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: INFERRING MICROEVOLUTION FROM MUSEUM COLLECTIONS AND RESAMPLING: LESSONS LEARNED FROM CEPAEA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Please see general comments.
Experimental design: Please see general comments.
Validity of the findings: Please see general comments.
Additional comments: The authors examine how the frequencies of genetically-based color morphs of Cepaea change from historical samples to the present, paying special attention to how conclusions can change depending on which specific year from a given time period is used for a comparison between time periods. In essence, conclusions as to how frequencies change from the past the present depend on which specific year from the past is used for comparison. The implication is that studies need to have replicate samples from each time period if they are to generate reliable estimates of change BETWEEN time periods.

This is all true but not especially surprising, as long term data sets (e.g., Darwin’s finches) show tons of year-to-year variation despite the lack of long term trends. I suppose there isn’t any harm in restating the point for another study system but the insight isn’t particularly novel (see also fig 2 of Hendry and Kinnison 1999). I do object to how the implication is sometimes stated as the lack of replicate sampling leading to incorrect or “misleading” inferences. Instead (as is implied at other parts of the MS), the robust conclusion is that short term evolutionary changes can be greater than long term changes. I would prefer that to be the point of motivation for the paper rather than the more obvious and less interesting point that somehow “incorrect” conclusions can result from incomplete sampling. Instead, the observed changes are “correct” but they don’t necessarily reveal long term average trends. Thus, the problem isn’t in how the comparison is done but rather in how an investigator might attempt to extend a particular temporal comparison to general statements about long-term trends. This is perhaps a subtle point but the wording in the MS could be much improved in this regard.

Technical comments:
1.	Line 38: cite general meta-analyses and quantitative reviews rather than a few arbitrary examples out of hundreds that could be cited.
2.	 Line 45: Of course, this point is obvious from essentially any long-term study.
3.	The emphasis seems to be on the fact that SIGNIFICANCE of temporal changes depends on year of sampling. However, significance is not what matters here (given that significance is also dependent on sample size). Instead, it is effect size that matters – that is, the actual frequency change. So the real question is how much allele frequency change differs depending on the year of sampling. Of course, these data are in the figure but the point is not clear in the text, nor is the figure optimal. For best inference, maybe prepare a graph of “change using one historical year” on the x-axis and “change using another historical year” on the y-axis. Deviations from the 1:1 line then reveal the extent to which the chosen year matters.
4.	Also, the allele frequency change that can occur is dependent on the starting allele frequency, so it would be good to examine if the two are correlated.
5.	As the lead author has shown in other work, the multivariate phenotypes of snails can vary among similar habitats. I would like to see a graph something like Fig 3 of Ozgo et al. (2011 – BJLS 102:251-262).
6.	The starting part of the Discussion essentially just lists the results again. I think the discussion could be much more interesting by focusing on the processes that shape short-term versus long-term change and how these process influence expectations under climate change (or something like that).


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: AUGMENTED CARTILAGE REGENERATION BY IMPLANTATION OF CELLULAR VERSUS ACELLULAR IMPLANTS AFTER BONE MARROW STIMULATION: A SYSTEMATIC REVIEW AND META-ANALYSIS OF ANIMAL STUDIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: Manuscript entitled “Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies (#18289)” is well written and discussed. However, following comments should take care during the revision.
1.	Manuscript lacking the future implication of this kind of analysis in cartilage tissue engineering. Please discuss the importance of the study in discussion and conclusion parts of the manuscript.
2.	Growth factors are the one of the important components of tissue regeneration along with scaffold and cells. It would be nice to include the growth factors description in the manuscript.
3.	Stimulation in form of bioreactor is again one of the crucial factors for differentiation of stem cells into chondrocyte lineage. Please also include the bioreactor in search, and discussion in the manuscript.
4.	Recently, cryogels special kind of the hydrogel which synthesized at sub-zero temperature to achieve good porosity and mechanical strength in the scaffold, gained significant attention in cartilage tissue regeneration. Please also include cryogels (PMID:28230077, 27886065, 27185069, 25498693 etc.) in the search study.
5.	In line 185, what’s I2? Please define and discuss the importance of I2.
6.	Line 132, what’s Safranin-O-staining does in cartilage research? Please discuss briefly.
7.	Please briefly discuss “Cochrance approach” in line 153.
8.	Conclusion lacking the importance of the study.
9.	Please include growth factors and bioreactor in figure 1 illustration of cartilage tissue engineering.


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: AUGMENTED CARTILAGE REGENERATION BY IMPLANTATION OF CELLULAR VERSUS ACELLULAR IMPLANTS AFTER BONE MARROW STIMULATION: A SYSTEMATIC REVIEW AND META-ANALYSIS OF ANIMAL STUDIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have used clear language throughout and present a well defined research question with good background information.

I recommend removing the word "unbiased" from line 80 and line 312. A systematic review is not an unbiased overview as it is subjected to biases at all stages of the review process. For example, the authors make decisions on types of study to include,  which databases to search and the methods to use.

Line 284-287. Please include effect size data for adipose-derived stem cells (mean and confidence intervals).
Experimental design: This is a primary research article with a well defined research question- to present a overview of all studies reporting regeneration of articular cartilage by implantation of cell-laden versus cell-free biomaterials in the knee and ankle joint after bone marrow simulation in animals comparing different cell types and methods.

Did the authors publish a study protocol before carrying out their review? Can you provide a link to this protocol or a copy of the protocol?

I would recommend that the authors include the specific search terms used in their search strategy instead of referencing other publications. This could be included in the methods or as supplementary information.

I would question whether the use of semi-quantitative histological scoring systems (which are observer-dependent and thus subjective (Ref. Rutgers et al. 2010) is the best method to determine the success of regeneration? I suggest discussing the limitations of this as outcome measure in the review.

I do not understand the meta-analysis methods used specifically, line 162-163. "modeled with a compound symmetry covariance matrix, as this resulted in the lowest Akaike Information Criterion value." Can you give more details?

I would recommend statistically testing for asymmetry in the funnel plot.

The reviewers do not report data extraction being carried out by two independent reviewers. I suggest discussing the limitations of this.
Validity of the findings: The included data has appropriate controls.

As requested above, I would like a bit more information on the meta-analysis  methods before assessing if the results are statistically sound.

The conclusions based on the results appear to be justified and linked to the original research question.
Additional comments: This is a well written review. I would recommend that the authors revise the manuscript bu clarifying some methods.


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: AUGMENTED CARTILAGE REGENERATION BY IMPLANTATION OF CELLULAR VERSUS ACELLULAR IMPLANTS AFTER BONE MARROW STIMULATION: A SYSTEMATIC REVIEW AND META-ANALYSIS OF ANIMAL STUDIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors of this manuscript have presented a summarized overview and meta-analyses on the previously published research articles on the augmented cartilage regeneration after bone marrow stimulation. This study utilized various tools for screening the suitable reports on this topic with full details of experiments to compare the results for concluding remarks. This review suggests that cellular biomaterials/implants have higher cartilage regeneration efficacy compared to acellular biomaterials/implants. In my understanding, this study of authors is the continuation of their previous finding (Ref. 8 of the manuscript), which demonstrated the role of acellular biomaterials in cartilage regeneration. The manuscript is written well, however, few grammatical errors have been noticed, that can be rectified in revision.
Experimental design: This is a systematic review and meta-analysis of the already published research. The findings are relevant to understand the suitable combination of biomaterials, biologics, and cells for the augmented cartilage regeneration. The study was started with search finding of  11,248 reference articles on this topic, which were further screened rigorously to obtain 146 full-text studies for further analysis.
Validity of the findings: The provided methods of research data screening and meta-analyses are suitable to demonstrate the unbiased conclusion on the role of cellular/acellular biomaterials in cartilage regeneration after bone marrow stimulation. Authors of this study concluded that cellular biomaterials have shown 18.6% higher regeneration capacity compared to acellular biomaterials.
I believe that the provided hypothesis on augmented cartilage regeneration using cell seeded biomaterials after bone marrow stimulation is not significant to understand the basics behind higher regeneration ability. I may suggest discussing more in this aspect in the discussion section using suitable reference articles will enhance the understanding and readership quality.
Additional comments: I have found few points that need to take care by authors of this manuscript;
1. Section 2.1_the provided ref. (like 32, 33..) are not clear. Can authors justify the relevance of these references? If these references are used in support of methods used, then they need to be cited with proper elaboration.
2. section 2.2, 2.4 etc., Authors have used the term 'reviewer' at few places to demonstrate their role, I believe that the correct terminology to indicate their role by the name of 'authors' of the present study.
3. I have found the repetition of many sentences in little-modulated form, for example; line 228-230 'cells were either.....' is providing the same meaning as provided in the next sentence, line 230-233, 'in some studies....'. Authors should revise the manuscript in this aspect to make more crisp and attractive text content.


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: AUGMENTED CARTILAGE REGENERATION BY IMPLANTATION OF CELLULAR VERSUS ACELLULAR IMPLANTS AFTER BONE MARROW STIMULATION: A SYSTEMATIC REVIEW AND META-ANALYSIS OF ANIMAL STUDIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Well-defined question, clearly written
Experimental design: Methods and analysis described clearly and included sufficient details.
Validity of the findings: The conclusion is well stated and directional for preclinical research.
Additional comments: Thanks to the authors for addressing my comments. The manuscript is significantly improved and readable well. Now, I am recommending the manuscript for publication in PeerJ journal.


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: AUGMENTED CARTILAGE REGENERATION BY IMPLANTATION OF CELLULAR VERSUS ACELLULAR IMPLANTS AFTER BONE MARROW STIMULATION: A SYSTEMATIC REVIEW AND META-ANALYSIS OF ANIMAL STUDIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: The modified manuscript is showing improvement in its technical information and better readership quality. The revised manuscript is now recommended for consideration for publication in Peer J.


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: MULTIVARIATE ORDINATION IDENTIFIES VEGETATION TYPES ASSOCIATED WITH SPIDER CONSERVATION IN BRASSICA CROPS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear, unambigous, professional English language used throughout.
Intro and background were used to show content.
Structure conforms to Peerj standards, discipline norm, or improved for clarity.
Figures are relevant, high quality, well labelled and described.
Raw data supplied.
Experimental design: Original primary research within Scope of the journal.
Research question well defined, relevant and meaningful. It is stated how the research fills an identified knowledge gap.
Rigorous investigation performed to a high technical and ethical standard.
Methods described with sufficient detail and information to replicate.
Validity of the findings: Data is robust, statistically sound and controlled.
Conclusions are well stated, linked to original research question and limited to supporting results.
Speculation is welcome, but should be identified as such.
Additional comments: The authors present an interesting research that confirms the importance of environmental heterogeneity when establishing populations of generalist predators useful for agricultural crops. In addition, the manuscript presents statistical tools that can be useful in research on agricultural crops that are conditioned by seasonality and extreme weather phenomena. If there is a weakness, it is in the way that some of the results are presented (as I have noted above) which should be improved upon before Acceptance.

Various references to supplementary material are made in the results section. It becomes difficult to follow the text with so many references to different figures that do not appear in the main manuscript that are mentioned profusely in the results. Please clarify it.

Specific comments:
Line 71: The reference to spiders studied as belonging to 'Araneida' is risky because the taxonomic organization of spiders (in terms of order and suborder) is still discussed. In any case if the authors wish to maintain their denomination they should explain which criterion they follow to define the spiders like 'Araneida' and not 'Araneae'.
Line 108: Indicate the bibliographic sources used to identify the spiders.


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: MULTIVARIATE ORDINATION IDENTIFIES VEGETATION TYPES ASSOCIATED WITH SPIDER CONSERVATION IN BRASSICA CROPS
Review round: 1
Reviewer: 2

Output:
Basic reporting: English should be carefully checked throughout. I pointed out a few issues and some paragraphs that need re-writing.

More background literature should be added to hypotheses and discussion. The discussion feels incomplete. With all the analyses done a lot more can be discussed.
Experimental design: The methods have some issues pointed out in the PDF. Also, the methods are not clearly described and make it confusing to understand.
Validity of the findings: The data would me more robust by adding suggested analyses (see PDF).

Discussion and conclusion need to be re-written and or expanded.
Additional comments: This is a great and valid contribution, however the paper has several flaws all pointed out in the PDF. Mainly the written english, some of the methods and the discussion.


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: MULTIVARIATE ORDINATION IDENTIFIES VEGETATION TYPES ASSOCIATED WITH SPIDER CONSERVATION IN BRASSICA CROPS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is globally understandable. However, there are numerous grammatical and spelling mistakes, as well as syntax errors that need to be corrected.

The introduction and particularly the discussion are often too general and miss concrete examples, especially the discussions about the pests/natural enemies/vegetation types. In addition, some parts of the discussion (quite general) would best fit in the introduction.

Some information is missing in the figure captions. Figure 6 is illegible. Some figures included in the Supplemental material would be best in the MS (e.g., RDA graphs). Also, one table could be added to summarize some pertinent information about the methodology.

Main results needed to answer the research question are provided. However, numerous figures are part of the Supplemental material (only figure about site 1 is provided in the manuscript).
Experimental design: The manuscript entitled "Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops" meets the aims and scope of the PeerJ journal.

The purpose of the study is well stated and relevant, and the justification of the research is provided. However, the hypothesis is too general and could to be more precise. It would be interesting to make hypotheses about which habitat types would provide the highest abundance and diversity of spiders in brassica fields and why.

The sampling design is acceptable to answer the research question. However, a more rigorous work could have been done by identifying the spiders to the species level (instead of the morphospecies) or by conducting the experiment over several years.

The most important issue with this manuscript is the methodology section (experimental design and statistical analyses) that needs to be further explained. There is a lack of details at several places in the manuscripts that limits the comprehension of the work done. For instance, a figure of the sampling design or a Table that summarizes all the essential information may help to understand how the samplings was performed (e.g., number of sampling points per site, number of sampling points per habitat types and per site). The statistical analyses section also needs further details to completly understand what was done and why.
Validity of the findings: The authors succeed to identify some habitat types that seem important for the conservation of spider abundance and diversity. However, the results greatly differ between the 3 sites and discussion remains often too general. The discussion may be improved by being more specific and, for instance, by giving specific recommendations (overall, which habitat types exactly should be present near brassica crops to provide a high abundance and diversity of spiders?).

The data consisted in only one year of sampling and, due to an exceptional event (typhoon), not all the sampling dates were taken into account in the analyses. However, the data seem correctly analyzed.

Because of the numerous analyses done, the "take-home message" is not always clear and needs to be better identified. The discussion may also be improved by adding critics of the methodology/results found. For instance, results and discussion should be moderated since 1) the study was performed in only one year and that an exceptional event happened during this year (typhoon), and 2) identification of the spiders were not performed at the species level (but morphospecies, so with possible bias).
Additional comments: General comments
The manuscript is globally understandable; however there are numerous grammatical and spelling mistakes, as well as syntax errors that need to be corrected.
The major issue of this article is the lack of important information, especially in the methodology and result sections, which limits the comprehension of the experimental design, the statistical analyses performed and the results obtained.
In addition, the introduction and particularly the discussion are often too general and miss concrete examples. The discussion could also be improved by adding critics of the methodology used and results found, and comparisons with other articles observing effects of habitats type on spider abundance and diversity (not only natural enemies in general).

Abstract
L16: “the importance of vegetation…”: You may precise “Natural vegetation”.
L17: Replace “disturbance” by “disturbances”
L18: Add “the” before “types of vegetation”
L19: Remove “into”
L19-20: “Here we explore… and non-crop vegetation”. You may consider rewriting this sentence, it sounds odd.

Keywords
I am not convinced about the term “Ecological Engineering”

Introduction
General comments
The introduction is overall well written but often lacks of details. It is often too general and may be improved by given some precise examples (see specific comments below).

Specific comments
L38-45: This part could be improved by adding an idea of the period of time you refer to. “Anthropogenic activities” since when (from few years ago, decades ago…)?

 L71-74: More information should be given regarding the spider communities found in brassica crops. You mentioned it in the discussion but it can also be described in the introduction. Actually, some information given in the discussion should actually be part of the introduction (e.g. L236-241). It is also important to precise in the introduction (not only in the discussion) that spiders are generalist predators. Furthermore, essential information is missing: Which brassica pests can be controlled by spider in brassica fields? Please provide more details.

L71-84: The last paragraph could be divided into 2 paragraphs: 1) One paragraph about spider communities found in brassica crops and their importance to control pests; so you can add more details about their biology and ecology (e.g., do they overwintered in non-crop habitats adjacent to crop fields?) and 2) second paragraph about the purpose of the study and hypotheses.

L81-84: The hypothesis remains very general. “different vegetation communities would share the spider fauna of brassica fields to varying degrees…”. Did you have an idea of which habitat types would share more species with brassica crops?

Material and methods
General comments
The most important issue of this manuscript is the lack of important information in the methodology. A lot of details are missing and prevent the complete comprehension of the study.
The methodology section could be improved by adding a table that compiled all relevant information for the comprehension of the sampling design: sites, total number of sampling points per site, number of each vegetation type sampled per site, details about the sampling period (exact dates of sampling)... Also, a figure of the sampling design may help understanding how the sampling where performed (e.g., how many sampling points in each habitat type?).
Finally, I wonder whether one year of data is relevant enough to make conclusions, as effects of landscape on insect communities can greatly vary from one year to another, and considering that one event had perturbed the samplings.

Specific comments
L90: Which brassica species? Were there different species? If so, it would be important to list the different species.

L91: “50 x 50 m grid”. Why this distance? You need to justify the choice of this specific scale. Is that because of the dispersal ability of spiders?

L95: “not uncommon”. So it is common?

L98-99: First, it is not clear in the MS whether you have 25-29 sampling points for each one of the 5 sampling periods or for the entire sampling period. Also, when looking at your dataset, it is not clear how many sampling grids you had per site. Did you initially have 30 sampling points for each date and site? In Minquing for instance, in the data file, the sampling points are numbered from 1 to 30, but 19 is missing. Why? So there are a total of 29 points, but only 28 in the other data file (Data_set_Sp). How can you explain that? All these details are essential to understand the experimental design. If there were 30 sampling points at the beginning you should say so. Same problems appeared with the other sites (Nantong 1: 25 or 26 grid points? Nantong 2: 27 or 28 grid points?)
Second, how many samplings were performed in each vegetation types? And how many vegetation types did you consider? These details could be summarized in a Table.

L99: “all vegetation types”: I do not understand the classification of the different vegetation types. This must be clarified in the methodology section. What does “non-crop vegetation” refer to? It is mentioned in the methodology (L92-94) that “non-crop vegetation consisted of adjacent field margins and fallow fields… as well as uncultivated areas…”. But in the results, non-crop vegetation, fallow and field margin are separated. So I wonder what were included in the “non-crop vegetation” category.

L100: “five occasions”. You need to precise the different sampling dates (could be included in a Table, as suggested before). Was all the vegetation types sampled during the 5 sampling dates? It is not clear.

L103-104: So how many sampling dates do you have overall?

L108-109 “(genus in some cases) and assigned to morphospecies”. It is not clear whether the analyses take into account the genus or morphospecies level. You need to be more precise. I assume that the morphospecies was used to calculate the diversity index. If so, it should be mentioned. You don’t need to say that some species were identified to the genus level if you don’t do analyses at this level.

Statistical analyses
General comments
The statistical analyses seem ok to me there are a lack of details and missing important information at numerous places, which limits the comprehension of the analyses done. I am familiar with RDA and variation partitioning analyses, but less with cluster analyses so I gave fewer comments on this part. In addition, the authors need to verify that the correct references are cited for all R packages mentioned.

L114 “spider abundance and diversity data”. What was the unit of replication in the analyses? Did you use the total abundance or mean abundance? As I understand when looking at your dataset is that you keep the data per sampling point. But, did you pool all the data from the 5 sampling periods? Did you use the genus or morphospecies level to calculate the Shannon index of diversity? All of this is not clear and need to be mentioned.

L117: Hellinger transformation: Also used when a lot of zeros in the matrix, like in your dataset.

L121: “differing vegetation types”. “different” instead of “differing”. What vegetation types did you include in the variation partitioning?

L121 “principal” instead of “principle”

L121-122. You may better explain why you decide to perform a variation partitioning between the vegetation type and the principal coordinates of neighbor matrices (PCNM). You may better explain what the PCNM is about.
L124: “effects of distance”: the distance between what and what? Is that the distance between the different sampling points within each site?

L128: It is said that the “adjacent land cover” is different between sites. It would be good to have a more precise idea of these differences. Can you add a characterization of the 3 different sites? For instance in a Table (e.g., including the proportion of the different land covers)?

L129-140. I am less familiar with this sort of analyses, so I am less able to criticize thoroughly this part. However, I have one comment about the dissimilarity index.

L145: “occurrence of spiders”. Occurrence per site? Per sampling point? For the entire season or per sampling dates?

L147: “spatial correlation”. Did you mean “Spatial autocorrelation”?

L148-156. The term “spatial variation map” is not clear. In addition, this part looks more like results than methodology.

L150-151. I am familiar with multivariate analyses and forward selection but I don’t understand what you did here. Why the “spatial variation maps” were included in a forward selection.

L155; “Whist”. ? Verify English.

L159: “p-value<0.00”. Replace by “p-value < 0.001”).

L159-161: You need to cite the references for all the R packages used.

Results
L163-164: It is important also to have the details of the captures per site (abundance and diversity). Moreover, why didn’t you identify to the species level? Did you confirm the different morphospecies with an expert? If not, you should discuss about it in the discussion (you may consider having an over/under-estimation of the diversity).

L164-171: “Variance partitioning showed that abundance of spider families was vegetation-type dependant…”. Important information is missing here. First, Fig 1a misses the total value of the effect of the variable X1=Vegetation and X2 = PCNM (by the way, you must change the second X1 in Figure 1 to X2, because you have 2 variables called X1). The value 0.13 means that the vegetation type alone explains 13% of the variation in spider abundance, which is not very high. What is the total effect of the variables X1 and X2 (unique contribution of each variable + share effect)? If the residual effect is 0.94, than the total effect of X1 and X2 is 6%, which is quite low.
Second, you precise in the following sentence that you have tested “the significance of each variance fraction”, but you precise only one p-value (p=0.07). Is that the p-value for the global model (including effect of X1 and X2)? Also, you mentioned that there are “strong effects” but I disagree with that. All the p-values you mentioned are > 0.05. I disagree also with the term “strong effect”. Actually, you have a strong effect when the R2 of your model has a high value, and the model is highly significant when p-value is very low. The description of the results needs to be rewritten.
Third, you mentioned only the results of the variation partitioning for spider abundance in Minqing, and spider diversity in Nantong 1 and Minquing. What are the results of the other variation partitioning? Even if you found no effect, you have to say it. It is not clear.

L174-176: I am not totally in agreement with you observations. According to me, when looking to Fig 3, Non-crop vegetation are associated with Thomisidae (maybe Oxyopidae), but Salticidae and Lycosidae are more associated with Fallow land than Non-crop vegetation.

L177 “pumpkin showed a strong association with Oxyopidae”. I disagree. The association is not so strong.

L177-183 It would be interesting to have all the RDA graphs in the MS.

L180: “Oxyopidae showed …” Oxyopidae abundance or diversity? Please, be consistent in the structure of the sentence. Put the species family first (e.g., Oxyopidae showed strong association with….) or the habitat first (e.g., Non crop vegetation are associated with…)

L181: Replace “Fig 2a” by “Fig S2a”

L184-185: Quite general. “most of the spider families” “Other surroundings vegetation types”. Can you be more precise. It is difficult to understand the results for people that have never done such analyses. Please explain in more details what do you mean by “same coulour in heatmap”. You should explain more precisely, at least in the figure caption, what does the color key correspond to (what is the unit of the value 0-10?).

L186-187: “Lycosidae showed strong differences in abundance between…”. You can add “and diversity” so that you don’t have to repeat Lycosidae in the next sentence.

L188-189: “Oxyopidae depicted strong differences in diversity among different vegetation types…(different colour)”. I disagree for Nantong 1 and Nantong 2 because it is actually the same colour for all the vegetation types (Fig S3b and S4b).

L189: Remove one “Fig”

L192-193: What does it mean concretely to have such AU-value and BP values? Can you explain briefly? It is important to give some precisions if you want people that are not familiar with such analyses to understand your results. Here, it looks like only a series of values, without explanations.

L196: “Spatial autocorrelation”: between sampling points?

L197: Spatial correlation or autocorrelation? Do you refer to the same thing?  Please explain what you mean. Be consistent in the writing and correct when needed

Figure 1: What is the meaning of the intercept?
Figure 2: Which site?
Figure 4-5: Did you sampled in brassica fields? It is not clear n the methodology. Why Brassica appears in Figures 4 and 5 and not in the RDA graphs? In the figure caption,
Figure 6 is very small and illegible.

Discussion
General comments
First, several part of the discussion are too general and need some precisions. Some hypotheses could also be added to explain some of the results found.
The discussion may also be improved by adding critics of the study (e.g., over/underestimation of the spider diversity because no identification to the species level…). What could have been done or analyzed (e.g., analyze of the effect of the vegetation type on the distribution of spider depending on the sampling periods…). Results would have been different if more than one year studied?

Specific comments
L208: “and non-cropped and non-sprayed zones”: You may rephrase (the two “and” are a bit redundant).

L210: “various pests”: can you give examples of pests controlled by spiders?

L214-216: “Requires….to require”: Replace one of the two “require”

L218-220: What did you mean by “conventional statistical approaches” and “advanced statistical approaches”? I am not sure that the pertinence of this section.

L224: 2a function of spatial distance”: Distance between what and what?
L224: “its intercept”: What does it mean exactly in an ecology point of view (not only statistics)?

L225-228: So it means that “cursorial families” are more widely distributed than “web-builders”? Can you explain why or at least give some hypotheses?

L227-228: “as observed (Blitzer et al. 2012…”. Correct the end of the sentence: “as observed by Blitzer et al. (2012) and Schmidt et al. (2003).

L230: “spatial distance”. It is not clear (between what and what?).

L230: “cabbage”. In the rest of the MS, the word “brassica” was used. Please, be consistent in the terminology.

L231: “meso-scale”. Is 50m really a meso-scale for spiders? I would have used the qualification “local scale” instead. Unless you can have  justifications.

L232: “alternative food”: Can you be more precise (e.g., examples of preys)?

L236-214: This part should be part of the introduction.

241-244: I do not understand. Are you referring to your results or to other authors (Schmidt et al 2003…)?

L244-246: Too general. “alternative food”, “place where spider have time and space…” Can you be more precise? What kind of food and what kind of habitat?

L252: Replace “this” by “which”

L253-255: “may be because of the availability…”. You may replace by “may be due to the availability”. Remove “may also be”.

L267 “vary in space”: Did you mean between habitats?

L269: “certain adjacent crop”: Can you be more precise and give some examples? Can you give some recommendations? Which habitat type should be present near brassica crops to provide a high abundance and diversity of spiders?

L278-280: Spatial correlation or autocorrelation?

L280: Replace “with” by “and”. “various vegetation types”: Can you precise?

L282: I don’t see the need here to emphasis again about the typhoon.

L283-284: I am not totally convinced.

L286: Replace “is” by “has been”

L287: Replace “likely” by “great”

L288: Replace “nearby to crop fields” by “nearby crop fields”. Replace “conservational” by “conservation”

L293: Replace “Further” by another word (In addition, furthermore…)

L294 “temporal effect”. As you have several sampling periods, it would have been very interesting whether the effect of vegetation type on the distribution of spider differ over time.


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: ANCIENT DIVERGENCE TIME ESTIMATES IN EUTROPIS RUGIFERA SUPPORT THE EXISTENCE OF PLEISTOCENE BARRIERS ON THE EXPOSED SUNDA SHELF
Review round: 1
Reviewer: 1

Output:
Basic reporting: The quality of written communication is excellent. There is a wide literature base employed, although literature from other homologous study systems (land faunas that were periodically connected via Pleistocene sea level fluctuations) was not employed. Many examples exist (Taiwan, Japan, Tasmania, New Zealand, Sri Lanka, England).

Tables and Figures were all of a high standard, although Fig1 needed the locality names on the figure for each sample, to avoid the need of cross-referencing with other sources. Likewise, Figure S1 only had codes for samples, and hence was uninformative without consulting other information. These figures need to be "stand alone" with respect to interpretation.

One of the main deficiencies was that the Introduction started straight with the study species. The question is very interesting and broadly relevant, so the paper should start with the over-arching issue, that is of broadest interest and significance (genetic history of taxa on landbridge islands, and predicting their past connectivity using SDMs as verified by genetics).
Experimental design: It was unfortunate that the previously studied specimens and DNA sequences could not be integrated into this study. As such, it comes across as the third study to make a "first attempt" at the phylogeography of this species.

In terms of phylogenetic reconstruction, concatenation of genes is only one option. The alternative, that is more realistic, is to build population trees that allow each gene to have evolved along an independent gene tree. There are methods out there that do this (including BEAST). That said, it seems most of your variation is harboured in mtDNA, and the nDNA are not adding much.

I was not sure about your models employed during tree building. I cannot see why the BEAST strategies needed to be different from MrBayes and RAXml, and vice versa (particularly with respect to codon models). Even if you need to fragment your datafile, you can make datasets of 1st codons all together, all 2nd codons together, and so forth, and then give them separate models in MrBayes or RAXml

Given the depth of divergences at play, is a coalescent tree prior likely to be the most appropriate for BEAST analysis, versus a Yule tree prior?

I am not very familiar with MaxEnt, but I am familiar enough to know that a basic acceptance of default parameters is inappropriate, and you should find good, more rigorous examples of its implementation to follow as a guide. This will indicate the degree of sensitivity to parameter selection.

No outgroup in the analyses? Although the Philippine split looks obvious, without an outgroup, you actually cannot say where the deepest split (phylogentically) occurs.
Validity of the findings: The findings are probably valid, but rely heavily on the mtDNA variation, which should be more adequately explored. Otherwise, the results may be given the impression that they are more reliable (strong multilocus support) than reality.

One of the big issues I have is an apparent contradiction. The species could not move across the Sunda shelf, to mix with other populations. However, the SDMs should that they also did not persist at most of the contemporary sample sites during the Pleistocene glaciations. So, if they couldn't move widely, and they could not persist where they are today, how did they come to have their present distribution, and indeed, deep genetic divergences?

I would be interested to know whether there are any modern day homologs of the glacial Sunda shelf habitat, and whether the species occurs there today or not. Essentially, is the Sunda shelf glacial habitat novel, relative to today's environment? If so, we have no evidence (from present species distributions) that they could not occupy this historical habitat, because there are no modern homologs.
Additional comments: The paper seems to end strongly on the point "we need more sampling". This weakens the study, because it points out your main deficiency, and leads to the question, why didn't you do more sampling?


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: ANCIENT DIVERGENCE TIME ESTIMATES IN EUTROPIS RUGIFERA SUPPORT THE EXISTENCE OF PLEISTOCENE BARRIERS ON THE EXPOSED SUNDA SHELF
Review round: 1
Reviewer: 2

Output:
Basic reporting: My main suggestions for revision are in "General Comments for the Author" below.  Included in these comments are suggestions for improving the focus of the text on the major discoveries made possible by the new data. Much of what exists in this draft seems largely extraneous to this central purpose.
Experimental design: I have no major changes to suggest on this topic.
Validity of the findings: Validity seems fine to me.
Additional comments: This manuscript reports new comparative DNA sequence data and phylogenetic analyses for skink populations of the species Eutropis rugifera. Geographic sampling is broad but sporadic, providing a historical biogeographic overview for this species. The results are worth publishing, but the manuscript needs a reasonable amount of revision to be effective in highlighting the new findings.

	The major problems with the presentation are evident from the abstract, which should describe the new data (genes, number of populations sampled) and analyses, and the major conclusions. For the latter, a verbal account of the contents of Figure 3 would be a good strategy: “The earliest phylogenetic divergence within E. rugifera separates Philippine populations from those of the Sunda Shelf with an estimated divergence of 16 million years ago; the Philippine populations thus cannot be considered conspecific with their Sunda congeners. Within the Sunda Shelf, the oldest divergence separated Borneo populations from a common ancestor of populations in peninsular Malaysia and the Mentawai Archipelago approximately 6 million years ago. Our data suggest that within Borneo, populations from Sabah and Sarawak separated approximately 4-5 million years ago in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Separation of continental Malaysian populations from those in the Mentawai Archipelago occurred approximately 5 million years ago. Divergence among samples from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 million years ago, and our samples from continental Malaysia appear to coalesce in the middle Pleistocene, about 1.5 million years ago.” With this temporal and spatial framework, focus the historical biogeographic analysis and discussion specifically on these events. Given the full temporal scope of the divergences revealed within E. rugifera, the emphasis on the Pleistocene in the abstract and elsewhere is misplaced; only the most recent divergences within Sarawak and coalescence of the continental Malaysian samples date to the Pleistocene, so these are the only events for which Pleistocene climatic history is particularly relevant. Limit your discussion of the historical climate of the Sunda Shelf to what should be your main point: the most parsimonious explanation of the historical events revealed by your data analysis. Your bar on Figure 3 showing episodic land connections probably suffices for this purpose. Extensive discussion of grasslands and rivers in the past history of the Sunda Shelf seems unwarranted by the data; introduce these considerations only if necessary to explain a specific case of cladogenesis on Figure 3.

Some additional problems in the abstract also recur throughout the manuscript. “Last Glacial Maxima” is a misnomer. The correct phrase is “Last Glacial Maximum,” the single most recent time that glaciation reached a maximum southern extension from the northern pole. The LGM occurred about 10,000 years ago, much too recent to be of explanatory value for the divergence events revealed by your data. Statements such as “unexpectedly ancient divergence” in line 26 are too vague to be informative; substitute the specific numerical estimates from your data and analyses for “ancient,” “recent,” “close” or “distant” in describing divergences, as illustrated in my suggested rewording of your main discoveries. In describing recurring cycles of inundation versus exposure of Sunda land areas, I favor “episodic” rather than “periodic,” the latter being a special case of “episodic” in which successive episodes have a constant temporal spacing. Figure 3 indicates that perhaps the Pleistocene cycles approach periodicity, but “episodic” is the more conservative claim.

	One important concept is missing from your discussion of historical biogeography: “incumbency” of populations in their interaction upon secondary contact. Vicariant populations of E. rugifera that have evolved as distinct lineages over many millions of years likely have made secondary geographic contact episodically following their initial divergence as climatic conditions temporarily removed a geographic barrier (for example, a drop in sea level permitting formerly separated populations to make contact by expanding into a newly formed land bridge between them). Because of their ecological similarities, each population lineage likely blocked the spreading of its geographic neighbor into its own range at these times of transitory secondary contact. The geographic pattern of vicariance thus persisted over many millions of years despite episodic removal of the physical barrier that initially led to allopatric speciation. Many authors have discussed this phenomenon, perhaps most notably John Wiens and Kenneth Kozak, although my recollection is that the term “incumbency” traces to writings by Elizabeth Jockusch and David Wake on Batrachoseps salamanders. Given your sparse geographic sampling, detailed discussion of incumbency is not advised here; the phenomenon nonetheless allows you to focus your explanations on what caused the initial cladogenesis of evolutionary lineages without having to explain why they subsequently maintained their patterns of vicariance despite episodic geographic contact during the Pleistocene.

	I focus next on the figures, which mostly succeed in conveying the main new discoveries, but which could be improved.

Figure 1 – Label all of the main areas discussed in your text. The Mentawai Archipelago is the most obvious omission; move “Eutropis rugifera Range” to the top of the circled area to make room to label the Mentawai Archipelago where “Eutropis rugifera Range” now appears. Within Borneo, distinguish Sabah and Sarawak. Because you mention them in lines 235-236, label Nicobar Islands, Bali and Bawean Island. Also, number the localities and use the same numbers to cross-reference taxa in Figures 2 and 3.

Figure 2 – After numbering the geographic localities shown on Figure 1, include the numbers in the tip taxa for cross-reference.

Figure 3 – Again, add numbers to the tip taxa to reference Figure 1 as requested also for Figure 2. Because the main purpose of this figure is to convey the temporal information, remove Bayesian support from the nodes and replace it with the estimated time of divergence. If you want to convey branch support, then perhaps put a small black circle at each node whose Bayesian posterior probability is 0.95 or greater. Then your numbers and confidence intervals on the figure will be synchronized. Because only one event of cladogenesis coincides with the transition from mesic to xeric climate at the late Pliocene, this point is perhaps overemphasized. The overall importance of this transition is to explain why episodes of land connection are much more frequent following this point, although your most important events of cladogenesis precede it.

Figure 5 – Perhaps cut this analysis entirely. My earlier comments explain why I consider it largely irrelevant to your data. You want to have some hypotheses of the geographic barriers that explain the initial cladogenesis of your main lineages. It is potentially of interest to identify what areas of refuge allowed these lineages to persist when unfavorable climate restricted their distributions; nonetheless, your geographic sampling is too sparse for giving too much emphasis to this point. Perhaps show one map that depicts the areas most likely to have been continuously occupied by lineages of E. rugifera through the cycles of fluctuating climate. This is the main point that your readers will want to know. The current presentation is too complicated to convey this point effectively.

	From my preceding comments, it is evident that I would greatly condense and rewrite the introduction and discussion sections to focus on explaining the main new results. Material on lines 210-224 of the Discussion should be consolidated with the introduction. Include at the start of the Results section a formal description of your new data before covering results of the phylogenetic analyses of those data. Organize your discussion section chronologically by summarizing the main divergence events and their best historical geographic explanations from the deepest to most recent cladogenetic events. As you reach the tips of the tree, identify the minimum number of separate geographic lineages that your data have revealed.

	Lines 267-271 are mostly a distraction. Where internal branches on a phylogenetic tree are small enough that topology cannot be resolved as successive dichotomies, emphasize instead the approximate time at which the various branches coalesce. Especially for cases of vicariance caused by interaction of a global climatic feature with details of topography, it is likely that some phylogenetic splits will be true polytomies rather than successive dichotomies. In such cases, the relevant phylogenetic resolution consists in putting a precise time estimate on the polytomy, not in trying to force it into a dichotomous scheme. Your main message then should be that the various lineages arose approximately simultaneously at the estimated divergence time that best fits your data.


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: CONSTRUCTING STAGE-STRUCTURED MATRIX POPULATION MODELS FROM LIFE TABLES: COMPARISON OF METHODS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Review of ``Constructing stage-structured matrix population models from
life tables: Comparison of method" by Masami Fujiwara and Jasmin Diaz-Lopez

Stage based demographic models are useful when life stages other than age of an individual
better capture survival and reproductive rates. Such models have been discussed in
ecological and demographic literature for some time though issues related to construction and
interpretation have persisted. This ms is a useful contribution that addresses a major issue
in linking age-based models with stage-based models. It provides some general clues about when stage-based models would work and provide guidelines for construction of such models.

Here are a few suggestions that I hope would help in improving the readability of the ms:

1) I would like to see a bit more clarity in the Discussion section about the discrepancy between age- and stage-based models with regard to estimates of $\lambda$ and generation time. It is shown that generation time as opposed to $\lambda$, is largely way off when derived from stage-based models.
Can authors provide some intuitive reasoning into why this is so? Is this a numerical issue or is there anything problematic when using equations 13-14 for stage-based models? Since only in the case of constant hazards (and constant fertility) stage-base models do well I am wondering which, the aggregation of age-groups to make stages, or individual heterogeneity contribute more to the error in estimates. Can this information be dished out from the results?

2) The ms is generally well written though it was hard for me to go back and forth between the text and the 16 tables at the end of the ms.
I would suggest converting the tables into figures if possible. You could plot deviations between estimates and true values, for instance. I would also think of moving some of the model details (equations 1-20) to an appendix leaving only qualitative information in the text. Please give citations to the different survival/mortality and fertility functions if they have been used previously. I would also suggest providing the codes as some of the methods used to compare different approaches can be used as tools to make models when data is available.

3) Line 177: why is $l(x) = n_1(x)+ n_2(x)$? If so, is it guaranteed that $l(x) \le 1$ for all $x$, as $n_1$ and $n_2$ are population densities?

4) Line 232: should be $l(z)l^{-1}(x-0.5)$?

5) Line 237:  what is $l(0.5)$?

6) Line 269 (and 278): what are the symbols L, M and O etc. inside the matrix? Never explained, I think.

7) Line 384: I am not sure if anything is said about the convergence; may be good to provide some details about how fast the methods converged etc.

8) Line 395: check sentence: ``higher threat than"

9) Line 403: ``age-range"

10) Line 453: check sentence

11) Lines 461-467: this paragraph is not very informative and seems redundant.

12) Line 481: ``We" recommend..(unless both the authors listed are same!)

13) The title should be "Comparison of methods" I guess (not "method")


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: CONSTRUCTING STAGE-STRUCTURED MATRIX POPULATION MODELS FROM LIFE TABLES: COMPARISON OF METHODS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is mostly clear, properly referenced, and put in adequate context.

Presenting the main results in a long series of tables is not the most effective strategy for communicating the results. I think you could use histograms to summarize results for lambda and generation time, perhaps also split by life-history type. Color coding could be used to embed more information into such histograms, e.g differentiate different types of averaging, or whatever you deem worth highlighting.

The language is a bit imprecise in some places. This issue is most serious for the terminology related to rates, ratios, and probabilities. To me a "rate" is something that has dimension 1/time. This manuscript starts with introducing "rates" that are not "true rates" thus defined. In a discrete time model, survival is not a rate but a probability. Reproduction and lambda are ratios. Of course, I readily admit that the use of term "rate" is often quite liberal, and people have tendency to include even when it is not needed or is "wrong" (I have also done so in the past). This is not necessarily a big issue - when the context is clear, they may not be a risk of confusion. But in this article some "rates" are "true rates" whereas others are ratios or probabilities. The text would greatly benefit if you could clean up this terminology.
Experimental design: This manuscript presents a useful comparison of different ways of aggregating data for stage-structured population models. The design of the analyses is adequate for the task.
Validity of the findings: No comments
Additional comments: Specific comments:
L19, abstract: I would shorten this, even though it probably is within the allowed limits. You would want to provide a concise overview of your work
L33: discretization ... introduce*s*
L44: "life history types" (simpler and less clumsy)
L47: "I recommend" should be "we recommend", assuming that both authors stand behind this recommendation.
L74: remove "However" that hints to a non-existent contrast
L90: usually simply "Euler-Lotka equation". In any case, no caps for "Renewal Equation" (also later)
L94 and below: why "a renewal equation" when you specifically have defined it as referring to the Euler-Lotka equation?
L105: remove the decimal from "1.0" because the  value is exactly "1"
L110: here you should write "*the* renewal equation"
L123: maybe you should define what "the second stage" is?
L132: I would call this "mortality rate" (this is a true rate because its unit is reciprocal of [x])
L134: why alpha_3 and beta_3 here, and alpha_2 and beta_2 in eq. 6 introduced later? If the notation has no mnemonic basis, at least the ordering should be logical.
L141: this equation is missing a scaling parameter (fecundity per length^3), otherwise R in this equation is completely different from R in equations 4 and 5. I would subscript the R's differently anyway because the exact interpretation is different even after standardizing the units.
L206: as L105
L269,278: in my pdf, I see L, M and O where there probably should be ellipses
L343: Should this be "similar"? They are the same under the chosen precision. Either say that or use "similar". Also further below - "same" literally means identical and should not be used loosely.
L380: you need to add "with the true values", otherwise "consistent" is ambiguous (or better "similar to the true values ")
L387: I don't understand what "and they performed poorly" refers to
L390: pompous, "two key parameters describing population demography" or something would be better
L390: insert "expected to be" before "declining"
L392: of population, not species
L414: there is a fundamental difference in that adults reproduce and survive while juveniles only survive, so the situation is unlikely to be symmetric
L429: only when growth is indeterminate, which is typically true for fish, but also for many other cold-blooded vertebrates as well as many invertebrates


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: CONSTRUCTING STAGE-STRUCTURED MATRIX POPULATION MODELS FROM LIFE TABLES: COMPARISON OF METHODS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors studied the convertibility between age-structured and stage-structured models with a life table and examined the convertibility using two basic demographic statistics. i.e., population growth rate and generation time. The description of the introduction is easy to understand the background of the issue they want to solve. It is written thoroughly citing many related references. The purpose is clear, that is, to investigate the performance of methods for such conversions. The manuscript is organized well according to PeerJ standards. The figures and tables are well-organized and well-labeled such that the readers can understand what they meant.
Experimental design: The original question is clear and well-defined, i.e., how to extent age-structured model can be converted to stage-structured model in obtaining the population growth rate and generation time. Most researchers, who have used population matrix models and the matrix database, would be interested in it and be eager to know the answer. It is definitely within the scope of the journal. Most of the assumptions made in the calculation are good and sufficiently described, but I have several complaints and concerns on a part of the assumptions (see comment 2 and 3).
Validity of the findings: Their findings, namely the conversion performed well in identifying the population growth rate for many life history strategies of organisms and performed poorly in estimating generation time, is astonishing and interesting. The recommendation in Conclusion is rationale and includes meaningful implication. However, the result on the discrepancy of generation time among the methods are not fully explained and compared (see Comment 1).
Additional comments: (1)	The most important point to be revised is on the description in the result of generation time (377l. to 382l.). The result showed that the discrepancy is substantial for most scenarios. However, the explanation is very short and insufficient to understand the discrepancy. Many questions arose when I read the result. Which scenario is the worst (or medium)? Does it depend on the maturation timing (early- and delayed-maturation)? Why does the discrepancy arise? I need more explanation about them in Results and Discussion including your speculation.
(2)	My second concern is the different assumptions of survivorship between early maturation type and delayed maturation type. The authors assumed two types of survivorship both for juveniles and adults (Eqs. 1 and 2) in early maturation, and assumed Eqs. 1 and 6 in juveniles and Eq. 1 in adults. I do not understand why the authors change the assumption because I think it is not necessary in this study. The difference leads to the difficulty in comparing the results between early- and delayed- maturations. The comparison must be very valuable.
(3)	The authors used 2 by 2 matrix in the construction of stage-structured matrix for early-maturation type. Several researchers cautioned that population growth rates strongly depend on matrix size. The variation in matrix dimensions complicates the comparison among the statistics of the matrices (see Salguero-Gomez 2010). Therefore, I expected that the results in tables 4 to 6 are very different from those in tables 7 to 9. Though they seem to be similar and not to affect the difference so much in your manuscript, it’s better to note lightly in Discussion.
(4)	This is just a comment. You explained the result of the estimation of population growth rate on lines 349 to 376. I recommend you to make a summary table in order to advise in which case we have to be careful when we used the converted stage-structured matrices. It would be useful for readers to understand the results at a glance.

Miscellaneous points:
(i)	On line 134: The parameter alpha_3 and beta_3 should be alpha_2 and beta_2. The subscripts should be numbered in order of their appearance.
(ii)	On line 173: “m_1 = 0.5 for x > x_2” There must be a mathematical contradiction here because x1=x2 in the first type of maturation. The equality symbol is necessary?
(iii)	On line 197: the stage -→ stage i
(iv)	On lines 231 and 233: l^-1(x-0.5) appears the product of l^-1 and (x=0.5). It’s better to use the fractional form here. Is the b(x)in the equation b(z)?
(v)	On line 260: Equation 13 is a typical formula of generation time. Please cite a good textbook on demography. Eqs.13, 14 and 18 are denoted as G using the same symbol. It’s better to denote them as G_1, G_2 and G_3. You should specify which generation time was used in the tables.
(vi) On line 266: at age x, respectively.  --→ at age x, respectively (in Eq. (7)).
(vii) On line 269:  f_2 -→ f_1.5?
(viii) On line 324: priori?  Is it “a priori”?


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: CONSTRUCTING STAGE-STRUCTURED MATRIX POPULATION MODELS FROM LIFE TABLES: COMPARISON OF METHODS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is reasonably well written but the results are still rather heavy to follow. This is because one has to refer to several figures at the same time, the figures are not made as accessible as they could, and the way of referring to their elements in the text is different from the figures itself. See also my "general comments".

I do not like calling everything as "rates", especially probabilities, but I acknowledge that there is no universal standard for this.
Experimental design: No new comments, this is fine
Validity of the findings: No new comments, conclusions reflect the results without over interpretations
Additional comments: Specific comments:
L41 "stage-structured" (hyphen, for consistency)
L52 Split this sentence after "and" --- the statement being made is not related to the first clause.
L79 It is never "necessary", so I would say something like "little is gained by converting..."
L180 I wonder if there is some reasoning behind using different means, or is it just ad hoc choice?
L322 Tell the reader which columns shoes this
L329 "(Models D-F in panels a-c of Figures 5-7" - the use of lower/upper case letters here is the opposite to their usage in the figures. Check this throughout, very confusing!
L339 The figure ref should be moved to the end of the sentence
L359 Figs. 11-13 do not include model B
L365 This should probably read "are generally not accurate", because they can be accurate in special cases
L391 "enable the estimation of"->estimate
L404 "it is possible that in reality" sounds odd and should be deleted, given that there are lots of insects that do exactly this, periodic cicadas being an extreme example.
L407 I would add here "In our model, the heterogeneity ..." because there are many other reasons, more in general
L478 Here you could advise against estimating generation time from stage-structured population models
L492 Remove the hyphen from "Orcinus-orca"

Table 1 None of the parameters are dimensionless. It would be good to make some statement about the measurement units or dimensions.
Figures:
* Each figure results from a 2x3 factorial design, but the panel order does not reflect this. With three rows and two columns, it would be logical and reader-friendly to let "H" with two levels to vary by column, and "F" with three levels by row. It looks like that you should fill the figures column-wise.
* The figures would probably benefit from marking the "a" column differently from the others, perhaps also adding a horizontal reference line
* More in general, indicating certain types of models with coloring or patterning would probably be helpful. Of course, this should not be overdone.
* Given that the figures 5-7 are structurally identical, you could probably merge them into one, with e.g. grouped bars or whiskers to show results for the three levels of lambda. The same applies to the other figure triplets.


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: CONSTRUCTING STAGE-STRUCTURED MATRIX POPULATION MODELS FROM LIFE TABLES: COMPARISON OF METHODS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no additional comment.
Experimental design: I suggested two points to be revised (Comments 2 & 3). It's now appropriately revised.
Validity of the findings: I commented "the result on the discrepancy of generation time among the methods are not fully explained and compared". It's now appropriately revised.
Additional comments: Most of my comments are appropriately responded. However, there are still several typos and points to be revised.

Reply to 1st comment: The expansion in discussion is good. It's now appropriately revised, I think.

Reply to 2nd comment: The author probably misunderstood what I meant in the comment. However, clarifying the reason or the mechanism of the difference between early-maturation and delayed-maturation is not a central theme in this paper. I agree with the author’s opinion, i.e. their recommendation is to use age-structured model to calculate lambda and generation time when age-specific vital rates are available.

Reply to 3rd comment: The revised discussion on 399l. to 406l. is enough to answer my comment.

Miscellaneous points:
(i)	On line 177: the stage begins at age x_i.  I understand “the stage” in the senetnce means stage i in stage-structured model, I think. Otherwise, there is no definition of i.
(ii)	In Eqs. (15) and (16): There are many 2s in matrix-element subscript and some of the subscripts are described as 1.5. I do not understand the inconsistency. Which is correct, 2 or 1.5?
(iii)	On line 362: They gave similar to the true values -→ They gave similar result to the true values?
(iv)	Table 4: You defined three types of generation time, G_1 to G_3. Please describe which generation time is use in which model type.
(v)	Figures to 16: Why do you use A to F in the panels. The capital A to U are used to identify the models you used in Table 4. It’s very confusing. The horizontal axes should be described using upper cases?


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: CONSTRUCTING STAGE-STRUCTURED MATRIX POPULATION MODELS FROM LIFE TABLES: COMPARISON OF METHODS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors have adequately addressed my residual comments. I have no further comments.
Experimental design: No new comments
Validity of the findings: No new comments
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: CONSTRUCTING STAGE-STRUCTURED MATRIX POPULATION MODELS FROM LIFE TABLES: COMPARISON OF METHODS
Review round: 3
Reviewer: 2

Output:
Basic reporting: No additional comments.
Experimental design: No additional comments.
Validity of the findings: No additional comments.
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: SPECIES–SPECIFIC CRAB PREDATION ON THE HYDROZOAN CLINGING JELLYFISH GONIONEMUS SP. (CNIDARIA, HYDROZOA), SUBSEQUENT CRAB MORTALITY, AND POSSIBLE ECOLOGICAL CONSEQUENCES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This MS by Carman, Grunden and Govindarajan is excellent, providing new data and observations on predation on the hydrozoan jellyfish Gonionemus by crab species both living in eelgrass habitats in Massachusetts, USA.

The MS is written clearly, with experiments, results and implications expressed in sufficient detail and fairly. Main conclusions include that the native majoid crabs Libinia dubia readily consume Gonionemus and that mortality of L. dubia increases in experiments when more medusae are consumed. In contrast, the introduced crab Carcinus maenus avoids consuming the jellyfish. Anecdotal evidence is presented that Callinectes sapidus may consume Gonionemus, but C. sapidus was not common enough to assess this relationship in any detail.

All told, these results are relevant because L. dubia and C. maenus live in the same habitat and consume many of the same prey items, suggesting that the differential feeding bahaviors on Gonionemus benefits the non-native C. maenus.

The complicating detail in this paper is that recent work has shown that the Gonionemus jellyfish likely in this region may include lineages that are particularly noxious to humans and that have recently been introduced. Some care should be taken to make clear that toxicity to humans is not necessarily a good proxy for toxicity to crabs, or evidence to the contrary should be presented.

Also, it may be helpful to explicitly lay out potential future work investigating whether there is differential impact when Libinia feed on the different lineages of Gonionemus.
Experimental design: The experiments are fairly straight forward.
Validity of the findings: The experiments are fairly straight forward, consistently showing that: 1) more medusae are consumed by L. dubia over time and in higher densities, and; 2) mortality increases as more medusae are consumed. The apparent inverse relationship between crab size and mortality (with smaller crabs being less likely to suffer lethal effects) is difficult to understand and the authors correctly assert that more evidence is needed to understand whether this relationship is real or not.
Additional comments: A few notes/suggestions, all minor.
1) I do not necessarily agree that "jellyfish" refers to gelatinous zooplankton. Perhaps this is true of the word jelly or jellies, but I tend to think of jellyfish referring to only the medusa phase of medusozoan species that have a medusa phase. In any event, it is a common name and it is unclear how that introductory sentence helps the overall narrative of this paper. It is not a big deal, but the authors could use the term "gelata" , as introduced by Haddock (Haddock, 2004 in Hydrobiologia) in order to move the focus to the medusa-bearing groups.
2) Line 223: "Even if the medusae were cling. . ." should have "were" deleted.
3) Lines 246-250. It might be worth providing a bit of caution into this discussion. Crabs and humans are quite different organisms and there is no evidence that the toxins behave similarly on the two groups. I think a caveat to this effect might be warranted. It is interesting to note the individual variation in human response to Gonionemus venom, and the fact that a single sting can elicit symptoms in a human, but this is merely suggestive of possibilities in regards to the crabs.
4) The discussion of jellyfish predators starts (lines 257-258) with a partial list (sea turtles, fish, molluscs, chaetognaths, ctenophores, and other cnidarians) and that through me off a bit. But it goes on to become more complete. Phyllosoma larvae should be added to the list (Biol Bull. 2012. 222(1):1-5. Predation by the phyllosoma larva of Ibacus novemdentatus on various kinds of venomous jellyfish.) and I have also seen images of galatheid crabs feeding on medusae in deep reef settings. I was unable to find anything in a quick literature search, but the authors might consider checking that.
5) Lines 288-290 states "The hard shells of the crabs probably provided protection from Gonionemus stings upon initial contact with the jellyfish. However, the soft interior tissues appear to be vulnerable." Is there really any evidence that the stings do not occur through the handling and manipulation of the jellies, rather than the consumption? I suspect that the authors have this correct, but it might be more fair to state " However, the soft interior tissues are more likely to be vulnerable."
6) Lines 308-312. Here again the authors suggest that what we know about Gonionemus toxicity to humans may be directly relevant to toxicity in crabs (when discussing Carcinus avoidance of Gonionemus). It could also be the case that Gonionemus in Europe is toxic to Carcinus even if the Gonionemus in Europe isn't particularly noxious to humans.
7) The authors may want to lay how to test (and the importance of testing) whether the less toxic lineage of Gonionemus (to humans) is also less toxic to Libinia.


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: SPECIES–SPECIFIC CRAB PREDATION ON THE HYDROZOAN CLINGING JELLYFISH GONIONEMUS SP. (CNIDARIA, HYDROZOA), SUBSEQUENT CRAB MORTALITY, AND POSSIBLE ECOLOGICAL CONSEQUENCES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a straightforward experimental paper on the effect of Gonionemus cf. murbachii on Libinia dubia and other crab species.
Experimental design: Very clear.
Validity of the findings: The results are sound and worth publishing.
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: SPECIES–SPECIFIC CRAB PREDATION ON THE HYDROZOAN CLINGING JELLYFISH GONIONEMUS SP. (CNIDARIA, HYDROZOA), SUBSEQUENT CRAB MORTALITY, AND POSSIBLE ECOLOGICAL CONSEQUENCES
Review round: 2
Reviewer: 1

Output:
Basic reporting: All clear, and reviewer comments addressed satisfactorily.
Experimental design: Well done.
Validity of the findings: Conclusions are well founded.
Additional comments: All reviewer comments have been addressed and the MS is ready to be published.


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: INDIGENOUS AUSTRALIAN HOUSEHOLD STRUCTURE: A SIMPLE DATA COLLECTION TOOL AND IMPLICATIONS FOR CLOSE CONTACT TRANSMISSION OF COMMUNICABLE DISEASES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Basic reporting is good, with clear presentation of the work. No concerns about this.

There is one typo in equation 2 (page 4): the minus sign in front of the lambda should not be there.

Perhaps there could have been a bit more of a discussion of the literature relating to measuring contact patterns relevant to infectious diseases and the potential limitations of relying on the number of household contacts alone. Some possible reference are

Ogunjimi B et al Mathematical Biosciences 2009
Xiao X et al Epidemics 2016
Melegaro et al Epidemics 2011
Zagheni et al AJE 2008
Stehle et al PLoS One 2011
Fournet et al PLoS One 2014

One limitation of relying on contact data alone is children have consistently been found to more infectious than others (for example, see Ghani et al 2010 paper cited, but several others as well such as Viboud et al Br J Gen Prac 2004).

Would be nice for the reader if Fig 3 could use colours corresponding to those chosen in Fig 2.

Minor point: "data are" is usually preferred to "data is"  (though I note the Peerj review website uses "data is" so I'm probably fighting a losing battle on this one).
Experimental design: I have no concerns about the experimental design. I believe this is relevant, original,  meaningful research with appropriate methods that clearly fills a knowledge gap.

The outbreak simulations are probably the weakest part of this (it seems a bit odd to collect good household data but then not look at a household model). However, this is not an essential part of the paper - this is more just to illustrate the point that contact patterns can be important. These simulations do not represent a novel finding and could easily be dropped without affecting the quality of the paper. If these stay in I think at least worth discussing limitations of this model (which can be contrasted with a household model), + also reporting R0 values for the three populations considered. Perhaps also worth mentioning that different methodology was used to collect data from the Melbourne site, so contact matrices are not necessarily comparing exactly like with like.
Validity of the findings: I have no reason to doubt the validity of the findings and the conclusions, though I think there could be more of a discussion of the relevance of the household data alone for informing transmission models. First because the number of effective contacts made by a single individual with household members may not necessarily scale linearly with the number of other household members, and secondly because many other factors (other than numbers of people per household and per room) may be important determinants for household transmission risk. Most importantly age, but other factors such as ventilation/humidity + hygiene practices may also be important.
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: INDIGENOUS AUSTRALIAN HOUSEHOLD STRUCTURE: A SIMPLE DATA COLLECTION TOOL AND IMPLICATIONS FOR CLOSE CONTACT TRANSMISSION OF COMMUNICABLE DISEASES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well-written (structure and language).

From my point of view, the analysis of the data should be deepened and better embedded in discussions around validity / reliability of measurements (see section 3) and relevant literature should be cited. I will suggest literature in section 3.
Experimental design: I have a few methodological questions:

1) How comes that the authors had more respondents for the magnetic board than for the questionnaire? I thought that questionnaire participation was mandatory and magentic board was not; hence the magnetic board respondents should be a subset of the questionnaire respondents? (ll. 94/95)

2) The authors state that the magnetic board was separated into four rooms. What happened if the respondent's house had more or less than four rooms? (l. 108)

3) How exactly was the weighting done (ll. 150/151)? Maybe an equation would help?
Validity of the findings: 1) The authors introduced a new method to measure contacts within a household. At least some data were measured with two methods (questionnaire and magnetic board). From my point of view, a new methods should be thoroughly assessed re how reliably data are collected. What are potential biases? Is the underlying contact definition the same as in other methods? If not, what are the potential implications of that?

There is a huge body of literature on contact measurement methodology. Some paper that might be helpful to deepen this analyses are the following (in reverse-chronological order):

BMC Infect Dis 2016, 16: 341
PLOS ONE 2015, 10: e136497
BMC Infect Dis 2014, 14: 136
Epidemiol Infect 2012, 140: 744-52
PLOS ONE 2012, 7: e37893
Proc Biol Sci 2011, 278: 1467-75

2) Since the numbers of respondents are at the lower end, it would be advisable to calculate confidence intervals when creating contact matrices for specific strata to assess whether apparent differences are statistically significant. This could be done with bootstrapping.

3) Since the authors have introduced weights for being in the same room, they also might want to discuss this in light of the literature around contact duration / intensity, e.g.

Biostatistics 2014, 15: 470-83
Epidemics 2011, 3: 143-51
R Stat Soc C 2010, 59: 255-77
Theor Biol Med Model 2009, 6:25
Epidemiol Infect 2007, 135: 914-21
Additional comments: - ll. 55/56: what kind of skin infections? Impetigo?
- l. 81: what is meant with "Top End"? The northern part?
- l. 153 what is a "shire council"?


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: INDIGENOUS AUSTRALIAN HOUSEHOLD STRUCTURE: A SIMPLE DATA COLLECTION TOOL AND IMPLICATIONS FOR CLOSE CONTACT TRANSMISSION OF COMMUNICABLE DISEASES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Changes are good. Just a few minor typos to be fixed (line numbers are from marked up version):

line 99 punctuation: ”. The questionnaire asked the question ?Who slept in the house last night?”

line 221 + 260 "NT" used inconsistently. I think better to spell out Northern Territory each time as abbreviation isn't used often.

line 252 "proportion of contact" ->"proportion of contacts"
line 276 "population" -> "populations"
line 277 "household" ->"households"
line 278 remove comma
line 290 "contribute" - >"contributes"
line 309 & 332   comma needed:   ...., however, ...

Also, no mention of methodology used to calculate the R0s which have been added in the results section in this revision. Presumably dominant eigen-value of next generation matrix, but worth saying and including the appropriate reference (Diekmann  + Heesterbeek).
Experimental design: no comment
Validity of the findings: no comment
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: KNOWLEDGE AND BELIEFS REGARDING CERVICAL CANCER SCREENING AND HPV VACCINATION AMONG URBAN AND RURAL WOMEN IN LEÓN, NICARAGUA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Line 7: Please define VIA.

Lines 7-10: The authors should clarify that the type of work described in lines 7-10 has not previously been conducted in Nicaragua specifically because it has been conducted elsewhere.

Line 16: Unadjusted linear regression is typically referred to as simple linear regression, “single variable regression” should be replaced with “simple linear regression.”

Lines 18-19: What was the overall goal of in-depth, qualitative interviews?

Line 27: The 3rd theme does not sound like a barrier.  Please revise to more clearly convey how this statement represents a potential barrier to screening.

Line 31-32: This sentence refers to an important finding (i.e., barriers to screening did not differ for urban and rural women); however, it is not mentioned in the Results section.  This sentence would be more appropriately placed in the Results section.

Line 47-48: The source of the data reported in the following sentence should be referenced: “Vaccination against HPV-16 and -18 can prevent nearly 70% of cases of cervical cancer.”

Line 54:  What is the cervical cancer mortality rate in Nicaragua?

Line 59-60: Please provide information on HPV and cervical cancer screening recommendations in Nicaragua. For whom (certain age groups?) is screening recommended in Nicaragua?  With what frequency is screening recommended?  Does the recommended frequency vary by age and risk?

Lines 73-74: Given that numerous studies have examined the acceptability of HPV vaccination programs, the authors should clarify that their statement in lines 73-74 refers to prior work in Nicaragua.

Line 91: When (i.e., months and year) was the study conducted?

Line 127: Does “diseases” refer to HPV and cervical cancer?

Line 133: Five weeks or six weeks as stated on line 92?

Line 141: Why were 92 surveys incomplete?

Line 188-189: The belief score clearly measures knowledge about and attitudes towards screening, but it is not defined in that way in the outcome variable section (lines 144-156), so it is unclear why the authors state that they examined correlates of knowledge and attitude (lines 188-189) in the quantitative data analysis section.

Line 189: Unadjusted linear regression is typically referred to as simple linear regression, “single variable regression” should be replaced with “simple linear regression”.
Line 190:  What “variables of interest” were considered?  Please clarify.

Line 247: According to Table 1, 52% of women were “just getting by” and 53% of rural women were “just getting by.”  Please correct line 247 or Table 1 depending on which is currently incorrect.

Line 255: If aged 18-49 was an eligibility criterion, how were data on age missing?

All statements made about qualitative findings in the Results section should be limited to what women actually said.  For example, it’s unclear whether the following statements reflect what women actually said during in-depth interviews or simply reflect the authors’ hypotheses about how women’s views about or attitudes toward screening might impact their willingness to undergo screening.  If they reflect the latter, then they belong in the Conclusions section:

•	Lines 287-289: “As these services are not affordable for many women in the population, the uncertainty of the gender of the provider may dissuade women from receiving Pap smears.”

•	Lines 289-291: “The embarrassment felt by some women receiving a Pap smear may be exacerbated by a male Pap provider – effectively discouraging some women from regularly seeking cervical cancer screening.”

•	Lines 334-335: “In addition, the perceived link between cervical cancer screening and sexuality could discourage women from seeking regular Pap smears.”

Line 337-338: The 3rd theme does not sound like a barrier.  It should be revised to more clearly convey how this statement represents a potential barrier to screening.

Lines 367-375: Everything other than the following sentence between lines 367 and 375 seems to reflect the authors interpretation of their findings and belongs in the Conclusions section: “Furthermore, as shown in Table 2, 26% of women who were surveyed at 372 health centers were unsure of the health benefits or purpose of a Pap smear.”

Line 403: Delete “of” between “against” and “cancer-causing.”

Line 788: In question 37, change “you” to “your.”

Line 806: Should question 40 be changed to: You would consult with YOUR partner before receiving a Pap test?

Line 984: In question 67, change the final word from “method” to “cancer”.

Line 1159: In the table of survey items included in the belief score, in item 6, change “you” to “your.”

Line 1160: In the table of survey items included in knowledge score, in item 9, change the final word from “method” to “cancer”.
Experimental design: The research question is well-defined and the authors state how this study fills an identified gap in knowledge.  However, the title of the manuscript, the first aim (lines 76-78), and the authors interpretation of findings from analyses addressing the first aim do not accurately reflect the quantitative data collected.  Barriers to screening were measured via the belief score, which the authors state “measures a woman’s likelihood of being screened based on her responses to 22 belief questions” (lines 348-349).  Although the beliefs measured likely have an effect on women’s decisions to undergo screening, the survey did not measure whether these beliefs actually serve as barriers to screening.  For example, women were asked whether they agree or disagree with the statement that “Pap tests are painful.”  Women were not asked whether they are unwilling to undergo screening because Pap tests are painful.  Thus, it is unclear how the belief questions measure women’s likelihood of being screened.  As such, the authors statement in line 348-349 requires justification.
Furthermore, the authors should either (1) address the discrepancy between the first aim of the study and justify their use of belief scores as the outcome of interest in quantitative analyses or (2) revise the Title, first aim of the study, and their interpretation of findings from analyses addressing the first aim to reflect the fact that barriers to screening were not actually measured in the survey.
Validity of the findings: Line 419-420: This statement is somewhat misleading.  While the identified themes may pose barriers to screening, most of the quotes provided from in-depth interviews suggest that the identified themes reflect women’s views about or attitudes toward screening.  Few of the quotes provided illustrate how a woman’s views/attitudes actually served as a barrier to screening.  This statement should be modified to better reflect the findings presented.

Line 439-440: The following is not reported in the Results section: “Our results indicate that there was no significant difference in barriers to cervical cancer screening for urban and rural women.”  All findings discussed in the Conclusions section should be reported first in the Results section.
Additional comments: I was able to open the raw data in Excel, but not in STATA.  I may have done something wrong, but when I tried to open it, I got the following error:

. use C:\Users\Desktop\peerj-18174-Rees_STATAdata2.dta
file C:\Users\Desktop\peerj-18174-Rees_STATAdata2.dta not Stata format


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: KNOWLEDGE AND BELIEFS REGARDING CERVICAL CANCER SCREENING AND HPV VACCINATION AMONG URBAN AND RURAL WOMEN IN LEÓN, NICARAGUA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a paper sharing results from a study in Nicaragua to understand knowledge, attitudes, beliefs about cervical cancer screening and HPV vaccination. Participants included a convenience sample of women recruited at 6 clinics (3 rural and 3 urban) in León, Nicaragua.
Experimental design: -This is a paper about beliefs and knowledge rather than “barriers” to screening. Please review and revise the aims, research question and focus throughout to reflect this.
- The methods section is very long, while it is clarify all methods there is some repetition. For example, it is stated several times that interviews were conducted in waiting areas.
Validity of the findings: no comment
Additional comments: Review of: Barriers to screening for HPV and cervical cancer among urban and rural women in León, Nicaragua (#18174)

This is a paper sharing results from a study in Nicaragua to understand knowledge, attitudes, beliefs about cervical cancer screening and HPV vaccination. Participants included a convenience sample of women recruited at 6 clinics (3 rural and 3 urban) in León, Nicaragua.

Major comments:
-This is a paper about beliefs and knowledge rather than “barriers” to screening. Please review and revise the focus throughout to reflect this.
-There is a lot of discussion in the results section, this should be moved to the discussion section.

Abstract:
-define the acronym VIA

Introduction:
-Line 59-61: You state that only 31.5% of women who are recommended to have a Pap test do have one each year. What are the screening recommendation for Paps in Nicaragua? This may be important to include. In the U.S. PAP screening is recommended every 3 years (not every year) for women age 21 to 65 years. On the PAHO Nicaragua cancer profile page (available here: http://www2.paho.org/hq/index.php?option=com_docman&task=doc_download&gid=23004&Itemid=270&lang=en) it states that screening is recommended every 3 years, so it wouldn’t be surprising that few women report having a Pap test in the past year.
-Line 77: No need to define the acronym HPV more than once in the manuscript.

Methods: The methods section is very long, while it is clarify all methods there is some repetition. For example, it is stated several times that interviews were conducted in waiting areas.
-Line 189: Single variable regression, please be specific and specify that this is linear regression.
-Please provide an explanation as to why so many surveys were incomplete and as to why those surveys were completely excluded.

Results:
-Line 346: “a multiple linear regression results” should be reworded.
-Most women report that that they have ever had a Pap test. How recent were those tests? This would be interesting to see since even though some women report that there are barriers to screening, they are still being tested.
-Move the discussion to the discussion section.

 Questionnaires:
-Question 19 asks about how long ago participants had a Pap test. These results would be interesting to include in the paper.
-Question 23 doesn’t make sense as written. Pap tests do not test for HPV.
-Question 24 asks for number of children, it would be interesting to know more about how likely parents would be to vaccinate their children for HPV among those women that have children.
-Question 58 is not clear. Is this a result of the translation or is this exactly how the question was asked? Please provide some explanation for this question.
-There seems to be an error in question 67.
-What was the reason that you only asked about if people would be willing to vaccinate their daughters and not their sons (Questions 80+)? How many of the participants actually had daughters?

Tables: Add more descriptive title to tables and figure.
-Table 3, add footnote describing the statistics used so that results can be interpreted without going back to the methods section.