MRG: Pyglmnet paper #313

jasmainak · 2019-09-18T21:31:25Z

closes #297

Hi everyone,

@pavanramkumar and I created a first draft of our paper for submission to JOSS. If you want to be listed as an author, please read the draft and leave comments. More importantly:

Check and/or update your name, affiliation and ORCID by leaving a "code suggestion"
Add to the acknowledgement section any grants that enabled you to contribute to pyglmnet
If you are a contributor but your commits don't show up in the contributor graph please make sure that you have the email id that you used to commit in your verified emails on Github. The instructions to do this are here

The guidelines for JOSS submission are here.

Compiling the paper

If you want to compile the paper
- go to: https://whedon.theoj.org/
- in the paper repository address, enter: https://github.com/jasmainak/pyglmnet/
- in the custom branch, enter: paper

Compile!

Tagging all contributors (check mark if we got a response)

codecov-io · 2019-11-02T19:38:55Z

Codecov Report

Merging #313 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #313   +/-   ##
=======================================
  Coverage   75.66%   75.66%           
=======================================
  Files           4        4           
  Lines         678      678           
  Branches      149      149           
=======================================
  Hits          513      513           
  Misses        128      128           
  Partials       37       37

Continue to review full report at Codecov.

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paper/paper.md

pavanramkumar · 2019-11-02T21:32:08Z

Thanks @jasmainak ! Looks good to me

jasmainak · 2019-11-08T14:28:29Z

hi @themantalope can you read the first comment and confirm your authorship by checking the affiliation and adding the orcid? Thanks.

koerding · 2019-11-08T14:33:56Z

I will be completely out until next thursday. Sorry guys. Huge grant deadlin

…

On Fri, Nov 8, 2019 at 9:28 AM Mainak Jas ***@***.***> wrote: hi @themantalope <https://github.com/themantalope> can you read the first comment <#313 (comment)> and confirm your authorship by checking the affiliation and adding the orcid? Thanks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#313?email_source=notifications&email_token=AA2XUNONXBZZ7SYJZZ5U263QSVZQ5A5CNFSM4IYD6K42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDSIUGI#issuecomment-551848473>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2XUNLV7FJQAEYXIQTOU63QSVZQ5ANCNFSM4IYD6K4Q> .

-- I love those that desire the impossible - Goethe. Konrad Kording @KordingLab, UPenn, Richards 404b cell:773 - liberat (5423728) office:(215) 898-5826 kordinglab.com

jasmainak · 2019-11-08T21:08:03Z

no worries, we are expecting you to make at least two pull requests since you are taking extra time now ;)

koerding · 2019-11-08T21:15:43Z

I have done my orcid ;) so just one?

…

On Fri, Nov 8, 2019 at 4:08 PM Mainak Jas ***@***.***> wrote: no worries, we are expecting you to make at least two pull requests since you are taking extra time now ;) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#313?email_source=notifications&email_token=AA2XUNIK66ITPVV664WPFTLQSXILHA5CNFSM4IYD6K42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDTLG2Q#issuecomment-551990122>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2XUNKATT3WYWNDI7G5G43QSXILHANCNFSM4IYD6K4Q> .

-- I love those that desire the impossible - Goethe. Konrad Kording @KordingLab, UPenn, Richards 404b cell:773 - liberat (5423728) office:(215) 898-5826 kordinglab.com

jasmainak · 2019-11-09T19:50:16Z

@AnchorBlues @BeibinLi @DreHar @the872 @themantalope @marquesVF @evadyer @tommyod @ravigarg27 @timshell

I have not heard from you in this thread. We do need you to confirm your name and affiliation if you want to be included as an author.

daniel-acuna · 2019-11-09T19:53:04Z

@jasmainak I am in a conference with one of the assoc. editors in chief of JOSS. perhaps there is some way of receiving feedback? maybe email me to [email protected]

pavanramkumar · 2019-11-09T20:05:23Z

Thanks @daniel-acuna for offering to do this. The JOSS review process seems super straightforward and transparent: one of the reasons why we chose the venue. @jasmainak will be in touch!

themantalope · 2019-11-10T15:02:54Z

Yes, my name and affiliation is correct as written. Thanks!

…

On Sat, Nov 9, 2019 at 2:05 PM Pavan Ramkumar ***@***.***> wrote: Thanks @daniel-acuna <https://github.com/daniel-acuna> for offering to do this. The JOSS review process seems super straightforward and transparent: one of the reasons why we chose the venue. @jasmainak <https://github.com/jasmainak> will be in touch! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#313?email_source=notifications&email_token=ABZ7OB2OPVBR523FQMC72ZTQS4JYLA5CNFSM4IYD6K42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDUOAUI#issuecomment-552132689>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZ7OB6ROX5OXD54U4NGBQTQS4JYLANCNFSM4IYD6K4Q> .

timshell · 2019-11-10T19:57:53Z

Name and affiliation are good for me. Thanks for including me! Not sure why I'm not showing up in the contributor graph. Perhaps the e-mail I used for that was my undergraduate university e-mail (which I don't have access to anymore)

jasmainak · 2019-11-10T20:23:07Z

@timshell okay then we have to do this by updating the .mailmap. Are you up to make a PR to fix it? If not, just tell me your new email address and I'll do it.

BeibinLi · 2019-11-12T01:14:37Z

Thanks! I would like to be part of this. My name and affiliation look all right.

tommyod · 2019-11-12T14:28:36Z

Verifying that my name and affiliation is correct as written. Thanks!

tommyod

Felt a bit guilty about having my name on something where I haven't contributed, so I added some quick comments. Hope it's helpful. I also hope to look more at the code in the future. Haven't had need to use GLMs in a while. Great work. 👍

paper/paper.md

tommyod · 2019-11-12T14:40:26Z

paper/paper.md

+| Group lasso | x | | | x | | | x |
+| Tikhonov | x | | | | | | |
+
+Pyglmnet implements the same algorithm described in [Friedman, J., Hastie, T., & Tibshirani, R. (2010)](https://core.ac.uk/download/files/153/6287975.pdf>) and the accompanying widely popular R package [glmnet].


"...implements the algorithm described in..." or "...implements the same algorithm as described in..."

paper/paper.md

jasmainak · 2019-11-12T20:36:15Z

paper/paper.md

+important to regularize the model to avoid overfitting the data.
+Regularization works by adding penalty terms that penalize the model parameters in
+a variety of different ways. This can be used to incorporate prior knowledge 
+about the parameters in a structured form. In Pyglmnet, we offer


Pyglmnet -> pyglmnet

comment from @DreHar

ravigarg27 · 2019-11-13T17:23:30Z

Thank you for including me. My name and affiliation are right.

* adding email * Update .mailmap Co-Authored-By: Mainak Jas <[email protected]>

AnchorBlues · 2019-11-17T08:20:18Z

Thanks for including me for the paper.

I verified that my name and affiliation are correct.

the872 · 2019-11-18T13:43:04Z

Thanks for the update, will be happy to represent the Loyola University Chicago commits.

pavanramkumar · 2019-11-18T18:06:03Z

@the872 thanks! any idea how we can reach out to @marquesVF -- pending confirmation needed from him

marquesVF · 2019-11-19T20:04:20Z

Hi guys!

Thanks for reaching me. That's correct. I was at Loyola.

I would only suggest to use my full name as Vinicius de F. Marques
Thanks and great work!

@pavanramkumar

jasmainak force-pushed the paper branch from 7acc64a to b5debfe Compare October 9, 2019 20:21

jasmainak added 8 commits November 2, 2019 15:26

ENH DOC: start writing paper

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ENH: move to paper/ folder

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FIX more tweaks

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ENH TST: Add test for readme

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ENH: Add references

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ENH: add more authors

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Tweaks

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FIX indexing

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jasmainak force-pushed the paper branch from 7830f8f to b5e0de2 Compare November 2, 2019 19:38

jasmainak added 4 commits November 2, 2019 15:52

Use proper format for refs

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One more pass

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MAINT: add paper to manifest

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ENH: acknowledge MNE grant

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pavanramkumar reviewed Nov 2, 2019

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Author order + pavan's comments

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pavanramkumar reviewed Nov 2, 2019

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jasmainak added 3 commits November 2, 2019 17:15

Address comments 2nd round

a895690

Use mathcal{L}

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Add another affiliation

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jasmainak force-pushed the paper branch 2 times, most recently from f27170f to f8dc2e2 Compare November 3, 2019 17:04

Update authors

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jasmainak force-pushed the paper branch from f8dc2e2 to dd34619 Compare November 3, 2019 17:10

Reorder affiliations

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jasmainak changed the title ~~WIP: Pyglmnet paper~~ MRG: Pyglmnet paper Nov 3, 2019

jasmainak mentioned this pull request Nov 11, 2019

preparation for JOSS paper #297

Closed

4 tasks

tommyod approved these changes Nov 12, 2019

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jasmainak commented Nov 12, 2019

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jasmainak commented Nov 12, 2019

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Adding Mayank E-mail (glm-tools#352)

3800c95

* adding email * Update .mailmap Co-Authored-By: Mainak Jas <[email protected]>

jasmainak and others added 5 commits November 23, 2019 13:23

Pass over comments

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Update book link

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Merge branch 'paper' of github.com:jasmainak/pyglmnet into paper

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Marques full name

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wordsmithing changes

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pavanramkumar merged commit dc89e29 into glm-tools:master Nov 23, 2019

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MRG: Pyglmnet paper #313

MRG: Pyglmnet paper #313

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MRG: Pyglmnet paper #313

MRG: Pyglmnet paper #313

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Compiling the paper

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Codecov Report

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