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JOSS Review: Improve documentation on geo-processing steps and its effects on the original geometries #53
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Thank you very much for these suggestions @Jo-Schie! I'll have a think about this and begin incorperating your feedback later this week. |
Sorry, I've been swamped and am only getting to this today. |
Thanks again for providing all these suggestions @Jo-Schie! I've created a PR with all the changes to incorporate your feedback (see #57). To help make it clear exactly how I've addressed each of your points, I've responded to each of them below (separately) and copied in the updated text from the PR. Since JOSS policies favor shorter publications [1], I've tried to address several of the comments in the same sentence or paragraph. I think I've responded to all your points, but please let me know if I have missed anything?
[1] JOSS policies state that the manuscript should be a "short paper" and less than 1000 words (https://joss.readthedocs.io/en/latest/submitting.html) [2] JOSS policies state the "the paper should not include software documentation such as API (Application Programming Interface) functionality, as this should be outlined in the software documentation" (https://joss.readthedocs.io/en/latest/review_criteria.html). |
Hi @jeffreyhanson : Thanks for the edits. Some quick remarks: -> What if there is an overlap of "old area/soft protection" with "new area/strong protection"? Is there some decision tree? If so it would be useful to illustrate it or link to the relevant literature that suggests the decision hierarchy at this specific point in the manuscript. As to 1). As to 7) I think an alternative could be that you include some graphics in your documentation (as in my comment above) that show how geometries are affected by different settings in the package. Nevertheless I think an interactive map is much better for the user to explore what happens then some graphics. I am thinking of this as a user who is interested in precise area information and I myself used your package with the default settings for quite some time without really checking what happened to the areas (because R is also not very convenient for that). The package vignette might be a great place to make users aware of that since it is the most relevant document that users of your package reference to. |
@Jo-Schie - thanks for getting back to me so quickly, I really appreciate it! I'll respond to each of your follow up comments below (seperately).
References Coetzer KL, Witkowski ET, & Erasmus BF (2014) Reviewing Biosphere Reserves globally: Effective conservation action or bureaucratic label? Biological Reviews, 89: 82--104. Runge CA, Watson JEM, Butchart HM, Hanson JO, Possingham HP & Fuller RA (2015) Protected areas and global conservation of migratory birds. Science, 350: 1255--1258. Updated vigntte html file is available here: wdpar.zip |
@Jo-Schie, I just wanted to follow up and ask if the PR address your concerns on this issue? |
Hi @jeffreyhanson . I did not really realize that you'd already worked on this. I put it on my todo list and will come back asap. |
No worries - thanks! Please let me know if anything's not clear and I'll get back to you as soon as I can. |
@Jo-Schie, I just wanted to follow up and ask if you'd a chance to go through the PR? |
@Jo-Schie, it's been over a month since I originally created the PR to address your feedback, is there anything I can do to help make it easier for you to review it? |
hi @jeffreyhanson. Documentation looks very good to me and I fully understand that you do not want to add the mapview package if it creates a dependency for the package. Also it makes sense to have the processing steps in the function documentation and I think you do explain it in a great level of detail. Sorry for the delays. Happy to close the issue now. |
Awesome - no worries - thank you very much! |
- Update paper for JOSS submission (fix #53, fix #54, fix #62). - Update vignette with new section on local scale analyses (fix #53). - Update `wdpa_fetch()` function to use the webdriver package for obtaining data (replacing Rselenium package as a dependency) (fix #63). - Update `st_repair_geometry()` to be more robust. - Fix failing tests for `st_repair_geometry()` function. - Update documentation for `wdpa_clean()` function. - Fix broken URL in vignette. - Fix CI.
Hi @jeffreyhanson .
I think it could be helpful for users to extend a little the documentation on the internal geo-processing steps and what they actually do to the data (geometries). This should be part of the vignette, but also of the paper (which so far very much focuses very much on describing the need, but not the internals of the package).
From my first test, there are a few things that should be discussed:
wdpa_clean
. -> maybe this could be also a graphical representation.wdpa_clean
affect the original geometries?If possible, I would recommend that you use interactive maps in your vignette instead of the map that you plotted (which does not allow to really see anything). Below you can find some sample code and some screenshots that might allow users to understand more intuitively what is done with the data. You could use and maybe extent this a little bit.
Original Data
Default Settings
Higher Geometry precision
HIgher geometry precision and overlaps
Link to review
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