whedon commented 2 years ago

Submitting author: @andrewmaclachlan (Andrew MacLachlan) Repository: https://github.com/andrewmaclachlan/CASA0005repo Version: 3.0 Editor: @ttimbers Reviewer: @TomasBeuzen @darribas Archive: 10.5281/zenodo.6375745

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/a05734775775d1ef968e582ce9a7cb17"><img src="https://jose.theoj.org/papers/a05734775775d1ef968e582ce9a7cb17/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/a05734775775d1ef968e582ce9a7cb17/status.svg)](https://jose.theoj.org/papers/a05734775775d1ef968e582ce9a7cb17)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@TomasBeuzen, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @ttimbers know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @TomasBeuzen

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: 3.0
[x] Authorship: Has the submitting author (@andrewmaclachlan) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @darribas

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: 3.0
[x] Authorship: Has the submitting author (@andrewmaclachlan) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @TomasBeuzen it looks like you're currently assigned to review this paper :tada:.

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/jose-reviews:

watching

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

TomasBeuzen commented 2 years ago

@ttimbers - I can't tick the check-boxes above, presumably because I didn't accept the invite in time and now the link has expired 😄 I'm keeping a copy of the checklist below for now, but can remove it once we figure out the issue.

@andrewmaclachlan - firstly, excellent work putting together this course. I can see that a lot of hard-work went into creating this content and I think it's an excellent resource for other in the field. I provide general comments below:

Review Comments

Content, Pedagogy, Instructional Design

All excellent and I don't see anything in particular to change here. The content is comprehensive, well presented, and uses modern tools (e.g., tidyverse). Admittedly I've been using Python for all my geospatial data analysis over the last few years, so not 100% sure what's new with R spatial world, but all the common tools are here, spatstat, sp, sf, etc.
I really enjoy the casual but informative style of teaching. I may be a little biased because it's quite similar to my own teaching style, but I find the conversational nature of the text, backed-up liberally with metaphors, examples, figures, call-outs, etc. to be an effective way of teaching what can be quite complex topics. Kudos.
I was a little sad to see interpolation dropped from the most recent version of the material. It's something I use frequently in my day-to-day as a data scientist, e.g., kriging, areal interp from one set of polygons to another, etc. Not saying anything needs to be changed here, just writing down my thoughts 😄
There are various spelling mistakes throughout the text (the most recent I saw was 8.10.1 Calucating tempearture from Landsat data). Again, this is completely understandable with such a large volume of material and I don't see any reason to need to go and correct every single mistake, just pointing it out as something to be aware of in future iterations.
May be worth updating to the new pipe operator? |>

Jose Paper

[x] The only thing missing is a reference to what the author's expertise is in the area, which is one of the review checklist items (Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?). Not sure how important that is to have though and it didn't bother me as the quality of the material speaks for itself.

Documentation

There are a few improvements I'd like to see here:

[x] The README is the first place I'll often visit when looking at other's material. I think it needs to include at least a brief paragraph (1-2 sentences) about what the material covers and who the target audience is.
[x] I would like to see clear instructions for how to install the material locally and develop it. Imagine someone wanting to use it with minimal experience with GitHub/Bookdown/etc, e.g., 1. Clone this repository git clone git@github.com:andrewmaclachlan/CASA0005repo.git. 2. Install R and RStudio. 3. Install Bookdown.... Or more helpful would be a Docker image - I wouldn't require it to pass this review but having personally worked with bookdown to build course materials like this, it's a life-saver for your future self and others trying to use your material, so worth considering.
[x] There are no contributing guidelines, as far as I could see. I note "Feedback" forms in the material itself. But I think some guidelines in the README of main repo are needed, i.e. are you accepting PR's or issues? If so, how would you like them structured, or what kind of things can someone contribute?
[x] There's an MIT license for the repo. It gets a little grey when sharing a repo with both original code and content. I usually associate an MIT license with software, but not necessarily written content, figures, etc. A CC license might be a more suitable option here? Or worth considering as an additional license that covers the content. Apologies if this is already covered somewhere and I missed it.
[x] Figures throughout the material are missing captions. In particular, I'm missing references to original sources. I note that you acknowledge these various sources in the welcome page, but as readers may not read that page, I think it's appropriate to add references to original figures when they are used in the text.

Temporary Checklist

(Until I get permissions to modify the checklist at the beginning of the issue thread)

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: Does the release version given match the repository release (2.0)?
[x] Authorship: Has the submitting author (@andrewmaclachlan) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

andrewmaclachlan commented 2 years ago

@TomasBeuzen Thanks so much for that detailed review of the submission, it really means a great deal to have someone external review our teaching resources. I agree with all your comments and will make the necessary changes. We decided to drop interpolation as we wanted to keep the content focussed on the what would be assessed in the new open book exam, but I was sad to see it go. I might reinstate it, to an extent, in my new MSc module called remotely sensing cities and environments.

ttimbers commented 2 years ago

@darribas - checking in on when you think you might be able to review this manuscript? Thanks again for agreeing to serve as a reviewer for this!

darribas commented 2 years ago

Hello! Apologies! I'll get to this this week or early next at the latest!

darribas commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

darribas commented 2 years ago

Comments by @darribas

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

Overall, all good. A couple of (very) minor point from my side:

I didn't find a release tag that ensured the materials on the repository were pinned to a version (e.g. 2.0). It might be good for historical reasons if someone would like to examine the version the paper is based on

[x] Repository: Is the source for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: Does the release version given match the repository release (2.0)?
[x] Authorship: Has the submitting author (@andrewmaclachlan) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

Again, this is very good in general. The statement of need in the paper makes a clear case. I wonder if parts of that blurb might even be ported to the "Welcome" or "Hello GIS" sections of the website.

One point where I am surprised I didn't find much is on the installation of the stack. There's clear documentation to install RStudio but, in a course like this, it's only half the job. From my own teaching experience, installing some of the libraries for geospatial (e.g. sf, rgdal) can be rather tricky, and students usually run into issues if they already have some versions and need updates, etc. The book mentions an online alternative at UCL but, for non-UCL students I wonder if a bit more signposting could be added? Or at least pointing to external install guides that'd help them?

On the topic on the stack, I tried several times to build the Binder instance and all resulted in failure to build. It is not critical but, if it doesn't work, is it work mentioning or removing?

I did not find a clear document detailing community contributions. This may not be as important as for an open source library, but it might be nice to have something that tells people how you expect them to contribute if they want (e.g. submit issues, PRs, etc.). I have personally found very useful: https://github.com/UofTCoders/rcourse/blob/master/CONTRIBUTING.md

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

I absolutely love the approach taken and the style. I think it is very conducive to build an inclusive environment that shows the students programming is not an obscure practice that requires lots of hard skills but is something everyone can try and enjoy. Plus, those music recommendations!

If there is something I miss a bit on is more guidance for instructors who want to take the materials and make them their own, or teach off them. I don't think this needs to be changed for the paper to be accepted at all, I'm just suggesting it in case the authors consider it might be useful to have an additional section or notebook at the end geared more for instructors than students. I think it'd help the course gain (even) more traction.

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?

Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

See some of my comments above, I think this is one of the key strengths for the course.

Another aspect I really enjoyed and I think contributes to the "inclusive vibe" of the course is the graphics.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

ttimbers commented 2 years ago

Thank-you very much for your review @@darribas!

@andrewmaclachlan - do you have an estimate on when you might expect to have a revision of this ready?

ttimbers commented 2 years ago

@andrewmaclachlan - pinging you on this again. If you think you may be unable to work on this for a while, please let me know and I can put a pause label on this review. Thanks.

andrewmaclachlan commented 2 years ago

Hi, sorry for the delay and thanks so much to both reviewers. I'm hoping to get to the comments in just over a week, but they may run over to the New Year as the University closes. But hopefully it won't be any longer than a few weeks.

andrewmaclachlan commented 2 years ago

Hi there, just a small update from me. I've gone through and addressed the majority of points raised by the reviewers with just a few left to do - i'm hoping to finish it off next week and then i'll give a full response.

andrewmaclachlan commented 2 years ago

Hi there, please see the response to @TomasBeuzen's review below. @darribas gave a few similar comments, but i'll address those in full over the next few days as well.

Jose paper

[ ] The only thing missing is a reference to what the author's expertise is in the area, which is one of the review checklist items (Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?). Not sure how important that is to have though and it didn't bother me as the quality of the material speaks for itself.
The paper now has a resource story section
Documentation
[ ] The README is the first place I'll often visit when looking at other's material. I think it needs to include at least a brief paragraph (1-2 sentences) about what the material covers and who the target audience is.
The README has been updated with a description, target audience, installation, license and contribution sections
[ ] I would like to see clear instructions for how to install the material locally and develop it. Imagine someone wanting to use it with minimal experience with GitHub/Bookdown/etc, e.g., 1. Clone this repository git clone git@github.com:andrewmaclachlan/CASA0005repo.git. 2. Install R and RStudio. 3. Install Bookdown.... Or more helpful would be a Docker image - I wouldn't require it to pass this review but having personally worked with bookdown to build course materials like this, it's a life-saver for your future self and others trying to use your material, so worth considering.
I did create a binder, more as an experiment, but as the material is rather large it would take a long time to load and in some instances wouldn't - i think Dani experienced this. As a result i've removed it and instead added a section on the bookdown website about how to adpot the course with specific instructions that include a renv snapshot which will install the correct version of the packages used. https://andrewmaclachlan.github.io/CASA0005repo/external-usage.html#how-to-adopt-this-course
[ ] There are no contributing guidelines, as far as I could see. I note "Feedback" forms in the material itself. But I think some guidelines in the README of main repo are needed, i.e. are you accepting PR's or issues? If so, how would you like them structured, or what kind of things can someone contribute?
I have added a how to contribute section in the bookdown website, and the README links to it - https://andrewmaclachlan.github.io/CASA0005repo/external-usage.html#how-to-contribute.
[ ] There's an MIT license for the repo. It gets a little grey when sharing a repo with both original code and content. I usually associate an MIT license with software, but not necessarily written content, figures, etc. A CC license might be a more suitable option here? Or worth considering as an additional license that covers the content. Apologies if this is already covered somewhere and I missed it.
I've added a badge and licence section on the REAME (changing it to CC and not MIT), included a license file (see the about section) and updated the bookdown website with the same license.
- [ ] Figures throughout the material are missing captions. In particular, I'm missing references to original sources. I note that you acknowledge these various sources in the welcome page, but as readers may not read that page, I think it's appropriate to add references to original figures when they are used in the text.
I've added figure captions under each figure where they have been taken from an original source.

General checks

[ ] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
See comments above, i have added this to the repo. https://github.com/andrewmaclachlan/CASA0005repo/blob/master/LICENSE

Documentation

[ ] A statement of need: Do the authors clearly state the need for this module and who the target audience is? Installation instructions: Is there a clearly stated list of dependencies?
There is a statement of need in the paper and i've added a target audience section to the README. The package section in the bookdown website holds all the package info, that can be replicated with renv
[ ] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
Addressed above, yes more specific adoption instructions
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support
Yes, clear contribution guidance is provided on the bookdown website - see link above.

Jose paper

[ ] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
Yes, i've added this to the paper.

andrewmaclachlan commented 2 years ago

@darribas see below the responses to the points in your review.

Thanks again to both reviewers for their useful insight. Let me know if any further clarification is needed. The edits have been made to the live version of the book - https://andrewmaclachlan.github.io/CASA0005repo/

General checks

[ ] Version: Does the release version given match the repository release (2.0)?
I did create the version myself which probably wasn't the best word to use. Version implies software to me, but i wanted to show and document how the content has been developed over the years. To rectify this i've added an updates section to the paper and README which reflects my intention for doing it in the manner I have. I've also changed the version section on the bookdown website to Updates. I could create the "release" area in GitHub if you think that would be better. I'd like to maintain having a repo and bookdown website for each year though as it's useful for me to look back on.

Documentation

I considered editing the statement of need and including it in the welcome section on the index but i felt it didn't read well, so I've included the whole statement of need.
Installing packages, the software installation section was actually written for when we used to use the computer cluster rooms. On the software installation I've added a lot more information about troubleshooting package issues (my process at least) and some reference links. Adam and i both use Windows machines the Mac sections are there for reference but usually there is some slight variation on the problem each year. A while ago i did manage to build the book with Travis and then GitHub actions (using multiple operating systems) but it caused more hassle that I've since spent developing the material. I'll keep a better log of how we resolve Mac issues going forward.
The binder instance was more of test of concept for me, however, i see your point so have removed it. Instead there is an renv snapshot which holds all the package information in and instructions to load it in: https://andrewmaclachlan.github.io/CASA0005repo/external-usage.html#how-to-adopt-this-course. We cover renv in week 4 content.
[ ] Installation instructions: Is there a clearly stated list of dependencies?
There is a list of packages used on the bookdown website and also now the renv snapshot.
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support
Yes, this was also picked up by Tomas. I've added a section on how to contribute following your suggestion. The README links to this section too: https://andrewmaclachlan.github.io/CASA0005repo/external-usage.html#how-to-contribute

Pedagogy / Instructional design

Tomas also commented about guidance for taking the materials and using them. I've added a section called how to adopt this course in the bookdown website. The README also links to this for students and for instructors.

TomasBeuzen commented 2 years ago

Thanks for addressing all my comments @andrewmaclachlan and congrats again on putting together a great course!

@ttimbers - I'm happy with how my review has been addressed 👍 🚀

ttimbers commented 2 years ago

Thanks so much @andrewmaclachlan for your revisions and @TomasBeuzen for confirming that your reviews have been addressed! As a next step I will rebuild the PDF and check it over, and then reply with further next steps.

ttimbers commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ttimbers commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

No archive DOI set. Exiting...

ttimbers commented 2 years ago

@andrewmaclachlan - I see we have not yet archived this. What we need for you to do next step is to archive this on Zenodo, issue a tagged release on the repository and generate a DOI. Please me know if I can assist you in any way on this. Once you have that, I will recommend accept again.

andrewmaclachlan commented 2 years ago

Thanks @ttimbers I have done that (i think!): DOI: 10.5281/zenodo.6375745

ttimbers commented 2 years ago

@whedon set 10.5281/zenodo.6375745 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.6375745 is the archive.

ttimbers commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

ttimbers commented 2 years ago

@openjournals/jose-eics - I ran @whedon recommend-accept but it seems stuck. It did not generate the PDF nor check the DOI's. Could you please provide some guidance as to how I should proceed here? Many thanks!

labarba commented 2 years ago

It seems neither of the reviewers has used the "official" checklist at the top of this review issue. This seems a bit messy. What happened?

labarba commented 2 years ago

@whedon re-invite @TomasBeuzen

whedon commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

labarba commented 2 years ago

@whedon re-invite @TomasBeuzen as reviewer

whedon commented 2 years ago

OK, the reviewer has been re-invited.

@tomasbeuzen please accept the invite by clicking this link: https://github.com/openjournals/jose-reviews/invitations

labarba commented 2 years ago

@whedon re-invite @darribas as reviewer

whedon commented 2 years ago

The reviewer already has a pending invite.

@darribas please accept the invite by clicking this link: https://github.com/openjournals/jose-reviews/invitations

TomasBeuzen commented 2 years ago

It seems neither of the reviewers has used the "official" checklist at the top of this review issue. This seems a bit messy. What happened?

I was unable to edit the original checklist so just copy-pasted it into a new comment. I accepted the new invite and was able to edit the original checklist now. Should be good to go from my end @ttimbers 😄

labarba commented 2 years ago

I see that @ttimbers added a checklist for the second reviewer in a separate comment. Is @darribas able to check off items there?

Normally the checklist is added automatically by whedon at the top of the thread when starting the review. I checked the Pre-Review issue to figure out why that didn't happen here. Bear in mind @ttimbers is a new editor. I think that running @whedon assign TomasBeuzen as reviewer actually swapped the original assignment and we needed @whedon add TomasBeuzen as reviewer to keep @darribas. But I'm not sure because I see both reviewers listed at the top of the Pre-Review.

labarba commented 2 years ago

Ah! @ttimbers, I see you manually edited the reviewers in the top comment of the Pre-Review. I think the @whedon add command is what we needed here.

ttimbers commented 2 years ago

Thanks so much for clearing all this up @labarba, and thanks for your patience @andrewmaclachlan ! I am new here in this role 😅

darribas commented 2 years ago

Hello! @ttimbers / @andrewmaclachlan sorry I've been out of the loop, is there any task on me to re-review? Happy to do it.

labarba commented 2 years ago

@darribas Can you check off items in this checklist?

ttimbers commented 2 years ago

@darribas - a gentle ping to follow-up on checking off the items in this checklist: https://github.com/openjournals/jose-reviews/issues/141#issuecomment-937324211

darribas commented 2 years ago

Hello, sorry for the slow movement on this front. I've checked all my original comments and @andrewmaclachlan answers and I'm happy with what it looks like now. I've ticked the missing boxes on the original comment but not sure if I need to do anything else, let me know and I'll go ahead. Congratulations @andrewmaclachlan on the course, it's fantastic!!!

labarba commented 2 years ago

@ttimbers @darribas — I cleaned up this review issue a little bit. There seemed to be some confusion as to where the reviewer should tick off items in their review checklist. When things start smoothly from the Pre-review issue, each reviewer gets a checklist in the top-most comment of the Review thread. If one reviewer is added later, we add the checklist manually by editing that top comment. Here, a checklist had been added as a separate comment down the thread, which required lots of scrolling and things getting lost. Thank you for your patience!

labarba commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/jose.00042 is OK
- 10.1016/0034-4257(82)90043-8 is OK
- 10.1016/B978-008044910-4.00447-8 is OK
- 10.1080/10618600.2017.1384734 is OK
- 10.1016/B978-044452701-1.00067-3 is OK
- 10.1080/22797254.2018.1474494 is OK
- 10.1080/13658816.2012.743664 is OK
- 10.1002/9781118944707.ch10 is OK
- 10.1080/00220480009596759 is OK
- 10.1016/j.isprsjprs.2015.10.012 is OK
- 10.1201/9780203730058 is OK

MISSING DOIs

- 10.1214/aos/1176344552 may be a valid DOI for title: Bootstrap methods: another look at the jackknife

INVALID DOIs

- None

whedon commented 2 years ago

:wave: @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/90

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/90, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

ttimbers commented 2 years ago

Thank-you for your help straightening this out @labarba and apologies to the author and reviewers for the mistakes I made earlier on in setting up the review that slowed things down. As @labarba said, this was my first review.

labarba commented 2 years ago

I notice that the tag in the release is jose: https://github.com/andrewmaclachlan/CASA0005repo/tags …whereas the version here was set as 2.0. These two should match. Which one do you prefer, @andrewmaclachlan?

andrewmaclachlan commented 2 years ago

I changed the tagged release to 3.0 as in the text it now says: This is the third iteration of the practical book - https://andrewmaclachlan.github.io/CASA0005repo/external-usage.html

openjournals / jose-reviews

[REVIEW]: An Applied Geographic Information Systems and Science Course in R #141

Status

Reviewer instructions & questions

Review checklist for @TomasBeuzen

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

Review checklist for @darribas

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

Review Comments

Content, Pedagogy, Instructional Design

Jose Paper

Documentation

Temporary Checklist

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

Jose paper

Documentation

General checks

Documentation

Jose paper

General checks

Documentation

Pedagogy / Instructional design