Please use this identifier to cite or link to this item: http://hdl.handle.net/10553/77688
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dc.contributor.authorBoulmezaoud, Tahar Zameneen_US
dc.contributor.authorAlvarez, Luisen_US
dc.contributor.authorColom, Miguelen_US
dc.contributor.authorMorel, Jean Michelen_US
dc.date.accessioned2021-02-11T09:05:59Z-
dc.date.available2021-02-11T09:05:59Z-
dc.date.issued2020en_US
dc.identifier.issn2105-1232en_US
dc.identifier.otherScopus-
dc.identifier.urihttp://hdl.handle.net/10553/77688-
dc.description.abstractWe describe a transparent method calculating an “effective reproduction number (ERN)" from the daily count (incidence) of newly detected cases in each country, in the EU and in each US state. We aim at getting a result as faithful as possible to the observed data, which are very noisy. The noise, being specific of administrations, shows a seven days period. Hence the incidence curve is first filtered by a seven days mean or median filter. Then the ERN is computed by a classic reproduction formula due to Nishiura. To do so requires knowledge of the serial interval function π(s) which models the time between the onset of symptoms in a primary case and the onset of symptoms in secondary cases, or equivalently the probability that a person confirmed infected today was actually infected s days earlier by another confirmed infected person. We fluse and compare several recently proposed evaluations of π, and verify that their variation has moderate practical incidence on the evaluation of the ERN. The method we present derives from Nishiura’s formula but we prove that for the adequate choice of parameters it is identical to one of the methods proposed by the classic EpiEstim (Estimate Time Varying Reproduction Numbers from Epidemic Curves) software. We find that the same method can be applied to compute an effective reproduction number from the daily death count, which yields therefore another prediction of the expansion of the pandemic. Although this application has no clear theoretical justification, we find good experimental fit of the ERN curves obtained from the incidence and from the death curve, up to a time shift. In most countries, both curves appear to be similar, with a time delay that depends on each country’s detection and administrative processing delays. Both ERNs can be consulted daily online in the demo tag associated with this paper. We refer the readers to the online demo1 to experiment by themselves. In the case of France, an ERN based on hospitalizations, new entries in ICU’s and deaths at hospitals is also computed daily2. The code is quite simple. To simplify its presentation we use a single file where all basic procedures are included, from the management of data to the parameter optimization. The reviewed source code and documentation for this algorithm are available from the web page of this article3. Compilation and usage instructions are included in the README.txt file of the archive.en_US
dc.languageengen_US
dc.relation.ispartofImage Processing On Lineen_US
dc.sourceImage Processing On Line [EISSN 2105-1232], v. 10, p. 191-210, (Enero 2020)en_US
dc.subject120602 Ecuaciones diferencialesen_US
dc.subject120326 Simulaciónen_US
dc.subject3202 Epidemologiaen_US
dc.subject.otherDaily Reproduction Numberen_US
dc.subject.otherEpidemicen_US
dc.subject.otherErnen_US
dc.subject.otherSars-Cov-2en_US
dc.titleA daily measure of the SARS-CoV-2 effective reproduction number for all countriesen_US
dc.typeinfo:eu-repo/semantics/Articleen_US
dc.typeArticleen_US
dc.identifier.doi10.5201/ipol.2020.304en_US
dc.identifier.scopus85099825901-
dc.contributor.authorscopusid6603787050-
dc.contributor.authorscopusid55640159000-
dc.contributor.authorscopusid55549886000-
dc.contributor.authorscopusid57203072257-
dc.identifier.eissn2105-1232-
dc.description.lastpage210en_US
dc.description.firstpage191en_US
dc.relation.volume10en_US
dc.investigacionCienciasen_US
dc.type2Artículoen_US
dc.utils.revisionen_US
dc.date.coverdateEnero 2020en_US
dc.identifier.ulpgcen_US
dc.contributor.buulpgcBU-INFen_US
dc.description.sjr0,359
dc.description.sjrqQ3
dc.description.esciESCI
item.fulltextCon texto completo-
item.grantfulltextopen-
crisitem.author.deptGIR Modelos Matemáticos-
crisitem.author.deptDepartamento de Informática y Sistemas-
crisitem.author.orcid0000-0002-6953-9587-
crisitem.author.parentorgDepartamento de Informática y Sistemas-
crisitem.author.fullNameÁlvarez León, Luis Miguel-
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