[PRE REVIEW]: PyNM: a Lightweight Python implementation of Normative Modeling

[editorialbot]

Submitting author: !--author-handle-->@harveyaa<!--end-author-handle-- (Annabelle Harvey) Repository: https://github.com/ppsp-team/PyNM Branch with paper.md (empty if default branch): joss_submission Version: 1.0.0b1 Editor: !--editor-->@dfm<!--end-editor-- Reviewers: @smkia, @saigerutherford Managing EiC: Kristen Thyng

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f"><img src="https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f/status.svg)](https://joss.theoj.org/papers/f9a276711945e53109bddab19646c85f)

Author instructions

Thanks for submitting your paper to JOSS @harveyaa. Currently, there isn't an JOSS editor assigned to your paper.

@harveyaa if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (209.3 files/s, 137427.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            334            720           1544
Jupyter Notebook                 7              0          10636            534
Markdown                         3             80              0            306
TeX                              1             11              0            240
YAML                             2              1              7             29
-------------------------------------------------------------------------------
SUM:                            22            426          11363           2653
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 863

[editorialbot]

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

OK DOIs

- 10.1038/s41380-019-0441-1 is OK
- 10.1016/j.biopsych.2015.12.023 is OK
- 10.1371/journal.pcbi.1009477 is OK
- 10.1371/journal.pone.0252108 is OK
- 10.1101/2021.08.08.455583 is OK
- 10.3389/fnins.2018.00662 is OK
- 10.3389/fpsyt.2019.00011 is OK
- 10.1038/s42003-020-01212-9 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.neuroimage.2021.118715 is INVALID because of 'https://doi.org/' prefix

[kthyng]

Hi @harveyaa and thanks for your submission! I saw your note that earlier versions of this software have been used in papers. This is fine, as long as the scholarly effort separate from those papers is large enough to justify another publication. Could you go into detail about what the other papers have been about (do they describe the software in detail or simply use the software?) and how much development has occurred on the software since the last paper? Thanks.

[editorialbot]

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

[deep-introspection]

Hi @kthyng! Only rudimentary implementations of LOESS/Centiles methods were used in the past papers. Not only the PyNM library covers other more advanced methods (GP and GAMLSS especially), but even the LOESS/Centiles implementations have been totally refactored for creating a real API. Overall, PyNM also contains many additions: a command-line interface for wide accessibility, automatic dataset splitting and cross-validation, five models from various back-ends in a unified interface that covers a broad range of common use cases, solutions for very large datasets and heteroscedastic data, integrated plotting and evaluation functions to quickly check the validity of the model fit and results, and comprehensive and interactive tutorials.

[kthyng]

@harveyaa, @deep-introspection thanks for that information. I will ping the greater editorial board with that information available so they can help decide if this is in scope for JOSS; this process will take 1-2 weeks. Thank you!

[kthyng]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[arfon]

For future EiC on rotation, @dfm may be a good handling editor here.

[danielskatz]

This has passed the scope review, and we'll now find an editor

[danielskatz]

👋 @dfm - as suggested by @arfon, are you willing to edit this submission?

[danielskatz]

@editorialbot invite @dfm as editor

[editorialbot]

Invitation to edit this submission sent!

[danielskatz]

Based on email, I'm going to assign @dfm as editor, but he won't start working on this until next week due to him currently being on leave

[danielskatz]

@editorialbot assign @dfm as editor

[editorialbot]

Assigned! @dfm is now the editor

[dfm]

@editorialbot add @smkia as reviewer

🎉 Thanks @smkia for agreeing to review this submission!

In our discussions, @smkia noted a potential conflict of interest: a publication from 2019 co-authored with @deep-introspection, a co-author of this submission. My understanding is that @smkia and @deep-introspection did not have direct contact related to that project, and neigher were the primary author, so I'd be happy to waive this conflict if the submitting authors (@harveyaa & @deep-introspection) agree. Please let me know here or via email if you have any concerns with this resolution.

[editorialbot]

@smkia added to the reviewers list!

[deep-introspection]

@dfm I can confirm that we did not have any direct contact with @smkia

[dfm]

@editorialbot add @saigerutherford as reviewer

Thanks @saigerutherford for agreeing to be our second reviewer!!

I'll get the review started in a separate issue where you'll find a lot more information about how this process proceeds.

[editorialbot]

@saigerutherford added to the reviewers list!

[dfm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4321.