Authors

M.J.M. Brown;  B.R. Holland;  G.J. Jordan

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  • pre-publication peer review (FINAL ROUND)
    Decision Letter
    2020/01/22

    22-Jan-2020

    MEE-19-11-849.R1 Hyperoverlap: detecting biological overlap in n-dimensional space

    Dear Ms Matilda Brown,

    It is a pleasure to accept your manuscript entitled "Hyperoverlap: detecting biological overlap in n-dimensional space" in its current form for publication in Methods in Ecology and Evolution. The comments of the Associate Editor who handled your manuscript are included below. Final instructions for your manuscript, and some promotion options, can be found at the end of this email.

    Please do note the Associate Editor's comment about archiving data.

    Thank you for your fine contribution. On behalf of all Editors of Methods in Ecology and Evolution, I look forward to your continued contributions to the Journal.

    Sincerely,

    Dr Aaron Ellison
    Senior Editor, Methods in Ecology and Evolution

    Reply to:
    Mr Chris Grieves
    Methods in Ecology and Evolution Editorial Office
    coordinator@methodsinecologyandevolution.org

    Why not become a member of the British Ecological Society? https://www.britishecologicalsociety.org/jointhebes

    Associate Editor Comments to Author:
    Associate Editor
    Comments to the Author:
    Thanks for dealing with the comments of the reviewers. Note that you'll have to properly archive your data before publication - github is not a stable archive so we suggest using dryad (which we cover the payment for) or zenodo (which you can link to your github) or similar. Chris in the MEE office will tell you more about this.

    Reviewer(s)' Comments to Author:

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  • pre-publication peer review (ROUND 1)
    Decision Letter
    2020/01/17

    17-Jan-2020

    MEE-19-11-849 Hyperoverlap: detecting biological overlap in n-dimensional space

    Dear Ms Matilda Brown,

    Thank you for submitting your manuscript to Methods in Ecology and Evolution. I have now received the reviewers' reports and a recommendation from the Associate Editor who handled the review process. Copies of their reports are included below. As you will see, the reviewers are positive about the value of the work but have also made a number of suggestions for improvement. I have considered your paper in light of the comments received and I would like to invite you to prepare a minor revision.

    In your revision, please make sure that you take full account of the above comments and those made in the reports below. Please note that Methods in Ecology and Evolution does not automatically accept papers after revision, and an invitation to revise a manuscript does not represent commitment to eventual publication on our part. We will reject revised manuscripts if they are returned without satisfactory responses to the reviewers' comments. When returning the revised paper, please show point-by-point how you have dealt with the various comments in the appropriate section of the submission form.

    Please return your revision by 07-Feb-2020. If you need longer, please let us know so we can update our system accordingly. Before resubmitting your manuscript, please read through the resubmission instructions below.

    We look forward to hearing from you in due course.

    Sincerely,

    Dr Aaron Ellison
    Senior Editor, Methods in Ecology and Evolution

    Reply to:
    Mr Chris Grieves
    Methods in Ecology and Evolution Editorial Office
    coordinator@methodsinecologyandevolution.org

    Associate Editor Comments to Author:
    Associate Editor
    Comments to the Author:
    (There are no comments.)

    Reviewer(s)' Comments to Author:
    Reviewer: 1

    Comments to the Corresponding Author
    This contribution is well written and succinct. The logic of the methodology is solid and comparisons with other approaches are clear. HYPEROVERLAP, with its ability to estimate simultaneously the ecological occupancy of organisms as two ecological hyperspaces and deal with low occurrence numbers (in one taxon), seems particularly valuable. The major drawback is that it provides purely qualitative results (overlap/ no overlap), lacking any quantitative measure of the degree of overlap. The authors discuss this and other limitations, however, and suggest routes of further development.

    I have neither the time nor expertise to evaluate the R package, so will not be able to comment on computational details of the methodology.

    I have just a few specific point for improving clarity of the presentation (below).

    Specific suggestions:

    1. Lines 29, 49, etc. Change ‘2017’ to ‘2018’ (throughout). (Early-View was 2017, final publication with page numbers is listed as Feb 2018.)

    2. Line 30. Change ‘which’ to ‘that’.

    3. Line 62. Replace first ‘them’ with ‘and then’. Comma not needed.

    4. Lines 264, 291, 294: Replace ‘which’ with ‘that’. These are restrictive-qualifier clauses, and as such, clarify your point. Check for this elsewhere. (Some journals do not enforce a distinction between ‘which’ and ‘that’; not sure about ME&E, but, in my opinion, worth doing regardless.)

    5. Line 325. Comma between independent clauses.

    6. Figure 4: This is a well designed figure, but ‘a’ and ‘b’ panels should be labelled. The caption should also explain that squares to the right of the diagonal decompose conflict squares (on the left side) into type of conflict, while no-conflict is decomposed on the left side... Also, why is Taxaceae absent from the axis of the upper figure (a)?

    Reviewer: 2

    Comments to the Corresponding Author
    Review of ‘Hyperoverlap: detecting biological overlap in n-dimensional space’
    General
    This is a very interesting manuscript that presents a new method and approach for investigating overlap among ecological (or other) entities. The authors present their concept succinctly, and demonstrate performance on an example dataset. The conceptual underpinnings of the new method are well explained, and the application of the algorithm is appropriate. Below, I provide feedback that is relatively minor in nature, and which mostly applies to presentation and contextualization. I hope the authors find these comments helpful.
    Abstract
    Line 17. Suggest that you delete ‘quantitatively’ and just leave this statement as ‘analyse’, as the answer from HYPEROVERAP is qualitative. This is one of the main features of this method (a qualitative answer).
    Line 19. Suggest revising to “detect qualitative overlap.....”
    Lines 27-30 and abstract in general. This is just my opinion, but I find these sorts of comparators to specific studies in abstracts irritating. HYPERVOLUME and HYPEROVERLAP approach similar questions differently, and the method that users choose to use will depend on the type of data they have, the question they are asking, what kind of answer they need (qualitative or quantitative), and how their data violates (or not) assumptions of these and other any other methods that are considered. Tell the reader in the abstract how your method is different, what obstacles it overcomes (compared to previous methods), and in what circumstances it will be especially useful as opposed to ‘it’s better than Blonder’s.”
    Main Manuscript
    Line 41. “The study of overlap is used in a broad range of studies….” This sentence could use a bit of work for grammar.
    Line 48. “…between these data…” Between what data?
    Lines 56-58. Expand on this more. Why might methods designed for prediction of entities not be well suited to descriptive data or questions?
    Line 59. In ecology? In other disciplines outside ecology? You haven’t yet defined SVM in the introduction.
    Line 75. “We analyse a real-world example to demonstrate these principles…” What principles?
    Line 84. “At present, machine learning methods provide the only viable approaches for analysing broad-scale, multidimensional data.” Compared to what? And what exactly do you mean by broad scale?
    Line 93. Awkward sentence; consider revising.
    Lines 94-97. It would be helpful for the reader who isn’t familiar with the NicheA software why they are not applicable outside ecology (and how this is a limitation for an ecological method….and paper). “Qiao et al” needs to go inside brackets.
    Line 110. Similar to above, define what you mean by broad-scale datasets. Broad spatial scale (i.e., landscape?)
    Lines 125-126. Consider citing an example, if possible.
    Line 130. You are arguing that the estimation of hypervolume overlap is simpler than the estimation of actual hypervolume, which could be made just a bit more clear by editing “is a much simpler task…” to: “is a much simpler task than….”. Also, why do you suggest that it is simpler?
    Line 180-181. Please cite the other hypervolume methods you are referring to here.
    Line 204. It’s not clear to the reader why this makes conifers an ideal group for evaluation.
    Line 208. Table 3 is missing (and there is no reference to a Table 2 anywhere – either in text or in the Tables & Figures section). Should this be a reference to supplemental information?
    Lines 217-218. Change ‘climate’ to ‘temperature,’ because precipitation (line 218) is part of climate.
    Line 219. When the authors say that they compared the overlap/non-overlap results, does this mean qualitatively compared? What exactly is meant by ‘requirements?’ Of the data?
    Line 230. In the first paragraph, consider adding a parallel sentence so the reader can easily compare the number of non-overlapping pairs of entities that results from HYPERVOLUME.
    Line 231. Consider replacing or deleting the word ‘significant.’
    Line 234. ‘Visualization confirmed all of the non-overlaps identified by HYPEROVERLAP.’ Revise and clarify – the authors are referring to the 133 non-overlaps that were classified as overlaps by HYPERVOLUME?
    Lines 235-236. Isn’t this Figure 4, not Appendix S4?
    Line 239. What further comparisons? Consider expanding in this part of your discussion how this particular result is applicable more generally to studies of overlap that involve species with constrained distributions.
    Line 254. Capitals needed for ‘HYPEROVERLAP’
    Line 250. I think what the authors want to state here is that the results were less stable than those produced by HYPEROVERLAP.
    Line 254. Computational advantage at higher dimensions, yes – but perhaps not at lower dimensions.
    Line 258. Suggest re-wording slightly to ‘reasons for conflicting results between….’
    Line 259. I think the authors mean Figure 3 here.
    Line 264. Specify what is meant by ‘this type’ – where HYPEROVERLAP finds no overlap but HYPERVOLUME finds overlap?
    Line 266. Suggest re-wording slightly to ‘we suggest that the result…’
    Line 269. The grammar of this first sentence is jarring – ‘narrowly endemic.’ Consider revising slightly.
    Lines 274-275. And does HYPEROVERLAP predict overlap for all pairs?
    Figure 6. ‘…the models produced by HYPERVOLUME do not intersect.’ Suggest expanding this/revising to state that the models produced by HYPERVOLUME do not overlap, despite obvious visual overlap.
    Lines 269-277. The reader is left wondering what the other causes for conflict were (see Line 273…”MOST of the these conflicts…”
    Line 280. Suggest italicizing ‘measure the amount’
    Line 288. Suggest ending this sentence at ‘did not find evidence of any in this study.’ The authors performed one study on one group of organisms with one set of 3 variables. It could be a bit of a stretch to say that these situations are rare in real-world data, and as the authors state, the situations can be identified with visualization so even if they are not rare it’s not an intractable problem.
    Lines 309-310. …’such as those described above.’ Consider being more specific at the end of this sentence so that the reader does not have to dig through the paragraph(s) to come up with which errors the authors are referring to here.
    Line 313-317. What do the authors mean by equivalent hypervolumes if this method does not measure or estimate size of hypervolumes? How can nestedness be further explored? Does the range expansion have to involve invasive species in order for it to be interesting? What about range expansion and contractions that are occurring as a result of climate change or other human perturbations? In general, this paragraph needs 1-2 more sentences that elucidate the ideas more fully.
    Line 322. How can HYPEROVERLAP be used to investigate likelihood of co-occurrence? At present the output is qualitative.
    Lines 321-323. This statement needs to be re-worded a bit so that the authors state that the HYPEROVERLAP method has applications in several possible disciplines and theoretical lines of inquiry, including…ecological partitioning seems like an obvious addition to the list.
    Lines 324-327. Suggest stating here that for many questions involving overlap, a qualitative answer is sufficient, and requires fewer assumptions…etc etc

    Decision letter by
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    Reviewer report
    2020/01/12

    Review of ‘Hyperoverlap: detecting biological overlap in n-dimensional space’
    General
    This is a very interesting manuscript that presents a new method and approach for investigating overlap among ecological (or other) entities. The authors present their concept succinctly, and demonstrate performance on an example dataset. The conceptual underpinnings of the new method are well explained, and the application of the algorithm is appropriate. Below, I provide feedback that is relatively minor in nature, and which mostly applies to presentation and contextualization. I hope the authors find these comments helpful.
    Abstract
    Line 17. Suggest that you delete ‘quantitatively’ and just leave this statement as ‘analyse’, as the answer from HYPEROVERAP is qualitative. This is one of the main features of this method (a qualitative answer).
    Line 19. Suggest revising to “detect qualitative overlap.....”
    Lines 27-30 and abstract in general. This is just my opinion, but I find these sorts of comparators to specific studies in abstracts irritating. HYPERVOLUME and HYPEROVERLAP approach similar questions differently, and the method that users choose to use will depend on the type of data they have, the question they are asking, what kind of answer they need (qualitative or quantitative), and how their data violates (or not) assumptions of these and other any other methods that are considered. Tell the reader in the abstract how your method is different, what obstacles it overcomes (compared to previous methods), and in what circumstances it will be especially useful as opposed to ‘it’s better than Blonder’s.”
    Main Manuscript
    Line 41. “The study of overlap is used in a broad range of studies….” This sentence could use a bit of work for grammar.
    Line 48. “…between these data…” Between what data?
    Lines 56-58. Expand on this more. Why might methods designed for prediction of entities not be well suited to descriptive data or questions?
    Line 59. In ecology? In other disciplines outside ecology? You haven’t yet defined SVM in the introduction.
    Line 75. “We analyse a real-world example to demonstrate these principles…” What principles?
    Line 84. “At present, machine learning methods provide the only viable approaches for analysing broad-scale, multidimensional data.” Compared to what? And what exactly do you mean by broad scale?
    Line 93. Awkward sentence; consider revising.
    Lines 94-97. It would be helpful for the reader who isn’t familiar with the NicheA software why they are not applicable outside ecology (and how this is a limitation for an ecological method….and paper). “Qiao et al” needs to go inside brackets.
    Line 110. Similar to above, define what you mean by broad-scale datasets. Broad spatial scale (i.e., landscape?)
    Lines 125-126. Consider citing an example, if possible.
    Line 130. You are arguing that the estimation of hypervolume overlap is simpler than the estimation of actual hypervolume, which could be made just a bit more clear by editing “is a much simpler task…” to: “is a much simpler task than….”. Also, why do you suggest that it is simpler?
    Line 180-181. Please cite the other hypervolume methods you are referring to here.
    Line 204. It’s not clear to the reader why this makes conifers an ideal group for evaluation.
    Line 208. Table 3 is missing (and there is no reference to a Table 2 anywhere – either in text or in the Tables & Figures section). Should this be a reference to supplemental information?
    Lines 217-218. Change ‘climate’ to ‘temperature,’ because precipitation (line 218) is part of climate.
    Line 219. When the authors say that they compared the overlap/non-overlap results, does this mean qualitatively compared? What exactly is meant by ‘requirements?’ Of the data?
    Line 230. In the first paragraph, consider adding a parallel sentence so the reader can easily compare the number of non-overlapping pairs of entities that results from HYPERVOLUME.
    Line 231. Consider replacing or deleting the word ‘significant.’
    Line 234. ‘Visualization confirmed all of the non-overlaps identified by HYPEROVERLAP.’ Revise and clarify – the authors are referring to the 133 non-overlaps that were classified as overlaps by HYPERVOLUME?
    Lines 235-236. Isn’t this Figure 4, not Appendix S4?
    Line 239. What further comparisons? Consider expanding in this part of your discussion how this particular result is applicable more generally to studies of overlap that involve species with constrained distributions.
    Line 254. Capitals needed for ‘HYPEROVERLAP’
    Line 250. I think what the authors want to state here is that the results were less stable than those produced by HYPEROVERLAP.
    Line 254. Computational advantage at higher dimensions, yes – but perhaps not at lower dimensions.
    Line 258. Suggest re-wording slightly to ‘reasons for conflicting results between….’
    Line 259. I think the authors mean Figure 3 here.
    Line 264. Specify what is meant by ‘this type’ – where HYPEROVERLAP finds no overlap but HYPERVOLUME finds overlap?
    Line 266. Suggest re-wording slightly to ‘we suggest that the result…’
    Line 269. The grammar of this first sentence is jarring – ‘narrowly endemic.’ Consider revising slightly.
    Lines 274-275. And does HYPEROVERLAP predict overlap for all pairs?
    Figure 6. ‘…the models produced by HYPERVOLUME do not intersect.’ Suggest expanding this/revising to state that the models produced by HYPERVOLUME do not overlap, despite obvious visual overlap.
    Lines 269-277. The reader is left wondering what the other causes for conflict were (see Line 273…”MOST of the these conflicts…”
    Line 280. Suggest italicizing ‘measure the amount’
    Line 288. Suggest ending this sentence at ‘did not find evidence of any in this study.’ The authors performed one study on one group of organisms with one set of 3 variables. It could be a bit of a stretch to say that these situations are rare in real-world data, and as the authors state, the situations can be identified with visualization so even if they are not rare it’s not an intractable problem.
    Lines 309-310. …’such as those described above.’ Consider being more specific at the end of this sentence so that the reader does not have to dig through the paragraph(s) to come up with which errors the authors are referring to here.
    Line 313-317. What do the authors mean by equivalent hypervolumes if this method does not measure or estimate size of hypervolumes? How can nestedness be further explored? Does the range expansion have to involve invasive species in order for it to be interesting? What about range expansion and contractions that are occurring as a result of climate change or other human perturbations? In general, this paragraph needs 1-2 more sentences that elucidate the ideas more fully.
    Line 322. How can HYPEROVERLAP be used to investigate likelihood of co-occurrence? At present the output is qualitative.
    Lines 321-323. This statement needs to be re-worded a bit so that the authors state that the HYPEROVERLAP method has applications in several possible disciplines and theoretical lines of inquiry, including…ecological partitioning seems like an obvious addition to the list.
    Lines 324-327. Suggest stating here that for many questions involving overlap, a qualitative answer is sufficient, and requires fewer assumptions…etc etc

    Reviewed by
    Cite this review
    Endorsed by
    Ongoing discussion (0 comments - click to toggle)
    Reviewer report
    2019/12/09

    This contribution is well written and succinct. The logic of the methodology is solid and comparisons with other approaches are clear. HYPEROVERLAP, with its ability to estimate simultaneously the ecological occupancy of organisms as two ecological hyperspaces and deal with low occurrence numbers (in one taxon), seems particularly valuable. The major drawback is that it provides purely qualitative results (overlap/ no overlap), lacking any quantitative measure of the degree of overlap. The authors discuss this and other limitations, however, and suggest routes of further development.

    I have neither the time nor expertise to evaluate the R package, so will not be able to comment on computational details of the methodology.

    I have just a few specific point for improving clarity of the presentation (below).

    Specific suggestions:

    1. Lines 29, 49, etc. Change ‘2017’ to ‘2018’ (throughout). (Early-View was 2017, final publication with page numbers is listed as Feb 2018.)

    2. Line 30. Change ‘which’ to ‘that’.

    3. Line 62. Replace first ‘them’ with ‘and then’. Comma not needed.

    4. Lines 264, 291, 294: Replace ‘which’ with ‘that’. These are restrictive-qualifier clauses, and as such, clarify your point. Check for this elsewhere. (Some journals do not enforce a distinction between ‘which’ and ‘that’; not sure about ME&E, but, in my opinion, worth doing regardless.)

    5. Line 325. Comma between independent clauses.

    6. Figure 4: This is a well designed figure, but ‘a’ and ‘b’ panels should be labelled. The caption should also explain that squares to the right of the diagonal decompose conflict squares (on the left side) into type of conflict, while no-conflict is decomposed on the left side... Also, why is Taxaceae absent from the axis of the upper figure (a)?

    Reviewed by
    Cite this review
    Endorsed by
    Ongoing discussion (0 comments - click to toggle)
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