[PRE REVIEW]: bayes_traj: A Python package for Bayesian trajectory analysis

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@jcross186@majensen<!--end-editor-- Reviewers: @gvieralopez, @lindemann09 Managing EiC: Kevin M. Moerman

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editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.20 s (263.6 files/s, 451156.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             11              0              0          76511
Python                          26           1178           1960           4743
Markdown                         7            395              0           2002
Jupyter Notebook                 5              0           5145            292
TeX                              1             16              0            139
YAML                             1              5              1             44
XML                              3              0              0              6
-------------------------------------------------------------------------------
SUM:                            54           1594           7106          83737
-------------------------------------------------------------------------------

Commit count by author:

   435  James Ross
    31  Fritz Obermeyer
     2  jcross186
     1  acil-bwh

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 663

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: pandas-dev/pandas: Pandas 1.0. 5
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: Longitudinal modeling of lung function trajectorie...
- No DOI given, and none found for title: Lung function trajectories in health and disease
- No DOI given, and none found for title: COPDGene\textregistered 2019: redefining the diagn...

❌ MISSING DOIs

- 10.2139/ssrn.3315029 may be a valid DOI for title: Bayesian estimation and model selection in group-b...
- 10.1016/j.alcr.2019.100323 may be a valid DOI for title: An overview of mixture modelling for latent evolut...
- 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a3725 may be a valid DOI for title: Dysanapsis Is Associated with COPD Trajectories At...
- 10.1109/tmi.2016.2608782 may be a valid DOI for title: A Bayesian nonparametric model for disease subtypi...
- 10.7196/10.2015.v21i3.83 may be a valid DOI for title: Lung-function trajectories leading to chronic obst...

❌ INVALID DOIs

- None

editorialbot commented 1 month ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

Kevin-Mattheus-Moerman commented 1 month ago

@jcross186 Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

[x] Please study the above reference check :point_up: and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
[x] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
[x] The paper YAML is not formatted as per our standards. Please review and edit the paper accordingly: https://joss.readthedocs.io/en/latest/example_paper.html

Kevin-Mattheus-Moerman commented 1 month ago

@jcross186 :wave:

jcross186 commented 1 month ago

Hi Kevin,

I have checked in changes that address previous issues. Please let me know if all looks good.

Kind regards,

-James

From: Kevin Mattheus Moerman @.> Date: Thursday, September 26, 2024 at 11:52 AM To: openjournals/joss-reviews @.> Cc: Ross, James Chapman,Ph.D. @.>, Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: bayes_traj: A Python package for Bayesian trajectory analysis (Issue #7252)

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Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1037/met0000359 is OK
- 10.1016/j.alcr.2019.100323 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.eclinm.2023.102408 is OK
- 10.1109/TMI.2016.2608782 is OK
- 10.1056/NEJMoa1411532 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: pandas-dev/pandas: Pandas 1.0. 5
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: Longitudinal modeling of lung function trajectorie...
- No DOI given, and none found for title: Lung function trajectories in health and disease
- No DOI given, and none found for title: COPDGene\textregistered 2019: redefining the diagn...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

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Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot invite @majensen as editor

editorialbot commented 1 month ago

Invitation to edit this submission sent!

majensen commented 1 month ago

@editorialbot assign me as editor

editorialbot commented 1 month ago

Assigned! @majensen is now the editor

majensen commented 1 month ago

Hi @jcross186 - if you have time, can you browse https://reviewers.joss.theoj.org/lookup for reviewers that you think might be appropriate? You can put usernames without the @ sign in this thread. This can help speed up the review process - much appreciated!

jcross186 commented 1 month ago

Hi Mark,

Here are a few:

gvieralopez limengbinggz mrazomej matteodelucchi gchure nhtran93 lindemann09

Kind regards,

-James

From: Mark Jensen @.> Date: Friday, September 27, 2024 at 2:31 PM To: openjournals/joss-reviews @.> Cc: Ross, James Chapman,Ph.D. @.>, Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: bayes_traj: A Python package for Bayesian trajectory analysis (Issue #7252)

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majensen commented 1 month ago

Hi @gvieralopez - would you be willing to review this work for JOSS? We could use your expertise. Thanks for considering! --@majensen

majensen commented 1 month ago

Hello @lindemann09 - would you have time to review this software for JOSS? Thank you for your consideration. --@majensen

majensen commented 1 month ago

Hi @mrazomej - would you consider reviewing this work for JOSS? We would appreciate your expertise. Thanks --@majensen

lindemann09 commented 1 month ago

Yes

gvieralopez commented 1 month ago

Hi @gvieralopez - would you be willing to review this work for JOSS? We could use your expertise. Thanks for considering! --@majensen

Yes

majensen commented 1 month ago

@editorialbot add @gvieralopez as reviewer

editorialbot commented 1 month ago

@gvieralopez added to the reviewers list!

majensen commented 1 month ago

@editorialbot add @lindemann09 as reviewer

editorialbot commented 1 month ago

@lindemann09 added to the reviewers list!

majensen commented 1 month ago

@editorialbot start review

editorialbot commented 1 month ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7323.

openjournals / joss-reviews

[PRE REVIEW]: bayes_traj: A Python package for Bayesian trajectory analysis #7252

Status