[PRE REVIEW]: NLSIG-COVID19Lab

[whedon]

Submitting author: @somefunagba (Oluwasegun Somefun) Repository: https://github.com/somefunAgba/NLSIG-COVID19Lab Version: v1.1.0 Editor: @majensen Reviewers: @agahkarakuzu, @kakearney Managing EiC: Kristen Thyng

: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.

Author instructions

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

The author's suggestion for the handling editor is @will-rowe.

@somefunagba 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]

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: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.

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.72 s (100.0 files/s, 22323.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Markdown                         3            102              0            201
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JSON                             1              0              0             23
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SUM:                            72           2006           5081           8990
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Statistical information for the repository 'be82677ff8c1b38096089f45' was
gathered on 2020/12/16.
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:

[whedon]

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

OK DOIs

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- 10.1007/978-0-85729-115-8_6 is OK
- 10.13140/RG.2.2.22509.95202 is OK
- 10.1101/2020.08.31.20185165 is OK
- 10.1063/1.3606555 is OK
- 10.1109/72.279181 is OK
- 10.1016/S1474-6670(17)45445-0 is OK
- 10.1016/j.ijnaoe.2018.04.002 is OK
- 10.1016/j.ejcon.2018.09.011 is OK
- 10.1109/ISCAS.2008.4541553 is OK
- 10.1109/IECON.1992.254474 is OK
- 10.1186/s12916-019-1406-6 is OK
- 10.1101/2020.07.03.20145672 is OK
- 10.1049/ic:19990713 is OK
- 10.1016/j.automatica.2006.07.018 is OK
- 10.1109/CDC.2003.1271825 is OK
- 10.1007/BF02551274 is OK
- 10.1017/atsip.2013.9 is OK
- 10.1177/1729881417703568 is OK
- 10.1007/978-3-642-36986-5_10 is OK
- 10.1038/s42256-020-00257-z is OK
- 10.1109/TNNLS.2016.2582924 is OK
- 10.1016/j.jtbi.2005.11.026 is OK
- 10.1038/35016072 is OK
- 10.1007/3-540-59497-3_175 is OK
- 10.1109/ICCV.2015.123 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.3201/eid1201.050396 is OK
- 10.1142/9789814261265_0009 is OK
- 10.1007/1-84628-259-4_10 is OK
- 10.1016/0005-1098(93)90052-U is OK
- 10.1007/1-84628-259-4 is OK
- 10.1016/j.conengprac.2007.03.010 is OK
- 10.1007/978-1-4842-2845-6 is OK
- 10.1109/IJCNN.2017.7966168 is OK
- 10.1007/3-540-49430-8_2 is OK
- 10.1371/journal.pone.0236860 is OK
- 10.1080/02664760903093633 is OK
- 10.1016/j.ecolmodel.2005.05.024 is OK
- 10.1063/1.4954543 is OK
- 10.1152/ajpheart.00219.2006 is OK
- 10.1109/ISTC.2014.6955084 is OK
- 10.1007/978-1-4899-7983-4 is OK
- 10.1109/JPROC.2020.2991885 is OK
- 10.3390/e21070627 is OK
- 10.3390/math8071174 is OK
- 10.1515/jee-2017-0069 is OK
- 10.1371/journal.pcbi.1002592 is OK
- 10.1016/S1474-6670(17)52049-2 is OK
- 10.1016/S1474-6670(17)58855-2 is OK
- 10.1155/2018/4231647 is OK
- 10.5772/60063 is OK
- 10.2307/2341367 is OK
- 10.1007/s13748-020-00218-y is OK
- 10.1109/ReCoSoC.2013.6581545 is OK
- 10.1016/j.neunet.2014.09.003 is OK
- 10.1073/pnas.1907373117 is OK
- 10.7641/CTA.2014.31117 is OK
- 10.7763/IJCTE.2009.V1.13 is OK
- 10.1016/j.ijid.2020.04.085 is OK
- 10.1080/10511979808965879 is OK
- 10.1049/cp:19991129 is OK
- 10.1109/JPROC.2017.2761740 is OK
- 10.1186/1742-4682-2-14 is OK
- 10.1007/s10462-011-9294-y is OK
- 10.1080/00031305.2017.1380080 is OK
- 10.1016/j.spl.2011.11.012 is OK
- 10.1109/5.58337 is OK
- 10.1007/s11071-020-05862-6 is OK
- 10.1109/IJCNN.2018.8489043 is OK
- 10.1016/j.jtbi.2012.07.024 is OK
- 10.1109/APEC.2016.7468308 is OK
- 10.1093/aob/mcg029 is OK
- 10.1109/TVLSI.2012.2232321 is OK

MISSING DOIs

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- 10.1561/9781680833294 may be a valid DOI for title: Multi-Period Trading via Convex Optimization
- 10.1201/9781315219165 may be a valid DOI for title: Feedback, Nonlinear, and Distributed Circuits
- 10.9790/4200-0702012633 may be a valid DOI for title: Performance Analysis of the Sigmoid and Fibonacci Activation Functions in NGA Architecture for a Generalized Independent Component Analysis
- 10.1007/978-1-4020-6949-9 may be a valid DOI for title: Handbook of Continued Fractions for Special Functions
- 10.1007/978-3-319-09330-7_7 may be a valid DOI for title: Training Deep Fourier Neural Networks To Fit Time-Series Data
- 10.1109/cvpr.2016.90 may be a valid DOI for title: Deep Residual Learning for Image Recognition
- 10.1109/ism.2016.0052 may be a valid DOI for title: Fair and Efficient Bandwidth Allocation for Video Flows Using Sigmoidal Programming
- 10.3390/info6030432 may be a valid DOI for title: Sliding-Mode Speed Control of PMSM with Fuzzy-Logic Chattering Minimization—Design and Implementation
- 10.23943/princeton/9780691197296.001.0001 may be a valid DOI for title: Statistical Inference via Convex Optimization
- 10.21468/scipostphys.9.4.053 may be a valid DOI for title: Neural Network-Based Approach to Phase Space Integration
- 10.1109/tnnls.2013.2281217 may be a valid DOI for title: Local Stability Analysis of Discrete-Time, Continuous-State, Complex-Valued Recurrent Neural Networks with Inner State Feedback
- 10.3390/books978-3-03897-522-9 may be a valid DOI for title: Biological and Biogenic Crystallization
- 10.1613/jair.251 may be a valid DOI for title: Mean Field Theory for Sigmoid Belief Networks
- 10.1007/978-981-13-1298-4_1 may be a valid DOI for title: Intelligent Adaptive Fuzzy Control
- 10.1109/icdar.2003.1227801 may be a valid DOI for title: Best Practices for Convolutional Neural Networks Applied to Visual Document Analysis
- 10.1016/j.physa.2010.01.035 may be a valid DOI for title: Improvement of Signal-to-Noise Ratio by Stochastic Resonance in Sigmoid Function Threshold Systems, Demonstrated Using a CMOS Inverter
- 10.46945/bpj.10.1.03.01 may be a valid DOI for title: WHO Coronavirus Disease (COVID-19) Dashboard

INVALID DOIs

- None

[kthyng]

Hi @somefunAgba, and thanks for your submission. I am trying to learn about this submission before deciding on next steps. Can you start by describing which of the code in the repository is specifically under review here, that is, written by you and your co-authors? I see for example the code in the helpers directories looks to be previously written by other people, so a list of the work (scripts/directories of scripts) described in this submission would be helpful.

[somefunAgba]

Hello. Thanks @kthyng.

All code in the repository apart from those in the helpers directory was written by me.

-- helpers directory The code in the helpers directory are also open-source matlab functions that can be found on Matlab's FileExchange.

1. LinePlotReducer.m and reduce_plot.m is an alternative to matlab's plot function.

   • Status: unused, added for possible use.

2. SLMtools is a custom matlab toolbox for fitting splines on data.

   • Status: minimal usage. This was used to smooth the noisy data, so as to reduce the time spent in finding zero-crossings.
   • active only when, bootstrapping action is specified by the user.

3. cprintf.m augments matlab's command-line print function for coloured text.

   • Status:. Actively used in the non-gui functions, mostly for coloured prints of debugging messages.

-- main directories

1. cvmain

   • contains the main functions for the NLSIG-COVID19Lab

2. applet

   • contains the MATLAB GUI Application file for NLSIG-COVID19Lab

3. local

   • local database directory for reference

4. data

   • actual database directory

5. ui

   • contains user application scripts for executing NLSIG-COVID19Lab

6. assets, measures

   • dynamically created directories: respectively:
   • stores plots of the infections and deaths growth model
   • stores the model metrics for the COVID-19 phenomena in each locale successfully queried.

7. osspaper

   • directory for paper.md submitted to JOSS.

[kthyng]

Thank you @somefunAgba, that is helpful!

[kthyng]

We can proceed.

@will-rowe Are you up for editing this submission?

[kthyng]

@whedon invite @will-rowe as editor

[whedon]

@will-rowe has been invited to edit this submission.

[will-rowe]

Hi all. I'd be happy to but I am on leave until early January now, as I imagine most reviewers will be. I can take this on in the new year if that suits everyone.

[kthyng]

@will-rowe Agreed. I will add you as editor now but with the understanding that you will start on it in the new year.

[kthyng]

@whedon assign @will-rowe as editor

[whedon]

OK, the editor is @will-rowe

[somefunAgba]

@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:

[will-rowe]

Hi @kthyng

I'm sorry but with the latest lockdown just announced in the UK, I'm going to be looking after my kids with them home from primary school. I will be working as I can but my editorial response times will be much slower. I can still take this submission on with the understanding that I may be slow to handle this at times but if there is another editor with more capacity, that may be better for the submitter. I'm happy either way.

[kthyng]

@will-rowe Sorry for my delay in responding. Of course things are super difficult right now! I'll try to find another editor to keep this off your plate.

@majensen Would you be able to edit this submission?

[kthyng]

@whedon invite @majensen as editor

[whedon]

@majensen has been invited to edit this submission.

[majensen]

@whedon assign me as editor

[whedon]

OK, the editor is @majensen

[majensen]

happy to do that @kthyng

[majensen]

Hello @nnadeau -- would you have some time to review this work for JOSS? It would be great to have your MATLAB expertise. Please let me know in this thread or via maj -dot- fortinbras -at- gmail -dot- com. Thanks for your consideration! -- @majensen

[majensen]

Hola @jsgalan - would you be willing to review this work for JOSS? Hope to tap into your MATLAB expertise. Please let me know in this thread or at maj -dot- fortinbras -at- gmail -dot- com. I appreciate your consideration! --@majensen

[engnadeau]

@majensen I no longer have access to a MATLAB instance, but if @somefunAgba can confirm it's compatible with Octave, then I can give it a proper review

[majensen]

Thank you @nnadeau -- @somefunAgba is your code Octave-compatible?

[somefunAgba]

@nnadeau @majensen I have not tested it with Octave. It was all implemented in MATLAB2020a. However, I doubt Octave supports Matlab's problem-based optimization workflow which I heavily used in the current version of my code.

[majensen]

@somefunAgba thanks. It looks as if the problem-based optimization is key to your implementation, and that MATLAB package seems very sophisticated and proprietary -- unlikely that there is an open source implementation as yet (quick search of Octave packages and Github doesn't yield anything promising). @nnadeau - let us know what you think - if you could recommend a reviewer that would also be very helpful.

[majensen]

@somefunAgba - if you have reviewer recommendations as well, I would be much obliged.

[jsgalan]

Hi all, I am not available to review at the moment.

Thanks for the invite.

[somefunAgba]

@majensen. Probably the following could be invited: @dsurujon, @ManuelaS, @kakearney, @castelao from similar reviewers of MATLAB code for JOSS

[majensen]

Thanks @somefunAgba. @jsgalan thanks for your consideration!

[castelao]

Interesting package @somefunAgba . I apologize but I can't commit to this at the moment. Good luck!

[ManuelaS]

It looks like a very interesting package @somefunAgba . However, I only have access to Matlab 2014b with a limited set of packages? What Matlab version and what packages does your package need?

[engnadeau]

@majensen if MATLAB is a requirement, then it would be best if someone else reviews it.

@somefunAgba, as a pre-review comment I would recommend updating the README with a robust requirements section such that reviews (and future users) know exactly what MATLAB version(s), toolboxes, and other dependencies are needed. This would avoid confusion and user experience impedance like @ManuelaS is facing.

[somefunAgba]

Thanks @nnadeau. I have modified the README with your comments.

[somefunAgba]

@ManuelaS because the optimization workflow used in the package is a problem-based, as opposed to a solver-based one, R2017b and above is needed. No external dependencies needed, other than the presence of Matlab's

• Optimization Toolbox, and
• Statistics and Machine Learning Toolbox.

[dsurujon]

I appreciate the invite, but I have to apologize that I cannot commit to reviewing this at the moment

[majensen]

@castelao @dsurujon thanks for your responses and consideration!

[majensen]

@agahkarakuzu - We at JOSS could use your MATLAB expertise on this work. Heads up that it requires a minimum version of R2017b. Appreciate your consideration - --@majensen

[agahkarakuzu]

@majensen I have the required toolbox & versions, happy to help out.

[majensen]

Awesome @agahkarakuzu , will add you as reviewer

[majensen]

@whedon assign @agahkarakuzu as reviewer

[whedon]

OK, @agahkarakuzu is now a reviewer

[majensen]

@kakearney would you have time and interest to review this work for JOSS? We could use your MATLAB expertise. Please let me know in this thread or at maj - dot - fortinbras - at - gmail - dot - com. I appreciate your consideration! --@majensen

[kakearney]

I would only be able to review this work from a technical (i.e. Matlab) standpoint. The topic itself is well outside my research focus, so I will have to accept the summary paper at face value, and assume the authors have properly described the state of the field, this entry's place in it, and that the chosen fitting techniques are appropriate. If that is okay, I should be able to provide a review by the end of the month.

[majensen]

@kakearney that would be fine. I will weigh in on the aspects you mention. I really appreciate your help.

[majensen]

btw @kakearney it goes without saying (but I am saying it anyway) that any scientific or methodological issues you raise will be fair game and very welcome

[majensen]

@whedon add @kakearney as reviewer