improved paper, with a much clearer focus. I recommend that you follow up further with Flajolet and Sedgewick's "Analytic Combinatorics" Cambridge UP 2009 for more about what you can do with these generating functions.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ACHIEVING HUMAN AND MACHINE ACCESSIBILITY OF CITED DATA IN SCHOLARLY PUBLICATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are some confusing aspects to Table 1. Please clarify how the HTTP(s) and PURL URI identifier schemes meet JDDCP criteria if they ‘fail’ upon object removal; this does not appear to agree with Principle 6. How can these ‘achieve persistence’ if they may not persist?

Further attention to clarity in the text, with an eye to removing possible ambiguities and redundancies, would make the article read better. I urge the authors to consider issues such as the following:
1.	Page 2, paragraph 2: use of parentheses
2.	Page 2, paragraph 3, sentence 2: what does ‘It’ refer to?
3.	Page 2, paragraph 3: introduce the acronym DCIG before using it later on the same page
4.	Throughout the manuscript: minor errors in spelling, punctuation, and sentence structure
5.	Page 3, paragraph 1, sentence 1: is ‘has’ the correct word here? Perhaps ‘reflects’ or ‘demonstrates’, etc?
6.	Page 3, paragraph 4: is ‘vend’ the correct word to use?
7.	Page 5: a bullet point related to #3 refers to “b”; do the authors mean “2”?
8.	Page 6, paragraph 3: do the authors mean ‘as a draft of NISO JATS version 1.1’, as ‘1.1d2’ denotes the second draft?
Experimental design: Many of these stated criteria for this area are not relevant to the article, which does not describe primary research in the Biological Sciences, Medical Sciences, or Health Sciences. However, the subject matter of the article (guidelines/proposed methods for improving access, citation, and deposition of data related to scholarly publications) is certainly applicable to Biological, Medical, and Health sciences. I leave it to the Academic Editor to determine whether the article is appropriate for this publication.
Validity of the findings: Please see my comments under Experimental Design above.
Additional comments: The guidelines are generally clear and contain sufficient detail for implementation. The manuscript is well-organized in presenting them.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ACHIEVING HUMAN AND MACHINE ACCESSIBILITY OF CITED DATA IN SCHOLARLY PUBLICATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper is a short note that provides practical guidance on the implementation of the standards for data deposition and discoverability formulated in the Joint Declaration of Data Citation Principles. The writing is generally clear, although a bit choppy in places. Please see the attached pdf for specific suggestions.

I found it hard to identify the intended audience for the paper. I suspect that the technical details will make most sense to web designers or database engineers that are making decisions on the design and appearance of data entries and the scholarly work that cites those entries. However, the introduction seems to be aimed at a broader audience, perhaps those in publishing, libraries or research institutions that are encountering the Force11 initiative for the first time and need to be convinced of the need for standardizing data citation and hosting practices. Even if that’s not the intent, it would benefit the article to add a little more detail and explanation throughout, and to strenuously avoid acronyms and other terms that outsiders (like me) may find opaque. A more accessible article would likely reach a broader audience, which can only be a good thing.
Experimental design: There is no original primary research being presented here – the work of choosing these particular standards while rejecting others has clearly gone on beforehand, and the paper presents the conclusions of that work.
Validity of the findings: I am not well placed to comment on whether the guidance presented here is valid or the best possible practice, particularly because there is no detail on how the presented solution was decided upon.
Additional comments: I'm supportive of this paper, as it's important to have a published version of record that others can point to when considering data citation issues. However, the paper is not obviously within the Biological, Medical or Health Sciences, and seems closest to Computer Science. Moreover, the paper does not present ‘research’ as such, as all the evaluation of various options (and the process behind that) is not presented. The article may therefore not be a good fit to PeerJ’s remit, and this is the reason behind my 'reject' recommendation. The final decision on suitability is, of course, up to the editor.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ACHIEVING HUMAN AND MACHINE ACCESSIBILITY OF CITED DATA IN SCHOLARLY PUBLICATIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Although this is intended as a brief piece to provide operational guidance, as it will be published as a journal article rather than a technical report, I suggest providing additional background and explanation throughout the paper. Consider that the relevant audience may be more than just repository managers who are highly proficient with technical jargon, but also other related stakeholders e.g., in managerial or other advisory positions. Additional explanation and clarification would make this paper more accessible and appropriate for the publication venue.

Title:
The title is broad considering the specific focus of the article. The current title reflects the overall goal of the Force11 data citation principles, rather than the specific points addressed by this article.

Introduction:
Provide some background on Force11 as not all readers may be intimately familiar with the organization. Why are they trustworthy? What is their mission? Why the JDCCP, given the existence of other guidelines for data citation? How does this relate to other guidelines for data citation and metadata? Consider that the reader might appreciate a listing of all 8 principles in the introduction for additional context.

You state that the JDDCP “deliberately” does not provide implementation guidelines. Why not?

Don’t leave me hanging: what are some other specific implementation issues that we can expect to be addressed in the future?

Provide parathenetical acronym for Data Citation Implementation Group (DCIG) the first time it is used.

What is Machine Accessibility?:
Only a very cursory definition/description of machine accessibility is provided, yet guidelines for machine accessibility is the main point of the article. Some additional description with attention to reasons for the importance of machine accessibility would be appreciated. Consider a brief description of RESTful Web services---although this is a standard for accessing functions for others to use they would need documentation. Is provision of documentation a best practice?

Unique Identification:
What do you mean by “long term commitment to persistence”?

If the criteria in Table 1 are important, why are they not introduced and discussed in the main body of the text? Is there a particular recommendation on any of these criteria?

Landing pages:
“First, as ‘mandated’ in the JDDCP – consider word choice here with ‘mandated’, may be too strong.

Sentence order in the first paragraph here does not flow appropriately. After the “First” point the sentence explaining more about metadata should follow. After the “Second” the sentence explaining credential validation should appear.

“Landing pages should combine human-readable and machine-readable information on a selection of the following items” – What selection should I choose from the list? Are these all optional items?

“Explanatory or contextual information” – Should the documentation be part of the landing page or a separate document?

“Dataset descriptions” – Need better definition of what “description” is in this context.
Regarding persistence and data availability, and the persistence of metadata beyond
de-accessioning: should this be parallel to journal articles? Why is data different?

Minimum acceptable information on landing pages:
Under 2, the 6th bullet, is there a particular ISO standard that can be referenced?

Best practices for dataset description:
What kind of description are we talking about here exactly? Why is it safe to say that a standard that has only been very recently released is already widely used and settled? Do you anticipate the release of any additional domain specific standards?

Data access methods:
Consider providing here some additional explanation. Points 1 and 2 are generically applicable. Point 3 follows a linked data model that is library applicable but might not translate to other stakeholders.

Persistence guarantee:
Can you make the relationship to persistent identifiers more explicit? This section feels somewhat overreaching. Is this a little much for citation practices? Or is this really a trusted repository issue?

Additional comments:
Are there any existing examples out there that already meet these criteria that you can share?

References:
In an article on citation standards, it is imperative that the reference list be correctly formatted and provide all necessary information to easily retrieve the listed documents. Check the author guidelines and make certain that both in-text and full citations in the reference list are done appropriately. For example, provide URLs and access dates for technical reports. It sends a mixed message to promote higher standards for data citation than document citation.

Should the JDDCP itself be included in the reference list?
Experimental design: Not applicable
Validity of the findings: Not applicable
Additional comments: No comments - covered above.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ACHIEVING HUMAN AND MACHINE ACCESSIBILITY OF CITED DATA IN SCHOLARLY PUBLICATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No Comments
Experimental design: No Comments
Validity of the findings: No Comments
Additional comments: The new draft is more thorough, clear, and readable.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SYNTHESIS AND CHARACTERIZATION OF BISMUTH(III) COMPLEX WITH AN EDTA-BASED PHENYLENE LIGAND AND ITS POTENTIAL AS ANTI-VIRULENCE AGENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript has been well-written and all information has been provided in a clear and concise manner. Literature cited is appropriate, albeit some missing, which have been mentioned in the reviewer report. The figures have been properly prepared and captioned accordingly. Overall, the manuscript quality is good with the conclusions arrived to by the authors backed by experimental data.
Experimental design: Experimental data has been reported appropriately, albeit with some missing information, which has been mentioned in the reviewer report. The inference drawn from the experimental data has been presented thoroughly in the manuscript.
Validity of the findings: The overall quality of the manuscript is good. The conclusions arrived to by the authors and thus stated are precise and backed by experimental results.
Additional comments: NA


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SYNTHESIS AND CHARACTERIZATION OF BISMUTH(III) COMPLEX WITH AN EDTA-BASED PHENYLENE LIGAND AND ITS POTENTIAL AS ANTI-VIRULENCE AGENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: Bismuth can form interactions with oxygen under basic conditions, but under acidic conditions, bismuth nitrate usually behaves as a salt. Bi(NO3)3 5H2O, which I assume is the one that was used, usually releases nitric acid into the reaction medium (and has therefore been described as a nitrating agent) so it is very likely that a complex is formed between edtabz and hydrated Bi(NO3)3 and that the nitrogens form ammonium nitrates; this would explain the high m/z close to 1000 found in the mass spectrum.
There is no consistency between the proposed formula (%. Calcd for BiC22H24O12N6 • 2NO3) and m/z 709.6 (the base peak). Also in this same context it is convenient to review the elemental analysis C, 33.39 %; H, 3.31 %; N, 10.62%.
The integrals of the NMR signals are not shown and the doubt remains as to whether they correspond to the proton in the ortho (2H), meta (2H) and para (1H) positions as suggested. It is convenient to clarify it because the signal assigned as "para" does not seem at first sight to integrate for one proton. There are unassigned signals that appear to be important, such as an apparent doublet at 3.9 ppm with a coupling J similar to the double signal at 4.2 assigned as Hc. It would be convenient to include the complete spectrum with the integrals indicated as supplementary material. I do not consider it necessary to explain the basics of interpretation for this spectroscopy for a specialized reader (HSQC explanation)
"The Hb protons are assigned to the signals at 4.31 and 4.23 ppm. These protons are from the carboxylate group in the acid" I assume that the text refers to the methylene protons neighboring the carboxylate and not to those of the carboxylic acid.
The biological results are very interesting, but it is convenient to use bismuth nitrate and edtabz solutions as a control and rule out that the effect is due to these compounds and not to the bismuth complex.
Validity of the findings: no comment
Additional comments: With more work on the spectroscopic interpretation, I consider that this work can be a nice contribution to the chemistry of bismuth as it is interesting from the chemical perspective as well as its microbiological application.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SYNTHESIS AND CHARACTERIZATION OF BISMUTH(III) COMPLEX WITH AN EDTA-BASED PHENYLENE LIGAND AND ITS POTENTIAL AS ANTI-VIRULENCE AGENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The suggestions of the previous version have been considered by the authors and I believe that the article can be published in its present form.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: X-RAY DIFFRACTION AND THEORETICAL STUDY OF THE TRANSITION 2H-3R POLYTYPES IN NB1+XSE2 (0 < X < 0.1)
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment'
Validity of the findings: no comment'
Additional comments: Title: X-ray diffraction and theoretical study of the transition 2H-3R polytypes in Nb1+xSe2 (0 < x <0.1)

The main conclusion for this paper is different structure switching between 2H to 3R by self-intercalation in the niobium diselenide system. Although this behavior is not new, but the data is useful for further study the polymorphism in the TMDs. Therefore, I suggest it can be accepted to be published in PeeJChemistry Journals after major revisions with answering the following questions:

Some issues to be address:

1. Introduction, it is well-known that 2H-NbSe2 is one of the most famous TMDs, where charge density wave （CDW） in coexistence with superconductivity. And the superconducting transition temperature is around 7.2 K which is the highest Tc among the pristine TMDs. However, the authors state that "The system NbSe2 has been the subject of many investigations, since it exhibits incommensurate charge density waves (CDW) and superconductivity phenomenon below to 4K (Wilson, Disalvo & Mahajan, 1975)." is obviously wrong. Evidently, the superconductivity can be seen above 4 K in 2H-NbSe2.

2. Introduction, up to now, there are innumerable reports on polymorphism in the TMDs by tuning systhesis temperature (such as MoTe2, from ref. 1966 Acta. Cryst. 20 268.), chemical doping (such as Mo1-xNbxTe2 from Ref.  2015, APL Materials 3(4); TaSe2-xTex from Ref. Proc Natl Acad Sci USA, 2015, 112 E1174) or self-intercalation (such as TaxSe2) and so on. The authors should mention these case and make the readers easily understanding.

3. There is a lot mistakes and typos in the whole manuscript. The authors should go through it and fix them, such as "formulaeTX2" in the introduction, 7x1x1 in line 131, Nb2Se6 in 173 and so on.

4. The authors should perform the resistivity and magnetic susceptibility measurements to check the CDW and superconductivity on these 2H and 3R-Nb1-xSe2 samples, compared with that of the 2H-NbSe2.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: X-RAY DIFFRACTION AND THEORETICAL STUDY OF THE TRANSITION 2H-3R POLYTYPES IN NB1+XSE2 (0 < X < 0.1)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Numerous language deficiencies are present, (e.g. out-of-place commas, adjectives without corresponding nouns or missing verbs, such as  "Both have been found stoichiometric;", etc.) .
Experimental design: Methods should be explained in more detail. For example, authors state: "The mixture was heated between 760-1050 C for 15 days" Does this mean that the temperature was changed from 760 to 1050 C over a span of 15 days, that several synthesis were performed at different temperatures (each constant during 15 days), or that the temperature was allowed to fluctuate between 760-1050 during that time?  Please clarify. I also cannot tell which conditions gave rise to each of the polytypes, or whether  a mixture wwas obtained and then the specific crystals were picked individually for further study.

" ...then slowly cooled to room temperature. Crystals of appreciable sizes were grown in the cold end of the tube. " This seems to imply that the cooling was not homogeneous, and a description of the non-homogeneity of the cooling process is therefore needed.

" an approximate ratio of 1:2 for Nb and Se [for 3R-Nb1.085Se2: Nb (at%) = 29,9 and Se (at%) = 70,1]" Authors should clarify whether the stated ratio is mass or molar ratio. If those are molar ratios, that translates to a 0.85:2  Nb/Se ratio. If those are mass ratios, they translate to a 0.725:2 Nb/Se ratio. In any case those are quite different from the claimed 1.085:2 Nb/Se ratio.

Some extra detail is needed for the theoretical computations: please provide (as Supporting information) the DFT energies of all systems, as well as their geometries. I also notice that the formation enthalpy you compute is not the actual enthalpy, but the energy divided by the number of atoms. Why? Also, at what temperature was enthalpy computed? Authors should state that. Why was enthalpy selected rather than free energy? Doesn't CASTEP allow the computation of hessians and vibrational/rotational contributions, ZPE, etc. , and hence the entropy
 and Cv/Cp values needed to compute G?
Validity of the findings: See below
Additional comments: in line 56 " since it exhibits [...] superconductivity phenomenon  below to 4K (Wilson, Disalvo & Mahajan, 1975)" I guess authors mean "below 4 K", but the quoted reference shows Tc as 7.3 K  (in its table 5, page 189)

line 74 "revisited by single crystals ". I guess authors mean "revisited by single crystal X-ray diffraction"

line 80 "By the fact of an excess of niobium, a transition 2H to 3R polytype should occur in order to minimize the Nblayer—Nbextra—Nbextra repulsions between these adjacent slabs. " I am afraid that the language here is again cryptic:  aren't both the 2H and 3R polytypes NbSe2? Do authors mean instead that as additional (supra-stoichoiometric) Nb is added the 3R polytype becomes energetically favored relative to the 2H?

lines 193-195 "it is quite clear, that the increase in the additional Nb , induces changes in the pressure of saturated Se vapor above the surface of the growing crystal, and then affects the concentration of selenium vacancies." Authors may suspect that, but I am afraid I do not think that is at all clear: did the authors monitor the Se vapor profile above the crystals duting growth? (Is that even technically possible?) I may be misreading, bu it seems to me that authors have only mentioned Nb vacancies before this sentence, and therefore I do not see how they can posit an explanation of the Se vacancies that (apparently) are not reported to be present (an on the next paragraph are stated to not exist "A free refinement of the occupancy of Se atoms in the three polytypes, leads to a fully occupied sites")

Figure 3 is not immediately readable, as the reader cannot tell whether the points at the upper right of each graph are calculated/experimental points or are a legend instead. Please correct that. I also fail to see a discontinuity around x=0.07, since (apart from the point that may (or not) be a legend, I see no other 2H points, and the 3R points are not discontinuous).

The legends in Figure 4 are barely readable. please correct.

The discussion of the computed stabilities is deficient: from the data in table 2, I compute formation enthalpies also  of - 66.5 kcal/mol for 2H-Nb1.1Se2  and -67.2  kcal/mol for 3R-Nb1.1Se2  (indeed indistiguishable with the computational methods used). The difference between the stoichoiometric compounds is much larger -76.8 kcal/mol for 2H-NbSe2 and 86.5 kcal/mol for 3R-NbSe2. Interesting as enthalpy differences are, stability cannot be directly inferred from that , but requires the computation of free energies.

line 252 "Moreover, the PDOS at EF decreases and upshifts (see Figs. S2B and S2D) compared to the pure polytypes, which implies that a large degree of electrons is transferred by Nb extra atoms into these pure polytypes"  This should be explained more fully (o at least a citation for a reference detailing how the DOS around Fermi level E(F) relates to the metallic/chalcogenide electron distribution).

There is an important typo in table 2: authors wrote Nb1.01Se2 , where they really should have written Nb1.1


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: X-RAY DIFFRACTION AND THEORETICAL STUDY OF THE TRANSITION 2H-3R POLYTYPES IN NB1+XSE2 (0 < X < 0.1)
Review round: 2
Reviewer: 1

Output:
Basic reporting: It is clear than before.
Experimental design: The data is enough for published.
Validity of the findings: It is meet the standards.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: X-RAY DIFFRACTION AND THEORETICAL STUDY OF THE TRANSITION 2H-3R POLYTYPES IN NB1+XSE2 (0 < X < 0.1)
Review round: 2
Reviewer: 2

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: I am generally satisfied with the authors responses. There are still a few issues to address:
A) I would have preferred the authors to explicitly state that their computations of free energy (performed using the methodology of Ivanova et al. 2019) only include configurational entropy due to intercalation .

B) I still do not understand how the Nb1.085:Se2 sample could afford a 29.9%Nb - 70.1 % Se mass (or molar) ratio. That should be clarified.

C) In line 224 authors still state  " As shown in Fig. 3, this ratio change is relatively small with the increase of x for both polytypes with a discontinuity around x = 0.07. " but no discontinuity can be seen. Please consider rephrasing this, for clarification of what you mean.