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Submit the package #12

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ibartomeus opened this issue Feb 18, 2018 · 49 comments
Closed

Submit the package #12

ibartomeus opened this issue Feb 18, 2018 · 49 comments
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@KevCaz @ibartomeus @JonasGeschke

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@ibartomeus
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The process is described here:

https://github.com/ropensci/onboarding#how-submit

Looks easy, but we need to check the guidelines first. Also, What do you think about submitting to JOSS (which is the same process)? For me and given the nature of this package, would be enough. This would give us a DOI, a line in our CV under peer-reviewed papers and a to be indexed in G scholar.

I am skeptical MEE would be interested. I am not sure which other Journals accept quick notes on R packages.
@KevCaz
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KevCaz commented Feb 18, 2018

JOSS + Ropensci... sounds like a plan!

This would give us a DOI [...]

Note that you can always add a DOI to your code using Zenodo!

By the way, if I recall correctly, the R client for the cites API was in the wishing of Ropensci, right?

@ibartomeus
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Yes, It was.

@KevCaz
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KevCaz commented Mar 6, 2018

So I have to stop working on the package for today but I can finish to boost the code coverage this week-end + improve the documentation. Then I'll consider the package as ¨submittable¨. What's your feeling?

@ibartomeus
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Kevin, thanks so much for all the effort you put! I didn't test it yet, but I am happy to submit it sooner than later. We should also clarify authorship and give credit appropriately, especially to Kevin and Jonas.

@KevCaz
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KevCaz commented Mar 6, 2018

I was happy to learn a bit more about web API and how to wrap around an API, so my pleasure!

I'll take care of the tests and double check the doc of our functions. If you have a good example in mind of what a user/researcher could do with this package, we should use it to build a vignette!

@KevCaz
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KevCaz commented Mar 12, 2018 •
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To me, we only need to build a nice / exhaustive vignette and we are ready to go.

@ibartomeus
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Awesome, I am swamped this week, but I can try to do the vignette next week. @JonasGeschke , what do you think about submitting to JOSS?

@KevCaz
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KevCaz commented Mar 12, 2018

I'll try to outline the vignettes this week.

@KevCaz
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KevCaz commented Mar 12, 2018

They make the submission quite easy!
https://joss.theoj.org/about#author_guidelines

@JonasGeschke
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JonasGeschke commented Apr 2, 2018 via email

@KevCaz
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KevCaz commented Apr 2, 2018

I may be able to write a little bit more about the vignette soon (within two weeks).
Any time frame for the ms?

@KevCaz
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KevCaz commented Jul 2, 2018

I may be able to put a little bit of energy in this project this summer, are you interested in finish this up by the end of the summer?

@JonasGeschke
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JonasGeschke commented Jul 2, 2018 via email

@KevCaz
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KevCaz commented Jul 2, 2018

Sure!
I'll be at the ESA by the way.

@ibartomeus
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Yes, and sorry for not kepig up with the project. Would be great to wrap it up and make it available. We can Skype this week anytime.

@KevCaz
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KevCaz commented Jul 2, 2018

What about Thursday? I guess you are both in Europe. What about 2pm in Madrid (i.e. 8am here in Guelph)?

@JonasGeschke
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JonasGeschke commented Jul 3, 2018 via email

@KevCaz
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KevCaz commented Jul 3, 2018

Next week works for me!

@ibartomeus
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ok, I am not sure If I will have internet, but if I do (hopefully), Monday 2 pm should be ok. If I can't make go ahead without me. My skype name is nachobartomeus

@KevCaz
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KevCaz commented Jul 3, 2018

works for me.

@JonasGeschke
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JonasGeschke commented Jul 3, 2018 via email

@ibartomeus
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14:00 to be clear.

@KevCaz
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KevCaz commented Jul 9, 2018

See you tomorrow

@ibartomeus
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Papers: look for Tella et al., is on parrots as invasive species. I'll see to find it when I got decent internet.

@JonasGeschke
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JonasGeschke commented Jul 9, 2018 via email

@JonasGeschke
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FYI: I contacted the coordinator of Methods in Ecology and Evolution in order to ask about publishing there. See the answer below.
So I guess we go with JOSS and then probably promote the publication via their blog.
Best greetings!

Hi Jonas,

Thank you for your email. It's wonderful to hear that your package is close to being ready for submission to rOpenSci or CRAN.

There are no publication fees for Methods in Ecology and Evolution unless you choose to make your article open access after submission. Your paper would fall under our ‘Applications’ article type, so it would be made freely available to the public upon publication (although not open access, as it would be published under a different license agreement). You can find out more about Applications articles here: https://besjournals.onlinelibrary.wiley.com/hub/journal/2041210x/author-guidelines#Article_types

The requirements for initial submission can be found here: https://besjournals.onlinelibrary.wiley.com/hub/journal/2041210x/author-guidelines#Quick_checklist

And you can see our aims and scope here: https://besjournals.onlinelibrary.wiley.com/hub/journal/2041210X/aims-and-scope/read-full-aims-and-scope

If you would like one of the Senior Editors to comment on whether your manuscript would be suitable for the journal, you just need to send us the abstract. I’ll then pass it along and let you know when I hear back from them.

Regardless of where you choose to submit a paper about your package, we would be happy to promote it through our social media channels and our blog. You can see how we have promoted a couple of other packages that arose from the hackathon here: https://methodsblog.wordpress.com/tag/hackathon/

I hope that this email has been helpful. If you have any further questions, just let me know.

Best wishes,
Chris

@KevCaz
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KevCaz commented Jul 10, 2018

Sounds like a very good plan to me, thanks Jonas!

@KevCaz
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KevCaz commented Jul 11, 2018 •
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JOSS has a new authors guidelines webpage https://joss.readthedocs.io/en/latest/submitting.html

@JonasGeschke
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JonasGeschke commented Jul 12, 2018 via email

@KevCaz
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KevCaz commented Jul 12, 2018

The submission to the CRAN doesn't worry me. Actually our package is ready for CRAN submission, and the steps to go through are fairly simple: https://cran.r-project.org/submit.html
However I would wait as there is still some work I want to do before submission!

@JonasGeschke
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JonasGeschke commented Jul 13, 2018 via email

@KevCaz
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KevCaz commented Jul 17, 2018

I've built a website with pkgdown, to add it I need you do something @ibartomeus !
Whenever you have some time to do so:

  1. go to the settings of the repo
  2. enable gh-pages for this repo, select the option using a docs folder
  3. it'll give you a url you should but on the first page (top right next to the short description)

More details here => https://help.github.com/articles/configuring-a-publishing-source-for-github-pages/

Cheers

@ibartomeus
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I think it's done. I also gave you both admin privileges.

I edited (minimally) the ms, help, and vignettes. I also placed Kevin as the second author if you agree. The package is working nicely. I think we are ready on my part!

The last issue is about coauthors. I noticed I don't have all peoples email, so if you agree I'll ask the 8 collaborators listed if they want to be coauthors by naming them in an issue.

Great job guys! It was a pleasure collaborating with you two!

@ibartomeus
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Update: It looks like I can not give you owner privileges (if you know a way, let me know).

Also, here is the webpage: https://ibartomeus.github.io/citesr/

@KevCaz
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KevCaz commented Jul 19, 2018

Can you add this on the top of the home page of the repo?

@JonasGeschke
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JonasGeschke commented Jul 19, 2018 •
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ohh its getting to many conversations streams/ issues now ...
somewhere I read about the token: I agree the token is personal and should not be screened. Either we take a placeholder instead or - which I think would be fine - we just use ***** instead of the last 5 characters. @KevCaz can you edit this? (as it also needs to be in in the website)

@JonasGeschke
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@KevCaz in the website citation info https://ibartomeus.github.io/citesr/authors.html some link to another package "inSilecoMisc" is provided. I guess there should be some other reference ...

@KevCaz
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KevCaz commented Jul 19, 2018

My bad!

@KevCaz
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KevCaz commented Jul 19, 2018

done

@JonasGeschke
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how do you access and edit the website? cause the one "Access" needs to be written small "a".
and in general: I wonder if we should chance the creation date of the package so it becomes a 2018 in the citation. e.g. to the submission date to CRAN? I dont know ;-)

tell me if you need me to do anything further. I am gone over the weekend and back available on monday. would be great to submit the paper (with CRAN link?!) on thuesday or wednesday!

@KevCaz
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KevCaz commented Jul 20, 2018

I'll follow your suggestions and I'll do some final change so everything is ready on Monday! Enjoy your week-end!!

@KevCaz
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KevCaz commented Jul 22, 2018

@JonasGeschke you do not access the website, you simply build it using pkgdown, using build_site() (a convenient wrapper). Basically it takes different piece of the documentation and build a website, isn't it neat? This means that if you want to change anything, you need to change the relevant piece of documentation! For instance, if you aim at editing the home page, then you edit README.md!

@KevCaz
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KevCaz commented Jul 22, 2018

I'm ready for the submission once I have your feedback about #23 @JonasGeschke.

@JonasGeschke
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did my feedback ;-)
thanks for the explanation about the website, got it.

@KevCaz
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KevCaz commented Jul 23, 2018

Well here is the plan for the next few minutes on my side. I'll tag the version and do the first official GH release. Then would you (@JonasGeschke ) like to do the CRAN submission? Then we are ready for the JOSS submission, right? I'm unsure whether or not we should get a DOI (via Zenodo) now or wait for the review.

@JonasGeschke
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sounds good!
yeah I can do the CRAN submissen, if you dont like to. I will do the JOSS submission once we have the cran link.
you can do the Zenodo now or wait until the JOSS paper is done. see the review process of the JOSS paper:

bildschirmfoto 2018-07-23 um 17 52 31

@KevCaz
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KevCaz commented Jul 23, 2018

It's up to you I can handle the CRAN submission and let you handle the JOSS submission.

@JonasGeschke
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JonasGeschke commented Jul 23, 2018 •
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yeah lets do it that way. I guess for the Zenodo deposit we should wait for the review, in case they ask for edits, right

@JonasGeschke
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alright. so I would close here so we can handle each submission separately (as we are doing already).

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