Authors since initial submission

cgreene commented 7 years ago

I wanted to track this so that we don't lose contributors.

Tagging @avctrh

New authors:

[x] @austinvhuang (formerly @avctrh)
[x] @SiminaB
[x] @michaelmhoffman
[x] @luzh2
[x] @lavenderca
[x] @zietzm

Acknowledgement -> Author due to approval after v1 went out:

[x] @swamidass

agitter commented 7 years ago

Perfect. I'll add new authors in one batch once we are nearing a new version.

agitter commented 6 years ago

I added @SiminaB to the list above after merging #588. That pull request alone may not meet ICMJE authorship criteria, but the discussion in #565 and incoming #566 do.

agitter commented 6 years ago

I added @michaelmhoffman after merging #620, noting that several other pull requests are still incoming.

michaelmhoffman commented 6 years ago

Thanks! Please don't forget to remove me from acknowledgments.

evancofer commented 6 years ago

This may be a silly question to ask on this pull request, but [how] do we plan on updating the author ordering? If we are still using the randomized hierarchies, are any transitions between them expected?

agitter commented 6 years ago

@evancofer It's a good idea to discuss this. The algorithm I proposed in #369, which is demoed here, would:

keep the random order for existing authors within each category
randomly order the new authors within each category
append the new authors to the end of the existing author list within each category
concatenate the category-specific author lists

The main objectives were to continue to emphasize the categories instead of the specific order and also minimize changes. I thought it would be confusing to have major permutations to the author list every time we add someone new.

michaelmhoffman commented 6 years ago

As a new author I think it is only fair that we get put at the end of whatever category we end up in.

agitter commented 6 years ago

Added @luzh2 above after merging #567

agitter commented 6 years ago

Added @lavenderca after merging #629

agitter commented 6 years ago

Added @zietzm after merging #638

cgreene commented 6 years ago

Talked with @swamidass at PSB. He contributed to the discussion of issues + writing on the first round (see Acknowledgements). He is now able to approve. I'm not sure what our procedure is this time around, but we should include him when we have things ready.

swamidass commented 6 years ago

Yes, I do approve.

agitter commented 6 years ago

@swamidass great, we'll add you in the next version. I'll post instructions for adding yourself here.

@aaronsheldon you also contributed previously but didn't give final approval. Do you want to review and approve this version to be added as an author?

@cgreene for the author-adding process, I'm thinking that we should once again have authors make pull requests to add their own information. That ensures accuracy and gives a commit as record of approval. I suggest that new authors add their information to a new file content/new_authors.yaml that I'll create using the format in content/metadata.yaml. After the text and new authors stabilize (at the end of next week?), I'll run the randomized ordering and move the new authors to metadata.yaml. Sound good?

cgreene commented 6 years ago

@agitter : plan sounds good to me. I agree with having the authors add their metadata via PR

agitter commented 6 years ago

@austinvhuang @SiminaB @michaelmhoffman @luzh2 @lavenderca @zietzm @swamidass we're ready for you to add your contact information to the author list.

Please submit a pull request to add your info to new-author-metadata.yaml, which will also indicate that you have read and approved the manuscript. This list is unordered so you can add yourself to the bottom. The funders entry is optional. The placeholder entries provide example formatting; see metadata.yaml for more examples.

Once all of the new authors are in new-author-metadata.yaml, I'll randomly order authors as described above and insert you into metadata.yaml, which will add you to the manuscript.

michaelmhoffman commented 6 years ago

How do we add multiple affiliations? I am planning to add Princess Margaret Cancer Centre, Toronto, ON, Canada; Department of Medical Biophysics, Toronto, ON, Canada; Department of Computer Science, Toronto, ON, Canada. I notice @agitter uses affiliations: Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison and Morgridge Institute for Research, Madison, WI. Does that mean I should use the ambiguous and as a way of adding additional affiliations? Better to switch to semicolon?

agitter commented 6 years ago

My example is wrong. You should use semi colon delimited as you suggested.

Better support for multiple affiliations is coming soon, but I'll update your affiliation formatting when we update the manubot package version.

agitter commented 6 years ago

I'm reminding myself that when I move the new authors from new-author-metadata.yaml to metadata.yaml I need to manually update the funding section. That part is no longer automatically generated.

edit: And the contributions section.

evancofer commented 6 years ago

@agitter This is related to the affiliations question. How should we go about adding a new affiliation for an existing author? Should we manually add them to metadata.yaml and submit a PR?

agitter commented 6 years ago

@evancofer yes, authors should feel free to update any of their own information via pull request. The affiliations in metadata.yaml are now a list, so you can either replace your existing affiliation or add an additional affiliation.

austinvhuang commented 6 years ago

Submitted my information as a PR, let me know if anything else is needed. Thanks!

agitter commented 6 years ago

All new authors have been added to new-author-metadata.yaml, and I don't anticipate any more authors for our next manuscript version. @cgreene do you agree that I can insert them into the ordered author list after we merge #777?

I'll review the new authors' commits to place them in a contribution category and then update the ordered list as described above.

cgreene commented 6 years ago

I agree that we should put these authors into a new contribution category and perform the ordering as was done for the other categories earlier.

agitter commented 6 years ago

New contribution category or existing categories? We can do either. I initially planed to use our existing categories:

Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion
Drafted one or more sub-sections
Revised specific sub-sections or supervised drafting one or more sub-sections
Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors

cgreene commented 6 years ago

Ahh - I would be fine with either, but putting new additions into a single category reduces shuffling of the author list.

michaelmhoffman commented 6 years ago

Should be no shuffling--I think what was discussed was putting in new authors in each of those categories after all previous authors in the category. (As a n00b I think it is far to put us after the authors for the first round within a category.) So up to four insertion points but no shuffling.

cgreene commented 6 years ago

@michaelmhoffman : sorry - misunderstood that then. 👍

agitter commented 6 years ago

I believe I have the same idea as @michaelmhoffman. For hypothetical categories and authors:

Category1: Existing1, Existing2, New1, New2, New3 Category2: Existing3, Existing4, New4

Suppose we currently have: Existing2, Existing1, Existing3, Existing4.

The updated list could become: Existing2, Existing1, New2, New3, New1, Existing3, Existing4, New4.

cgreene commented 6 years ago

As a heads up, I need all of our authors since the initial submission (others did this before the first submission) to create an account at JRS-I so that I can associate it with the manuscript. Please post here when you've done it. Please use the email address listed in the metadata file.

Go to this address: https://mc.manuscriptcentral.com/jrsi

Click "Create An Account" and associate your ORCID with the new account.

Post here that you have created your account.