joss-reviews
joss-reviews copied to clipboard
openjournals
[PRE REVIEW]: The ppmData R-package for setting up spatial point process models
Submitting author: @skiptoniam (Skipton Nicholas Charles Woolley) Repository: https://github.com/skiptoniam/ppmData Branch with paper.md (empty if default branch): joss_submission Version: v1.0.0 Editor: @elbeejay Reviewers: Pending Managing EiC: Arfon Smith
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/b5288481bbd5f97602a71ce7b66273ef"><img src="https://joss.theoj.org/papers/b5288481bbd5f97602a71ce7b66273ef/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/b5288481bbd5f97602a71ce7b66273ef)
Author instructions
Thanks for submitting your paper to JOSS @skiptoniam. Currently, there isn't a JOSS editor assigned to your paper.
@skiptoniam if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).
Editor instructions
The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:
@editorialbot commands
Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Couldn't check the bibtex because branch name is incorrect: https://github.com/skiptoniam/ppmData/tree/joss_submission
Couldn't check the bibtex because branch name is incorrect: https://github.com/skiptoniam/ppmData/tree/joss_submission
Software report:
github.com/AlDanial/cloc v 1.88 T=0.03 s (970.7 files/s, 133566.1 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
R 16 342 439 1141
C++ 4 166 27 698
XML 1 0 2 441
TeX 1 34 0 356
Markdown 3 61 0 177
C/C++ Header 2 44 0 126
YAML 3 20 9 90
Rmd 2 50 106 74
-------------------------------------------------------------------------------
SUM: 32 717 583 3103
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Just had a search through your list of reviewers, here are some suggestion: mhesselbarth; lionel68; OwenWard
@editorialbot invite @elbeejay as editor
:wave: @elbeejay – I realize this is a little left-field for you but would you be willing to edit this submission for us?
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@skiptoniam thank you for this submission to JOSS. Before asking any potential reviewers to have a look and decide if they are up to reviewing this submission, I have a number of comments and suggestions relating to the text of the manuscript. I encourage both you and your co-author to review the text of the manuscript after making any revisions before letting me know you are ready to proceed. To have the bot regenerate a PDF, write a comment that begins with @editorialbot generate pdf. My comments and suggestions are below and refer to line numbers in the PDF as generated above:
- Figure 1 runs off the page, please adjust its width using syntax like:
{ width=20% } - L 9: Do you mean to say "process models" rather than "processes models"?
- L 16: Should the "m" in "models" be capitalized as it is part of the IPPM acronym?
- L 17: I suggest changing to either "spatially referenced" or "spatial reference"
- L 26: Consider changing to read "package is setup" rather than "was" (similar suggestion for other instances referring to package design, as hopefully the software will continue to evolve and be maintained/developed)
- L 33: capitalize "Poisson"
- L 40: seems like "involved" should be "evolved"
- L 41: I'd suggest changing "process" to "processes" here
- Should it be "process" or "processes" in the IPPM acronym? Also is there a P missing in the acronym (Poisson Point Process)? The definition seems inconsistent between line 16 and the first subsection within Methods
- L 48: I found this sentence to be unclear, particularly the terminology "pattern in which n observed locations, say, makes over a spatial window" - is this a pattern made over some spatial window?
- L 57: should "point" be pluralized: "of the m quadrature points"?
- L 88: I would suggest deleting "which" after "rQuasi function"
- L 90: seems like a typo, "non" should be "not"?
- L 97: delete "While" or alter the structure of these sentences
- L 98: I would add words after "The reason for this" so that "this" is clear. For example: "The reason for this difference" - later in the sentence I think it either needs to be "due to the computational complexity of calculating" or "due to the computational complexities associated with calculating" or similar
- L 103: there is a period missing at the end of the sentence here
- L 117: "a" to "an" - I also found the next sentence to be unclear, especially the phrasing "under this scenario pass"
- L 119: consider changing "not distinguishing" to "not unique to"
- L 128: typo "the the"
- L 134, 136, 150: should be "an inhomogeneous" not "a"
- L 163: consider deleting "be" after "could"
- Overall, be consistent with the use of back-quotes ` to typeset references to code objects. For example sometimes ppmData is surrounded by back-quotes, other times it isn't.
Thank you, Jay
@elbeejay thanks so much for the suggestions and edits. I've tried to clean up those paper. I have also remove a bit of text including the future work section as the paper is fairly long. I was using rmarkdown to build the document, so hopefully the .md is OK now.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks for making some revisions @skiptoniam - I'll re-read and begin to contact reviewers this week
@skiptoniam I still have a number of questions relating to the text of the manuscript, some of which are repeats of my previous comments that were not addressed.
- L 9-10: Shouldn't "e.g.," come before the references? Re-order this in the markdown file to read:
[e.g. @baddeley_practical_2000; @cressie_statistics_1993]and this should be resolved - L 18, 33-34, 46, 48: Is there a reason the IPPM acronym isn't being used in these instances?
- L 40: Should the word "involved" be "evolved" in this sentence?
- L 42: Should there be an "a" before "how" in this sentence? Should it be "an" rather than "a" preceding "inhomogeneous"?
- L 52: Why is "for example" in parentheses? Typically this would be written as a clause, e.g., "for particular spatial locations, for example, \Lambda_i ..."
- In the caption for Figure 1 is there a reason this "ppmData" is not typeset with backquotes?
- L 101: Is "be come" intentionally written this way? I'd have expected the single word "become"
- L 126: Is the repetition of the word "the" intentional in this sentence? This was a previous comment so I wanted to ask again, please let me know if this is intentional, maybe it is supposed to be "that the"?
- Figure 3: Is "recoreded" a typo? Maybe "recorded" is the intended word?
Again I'll encourage both you and your co-author to review the text of the manuscript after making any revisions. For the sake of clarity, please reply directly to any of the above questions if you are not planning to change the text in response to a given query. To have the bot regenerate a PDF, write a comment that begins with @editorialbot generate pdf.
Thanks!
@skiptoniam following up here to ask if you have any outstanding questions or problems making these revisions to the text of the paper. Thanks!
Jay
@skiptoniam I have marked this pre-review issue as "paused" as I have not heard from you in several weeks on these minor revisions to the paper text. If I do not hear from you in another 2 weeks (by September 20) I will be closing this issue and you will have to re-submit when you are ready.
@elbeejay sorry I was leave the last few weeks. Back at it now. I'll try make those changes asap
Hi @elbeejay,
@skiptoniam I still have a number of questions relating to the text of the manuscript, some of which are repeats of my previous comments that were not addressed.
- L 9-10: Shouldn't "e.g.," come before the references? Re-order this in the markdown file to read:
[e.g. @baddeley_practical_2000; @cressie_statistics_1993]and this should be resolved This has been resolved. I removed the e.g all together
- L 18, 33-34, 46, 48: Is there a reason the IPPM acronym isn't being used in these instances? I decided to remove the acronym for clarity. I'm not normally a fan of them, but it is quite a mouthful, so decided to use them originally. I have removed for now.
- L 40: Should the word "involved" be "evolved" in this sentence? Fixed. Good catch.
- L 42: Should there be an "a" before "how" in this sentence? Should it be "an" rather than "a" preceding "inhomogeneous"? I have fixed this sentence.
- L 52: Why is "for example" in parentheses? Typically this would be written as a clause, e.g., "for particular spatial locations, for example, \Lambda_i ..." I'm not sure why I did that. The clause reads better :)
- In the caption for Figure 1 is there a reason this "ppmData" is not typeset with backquotes? Fixed with a bit of latex.
- L 101: Is "be come" intentionally written this way? I'd have expected the single word "become" Typo. Fixed
- L 126: Is the repetition of the word "the" intentional in this sentence? This was a previous comment so I wanted to ask again, please let me know if this is intentional, maybe it is supposed to be "that the"? Apologies, that was an oversight by me
- Figure 3: Is "recoreded" a typo? Maybe "recorded" is the intended word? Typo. I have reworded this caption
Again I'll encourage both you and your co-author to review the text of the manuscript after making any revisions. For the sake of clarity, please reply directly to any of the above questions if you are not planning to change the text in response to a given query. To have the bot regenerate a PDF, write a comment that begins with @editorialbot generate pdf. We have looked over it again. Thank you for all your careful and considered edits, it is greatly appreciated.
Thanks!
Once again apologies for the delay, I should have let you know I was away.
Regards,
Skip.