[PRE REVIEW]: fctSPM: Factorial ANOVA and post-hoc tests for Statistical Parametric Mapping in MATLAB

[whedon]

Submitting author: @tramarobin (Robin Trama) Repository: https://github.com/tramarobin/fctSPM Version: 1.4 Editor: @cMadan Reviewers: @0todd0000, @nicholst Managing EiC: Kristen Thyng

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Author instructions

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

The author's suggestion for the handling editor is @csoneson.

@tramarobin 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

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[whedon]

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1016/j.jbiomech.2010.03.008 is OK
- 10.1016/j.jbiomech.2010.03.008 is OK
- 10.1109/TBME.2020.3035838 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1002/hbm.460020402 is INVALID because of 'https://doi.org/' prefix

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.60 s (989.1 files/s, 41876.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                         591           6048           3866          14981
Markdown                         3             59              0            198
TeX                              1              5              0             34
-------------------------------------------------------------------------------
SUM:                           595           6112           3866          15213
-------------------------------------------------------------------------------

Statistical information for the repository '2c1b233853851da820e7464a' was
gathered on 2020/11/13.
No commited files with the specified extensions were found.

[whedon]

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

[kthyng]

@tramarobin Can you address the DOI note above?

[kthyng]

@csoneson Can you edit this submission?

[kthyng]

@whedon invite @csoneson as editor

[whedon]

@csoneson has been invited to edit this submission.

[tramarobin]

The DOI issue was corrected. Trama RobinPhD student De : Kristen ThyngEnvoyé le :samedi 14 novembre 2020 20:08À : openjournals/joss-reviewsCc : tramarobin; MentionObjet :Re: [openjournals/joss-reviews] [PRE REVIEW]: fctSPM: Factorial ANOVA and post-hoc tests for Statistical Parametric Mapping in MATLAB (#2839) @tramarobin Can you address the DOI note above?—You are receiving this because you were mentioned.Reply to this email directly, view it on GitHub, or unsubscribe. 

[csoneson]

@kthyng - this is a bit outside of my expertise, I'm afraid. I wonder if one of the more MATLAB/neuroimaging-oriented editors would be more suitable (if available).

[kthyng]

@csoneson no problem!

@cMadan Are you interested in editing this one?

[kthyng]

@whedon invite @cMadan as editor

[whedon]

@cMadan has been invited to edit this submission.

[cMadan]

@whedon assign @cMadan as editor

[whedon]

OK, the editor is @cMadan

[cMadan]

@tramarobin, it looks like the references aren't working here. Are you still working on this, or do you need help debugging it?

[tramarobin]

@cMadan yes it seems I can use some help. I think I correctly modified the DOI issue, and I did not receive other issue with references.

For what I read, I attached my bibliography in the article by writing "bibliography: paper.bib", and I called my reference that is listed in the paper.bib file as '[@myreference]'

It is the first time I am using bibtext format for references, am I missing something ?

[cMadan]

@tramarobin, I think there are probably a few things that need fixing. Let's fix the ones I noticed and see if there are any more that still remain.

(1) https://raw.githubusercontent.com/tramarobin/fctSPM/master/Article%40JOSS/paper.md

Please remove the single quotes around the square brackets for each reference. It might be useful to take another look at the example: https://joss.readthedocs.io/en/latest/submitting.html

I think you used the examples at the very bottom and followed them too literally, look instead at the references in the Statement of Need section.

(2) https://github.com/tramarobin/fctSPM/blob/master/Article%40JOSS/paper.bib

You need and between authors, not just at the end. If you have initials after the last name you need a comma, e.g., {Nichols, T E and Holmes, A P}. See the first bib example in https://joss.readthedocs.io/en/latest/submitting.html, which shows a paper with three authors.

Your last reference is missing the volume and page numbers.

[tramarobin]

@cMadan, thank you for your help. I took the examples too litterally indeed.

I previewed the paper at https://whedon.theoj.org/ and I think it is ok now (last time the website wasn't working and I could not check the paper once compiled)

For the last reference, the paper was only accepted recently and there is no volume and page number yet. On the jounal website, the BibText citation has an empty volume number and '{1-1}' for page numbers. I added these fileds to the reference, I hope it is ok.

[cMadan]

@whedon generate pdf

[whedon]

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

[cMadan]

@tramarobin, thanks for fixing those errors. I would remove the 1-1 page range for the recently accepted paper since this isn't the actual publication information and is just a placeholder.

Now that some of the initial issues are resolved, it would be good to revise the text a bit. Your current Statement of need section doesn't really explain the 'need' that this software is designed to fulfil. I also found that the section of the software itself could use some proof reading. For instance the sentence beginning with "Numerous figures are also created, ..." is a bit awkward. The late sentence about "Many parameters also exist..." would benefit from more details on what these parameters are. I would suggest you ask a colleague not involved in the project to look over the text and ask them where they found it too unclear. These are intended to be short papers, but they also need to explain what the software does, so that an interested reader might follow up and try using the software.

Here are a few examples I felt that should be relatable, to help you get a better idea of what the paper should be like: https://joss.theoj.org/papers/10.21105/joss.02670 https://joss.theoj.org/papers/10.21105/joss.02166 https://joss.theoj.org/papers/10.21105/joss.02668

[tramarobin]

@cMadan, thank you for your helpful feedbacks. We have modified the article as recommended and some colleagues not involved in the project helped us to clarify some points. The new version has been updated on the GitHub repository.

[cMadan]

@whedon generate pdf

[whedon]

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

[cMadan]

@tramarobin, the text is much improved--well done!

As a minor comment, I'd suggest against jet as the default colormap. (For some background, see https://onlinelibrary.wiley.com/doi/full/10.1111/ejn.14430.)

Can you look through the list of JOSS reviewers (linked in the first comment in this issue) and suggest some who may be suitable?

[tramarobin]

@cMadan, thank you for the link to your paper. I had never considered the luminance or the sequential or diverging characteristics of a color scale.

I included the cbrewer funtion in the package as it allows to chose between more colormaps. (Charles (2020). cbrewer : colorbrewer schemes for Matlab (https://www.mathworks.com/matlabcentral/fileexchange/34087-cbrewer-colorbrewer-schemes-for-matlab), MATLAB Central File Exchange. Retrieved December 11, 2020.)

Two optional inputs are now available to define colormaps for mean maps and map of differences independantly.

• colorMap is the colormap used for means, standard deviations, ANOVA and effect sizes plots. Default is cbrewer('Reds').
• colorMapDiff is the colormap used for differences, relative differences and post-hoc spm plots. Default is cbrewer('RdBu').

Consequently, jet is not the default colormap anymore. I modified the readme.md file to reflect these changes, and created a new release of the function (v1.4.1)

Maybe @EtienneCmb ?

[EtienneCmb]

Hi all !

Agree with @cMadan , I wouldn't use jet neither. There's a recent Nature Comm paper about it, also comparing several colormaps : https://www.nature.com/articles/s41467-020-19160-7

[cMadan]

@EtienneCmb, would you be interested/available to review this submission?

@tramarobin, can you suggest anyone else? We normally have two reviewers for each submission.

[tramarobin]

@cMadan, oh yes sorry I can suggest @katschueler

[tramarobin]

@cMadan, Hi ! Hope your doing well As I am not familiar with this kind of review, should I suggest other reviewers as we have no answers from the previouly suggested ones ?

[tramarobin]

@cMadan & @kthyng, is there something I can do as I don't have any answers ?

[kthyng]

Hi @tramarobin! Do you mean with respect to reviewers to suggest? We do ask submitting authors to look through the list of volunteers to find matches for your submission since you know your code best, and then list them here without using "@" so they aren't preemptively pinged. I see you've found 2. Can you find a handful more? You may also know people from your own science community and network who may be good reviewers, as long as they aren't conflicted with you. @cMadan will then request reviewers from your suggestions and/or others.

Please let me know if you have other questions.

[tramarobin]

@kthyng, thanks for your answer, i didn't get the nuance of "without @"

@cMadan, I suggest EtienneCmb, katschueler, daviddewhurst, marcoapintoo Outside the list, I can suggest 0todd0000 who created the statistical analysis which is employed in my function.

[cMadan]

@EtienneCmb @daviddewhurst @0todd0000, would you be available and interested in reviewing this submission?

[EtienneCmb]

Hi @cMadan, sorry for the delay, unfortunately I'm already in the middle of multiple reviews.

[cMadan]

@EtienneCmb, no problem, thanks for letting me know!

[tramarobin]

@cMadan, do you want me to suggest other potential reviewers ?

[0todd0000]

Apologies for my delayed reply, I saw the invitation a while ago but then lost it, so thank you for the reminder. I'd be happy to review. I don't see instructions for reviewers in this discussion, but please let me know if I've missed something.

[cMadan]

@0todd0000, that would be great, thank you! The detailed instructions, and review itself haven't started yet. Ideally we'd have two reviewers before we begin.

@typically, would you be interested and available to review this? I think it is related to some of your current work and may even be useful to use there.

[cMadan]

@whedon add @0todd0000 as reviewer

[whedon]

OK, @0todd0000 is now a reviewer

[tramarobin]

@cMadan, as typically does not seem to answer, I can suggest nicholst. He is working in Matlab about Statistical non Parametric Mapping (SnPM), which is the approach chosen in my function to analyse two-dimensional data.

[cMadan]

@nicholst, would you be interested/available to review this submission?

@tramarobin, sorry we haven't been able to start the review yet. Hopefully we'll be able to soon!

[nicholst]

Sure @cMadan ... first time reviewing for JOSS... is there a reviewer's guide?

[tramarobin]

@cMadan, no problem I know it is sometimes difficult to find reviewers.

@nicholst, thank you for accepting to review this paper. I think @cMadan will give you instructions soon as there are now two reviewers.

[cMadan]

@nicholst, thank you, that's great!

The reviewer guide is here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. When the review is started (moments from now), you'll have a checklist of what you're supposed to assess in the work--a bit different than with other journals since we're reviewing software, but same spirit of giving feedback and making sure it meets set expectations. That link has some related pages linked on the far-left that provide further guidance. Of course, I'm happy to answer questions as you do the review and there will be another reviewer as well. It's a relatively interactive and transparent process, so not in discrete rounds/etc as with most journals.

[cMadan]

@whedon add @nicholst as reviewer

[whedon]

OK, @nicholst is now a reviewer

[cMadan]

@0todd0000, it's been awhile, but hopefully you are still able to review this as well. I am going to start the review now, but do let me know if your availability has changed. You may also want to see the reviewer guidance I just commented above.