[PRE REVIEW]: treesiftr: An R package and server for viewing phylogenetic trees and data about jose-reviews HOT 36 CLOSED

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👋 @wrightaprilm — Thank you for your submission to JOSE. I see that you describe this as an R package for visualizing phylogenetic trees, and that the package has been used in support of workshops and a university course.

As described, however, this submission appears to be unsuitable for publication on its own. I point you to the JOSE Author Guidelines, which explains the type of submissions we consider.

JOSE accepts two types of submissions: (1) computational learning modules, created as open educational resources (OER), and (2) open-source software, created as educational technology or infrastructure.

In the first type, what would fit is a written-out tutorial, or a learning module used within the graduate course you mention in the paper, which uses this package such that the interactive computational parts are essential to complete the learning objectives.

Note that the guidelines also say:

Computational learning modules should be complete and immediately usable for self-learning or adoption by other instructors.

In the second type (software submissions), the JOSE scope covers educational technology or infrastructure software (e.g., auto graders, course-management solutions, etc.).

We have seen in the first few submissions some software that's meant to be used in the classroom, to support specific teaching contexts. We (the editors) have been discussing how to adapt to this demand, and are still working this out. But one thing we quickly agreed on is that this type of software can only be useful to other instructors (or self-learners) if it contains fully worked-out examples as part of the documentation.

Furthermore, the expectations for the JOSE paper are greater than shown in your submission. Note that a required section is the Statement of Need:

A key component of the JOSE paper is a statement by the authors, explaining the contribution made by the submitted artifacts to computationally enabled teaching and learning, and describing how they might be used by others.

Further below, it says:

The goal is that someone reading the JOSE paper has enough information to decide if they'd be interested in adoping the learnig module or software. Readers will want to know how the content/software has been used, and how they would adopt it. They may also want to be persuaded that the authors have put careful work on creating the material, and have experience teaching with it.

Please let me know what you want to do with the submission, given this feedback. For now, it's not ready to go into review.

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Well, shoot. I wish the innappropriateness of the package would have come up in my presubmission inquiry before I went to the trouble of getting the tutorial files and submission files in order.

I'll withdraw and submit it to a journal that supports more specific educational tutorials in my field.

Thanks!

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I'm sorry I missed that issue conversation.

It looks like @moorepants was pointing you to make a submission that combines the software with the accompanying learning materials, together, as a learning module.

It's possible I'm missing something. I'm not an R person and I can't view the files directly on the repo, so I don't know if you have written-out learning materials there. If you do, perhaps the README and the paper need to explain how a reader would approach this.

Are you submitting learning materials, in addition to the package? If yes, how would I inspect the material?

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@labarba, @wrightaprilm submitted openjournals/jose#20 for a pre-inquiry and I took it upon myself to respond.

I reviewed that inquiry and saw an educational software package, worksheets, and slides that looked like a reasonably complete set of teaching materials. Furthermore, the content was written as plain text sources. I told her it looked valid to submit based on these things. Her preliminary question was wrt to the fact that the submission was a mixture of both types of submissions we accept. I suggested submitting it as an educational software package and to treat the learning module materials as supplementary materials.

@wrightaprilm I apologize for leading you astray. I wrongly assumed that software packages designed to facilitate teaching and learning were valid. It seems that only things that are considered infrastructure are allowed. Maybe there are some things that can be added or improved to meet the submission criteria.

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I'm also not an R person - but alas, it seems to be the more popular language in my field. I've been keeping the worksheets in my vignettes folder.

I'm not sure if you have R Studio installed, so I made PDF files for a worksheet for use with the web-based GUI and a [worksheet](https://github.com/wrightaprilm/treesiftr/blob/master/vignettes/02-treesiftr-advanced.pdf] for the RStudio exercise. I keep the visual outputs collapsed in the actual .Rmd files for students, but I've included them for you in the PDF here. There's also a slide deck in inst/slides, which I figured would be supplemental. Unfortunately, they don't make too much sense as html renders, unfortunately, as the ability to execute code within is a little bit integral. So they're harder to view without RStudio.

Anyway, it sounds like this is out-of-scope, per the replies above. That's no problem. There are some field-specific educational resource journals in my field (biology/paleobiology). I was just interested in trying the publication model, since I'm a primarily undergrad institution coordinator for a local research network, and publication of reusable, collaborative, living materials is something we're interested in.

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I wrongly assumed that software packages designed to facilitate teaching and learning were valid. It seems that only things that are considered infrastructure are allowed. Maybe there are some things that can be added or improved to meet the submission criteria.

Please see above, where I stated: "We (the editors) have been discussing how to adapt to this demand, and are still working this out."

We are not ruling out these types of submissions. We were just a bit blindsided by them, as they weren't included originally.

In any case, full worked-out examples (a.k.a. tutorial) is essential.

I am not able to see slides or tutorial material on this submission. Perhaps we need breadcrumbs in the README. Also, the paper needs work, as I explained.

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@wrightaprilm — Are you able to export your worksheets to a portable format, viewable on the repo? (like markdown). I don't have RStudio, so am not able to see this material. Also, the material is not described in the paper so I didn't get that it existed.

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To clarify, the submission of the worksheets, together with the software, may be eligible under the "learning module" category.

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Thinking about viewing worked examples without RStudio: I made a website for the software + exercises, which renders both exercises under the "Articles" tab. There's an instructor's guide, with the output that students will see via the RStudio interface, as well as screenshots of the GUI exercise answers.

In re: the Paper. I was looking at the paper on my local machine, and I couldn't see the problem. Then I looked at the repository and realized the text had gotten lost in the rollback of a prior commit. Sorry about that. The text is here. I'm not sure how changes come through the journal interface.

Supplemental slides - I saved these to HTML and PDF. I have to think a little more about how best to serve these outside of the RStudio application - the PDFs look fine (though figure citations aren't appearing right), but the HTML slides look a little odd. I'm certainly willing to look more into this, if you think the module is OK to go out for review.

I'm just coming off maternity leave, and a bit slow on the uptake, so I need this next bit to summarize and keep me on track:

• Slides viewable via Git repository.
• Instructor's guide with worked examples that does not require RStudio to view.
• Paper text actually present in paper (sorry about this again).

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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--> Check article proof 📄 <--

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@wrightaprilm Great going! I've not had a chance to go over it yet… currently I'm in report-writing purgatory. Will get back to you as soon as possible.

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@whedon assign @juanklopper as editor

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OK, the editor is @juanklopper

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👋 @juanklopper — I've assigned this submission to you as handling editor. Since this will be your first editing assignment, let me know if you need to bounce ideas about selecting reviewers. Check out the Editor's Guide I put together: it describes the editor workflow, including needed @whedon commands.

@wrightaprilm — My apologies for the delay in handling this submission! The beginning of semester hit me like a hurricane.

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@labarba I'm in grant writing jail, and hadn't noticed the passage of time. Thanks for your help handling this!

Let me know what you need from me and when you need it. I'm happy to provide some suggested reviewers who are working at the intersection of evolution and education.

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@wrightaprilm I was originally assigned as editor for your submission. Unfortunately, it has taken me this long to be in a position to assist you in taking this proposal forward. Thanks to our editor-in-chief (EiC), @labarba for helping out. Not to mention @moorepants . Thanks everyone.

I note that you are in grant writing jail! It is a special place isn't it!? :-) I wish you all the luck.

Now that I have had some time to look at your work, I have some suggestions and questions. Let's start with the latter. Your last post above mentioned that you wanted to suggest a couple of reviewers. Have you progressed with this?

@labarba has intimated to the fact that we are still negotiating the perils of inclusion criteria for the journal, and quite rightly so. At this time, though, I want to support your submission. Creating learning resources that others can use is something that is close to my heart. I want to suggest that you have a look at one of the papers in our journal: Pynamical: Model and visualize discrete nonlinear dynamical systems, chaos, and fractals. It is available here . Much like your project, it is a novel software package (in python), combined with a well developed resource infrastructure that makes it ideal for someone else to pick up and use as an educational resource.

To this end, I love the website that you added and can only suggest that you expand on it a little bit. The same goes for the great Shiny app. From viewing your work submitted for this proposal, I sense that your are an expert in your field. Something, I suppose, not all of your colleagues are. I would really recommend then that you expand on both the website and Shiny app. Just to make it a pick-up-and-use for the less fortunate.

I also want to suggest a quick rewrite of you actual paper. I come from a world where we have very structured papers. As our EiC once mentioned, the papers for JOSE are just the entry-portal to your work (for our readers). I wouldn't mind, though, if you would consider the following structure for the rewrite:

Summary

A summary of the R package (one paragraph).

A summary of the R Shiny app (one paragraph).

A summary of the accompanying resources detailing the use (how to) of the package / app / accompanying resources (one paragraph).

Introduction summary on phylogenetics (one to two paragraphs).

Statement of need

Explain the need for this R package / Shiny app / accompanying educational resources within the context of its use (one paragraph).

Explain a use-case of the software / learning resources with inclusion of screenshots.

Let me know what you think. And now, I'll go read up on the phylogenetics of trees, because you made me interested in it.

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Hi Juan-

Happy to do a restructure; I'll probably get to it Friday afternoon. I send off one of two grants Friday morning, which means I get to do something fun:)

I'm happy to suggest reviewers. I have two other primarily undergraduate institution faculty in mind (one an R expert, one not) - I'll send along names and emails when I commit the restructure.

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Alright, I committed changes to the paper that are more in line with what you've suggested. Let me know what you think.

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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👉 Check article proof 📄 👈

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@wrightaprilm I have read your rewrite. Thanks a lot. Just to keep you informed, we have now moved on with the process and have approached some potential reviewers (I do note that you might have some suggestions and we'll keep this in mind). Hopefully, we can update you shortly.

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I'd like to suggest Cathy Newman, who is another primarily undergrad institution faculty member serving similar educational audiences. Rowan Lockwood is another one who would be good.

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@wrightaprilm we have our first reviewer to look at your submission. Please hang in there until we hear back from our other requests (we will keep your suggestion in mind).

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@whedon assign @ethanwhite as reviewer

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OK, the reviewer is @ethanwhite

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@ethanwhite great to have you review this submission! Thanks.

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@whedon add @rachelss as reviewer

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OK, @rachelss is now a reviewer

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@whedon start review

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OK, I've started the review over in #35. Feel free to close this issue now!

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