PONE-D-20-21676

Spatial and temporal regularization to estimate COVID-19 Reproduction Number R(t): 

Promoting piecewise smoothness via convex optimization

PLOS ONE

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Academic Editor

PLOS ONE

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The paper, after minor revision according to the attached report, could be accepted for publication.

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Reviewer #1: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: PLOS ONE

Manuscript Number: PONE-D-20-21676

Manuscript Title: Spatial and temporal regularization to estimate COVID-19 Reproduction Number R(t): Promoting piecewise smoothness via convex optimization

This is a really interesting paper.

The study presents the results of original research. The paper is interesting and, useful both in a mathematical sense and in medical one.

The author suggested a new estimation procedure to quantify the spread of a new epidemic in order to permit the monitoring of the evolution of the reproduction number.

Research work is motivated by the need to find a new method to monitoring the pandemic evolution in real time. The work proposed a new framework for the estimation of R(t).

Incidence data referes to the number of daily new infections in several conutries and secondarly in France departments.

1. INTRODUCTION

Context

To enrich the work of interest it might be useful to explain the practical usefulness of having new predictive models inserting some sentences such as:

“The ability to provide a predictive model is extremely useful for management of patients and also for medical resource allocation. What was in fact achieved in recent months of February and March was the difficulty to have models that could predict the number of patients (not only the infected) and what was the real need for personal protection and support for patients in hospitals.

At that time, in fact, the data and methods of spreading the epidemic in China were not fully available, but already in Europe, primarily in Italy, the epidemic was spreading. In fact, we were not talking about a pandemic yet and we were not able to meet the needs of gloves, disinfectant, facial mask, mechanical ventilators and beds of intensive care”. The goal of the entire research community is to find a solution to provide timely data to prevent future health crises.

To support these sentence authors can cite these COVID-19 update articles or others that they can choose:

Coccia M.

Factors determining the diffusion of COVID-19 and suggested strategy to prevent future accelerated viral infectivity similar to COVID.

Sci Total Environ. 2020 Aug 10;729:138474. doi: 10.1016/j.scitotenv.2020.138474.

Petkova E, Antman EM, Troxel AB.

Pooling Data From Individual Clinical Trials in the COVID-19 Era

JAMA. Published online July 22, 2020. doi:10.1001/jama.2020.13042

Ing, RJ; Bills, C; Merritt, G et al.

Role of Helmet-Delivered Noninvasive Pressure Support Ventilation in COVID-19 Patients.

J Cardiothorac Vasc Anesth; 2020 May 08. doi: 10.1053/j.jvca.2020.04.060.

The part “issue and related work” is too long: it is recommended to eliminate the details that will be described later to better focus the work points.

MATHERIALS AND METHODS

To make the reading clearer it is necessary to delete parts already described or comments and just describe the data.

Model and estimation procedures represent the core of the work and unnecessary or repeated parts should be eliminated (for example line 125-127 “to enable..basis”or line 151-152 “outliers…ways” or line 167-169 “as…outbreak”).

RESULTS

The study presents the results of original research.

Results reported have not been published elsewhere.

Methods are described in sufficient detail for another researcher to reproduce the experiments described.

CONCLUSIONS

In order to clarify the conclusions it is necessary to delete some phrases or concepts already described (for example line 520-532 “Estimation….analysis”; line 546-552 “As previously… address”).

I suggest to move the sentence “when decisions need to be taken and action need to be made 525

under emergency” (line 525-526) at the end of the conclusion paragraph (line 566).

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Reviewer #1: No

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Spatial and temporal regularization to estimate COVID-19 Reproduction Number R(t): 

Promoting piecewise smoothness via convex optimization

PONE-D-20-21676R1

Dear Dr. Abry,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Maria Alessandra Ragusa, PhD Professor

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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