Estimating the basic reproduction number at the beginning of an outbreak
We compare several popular methods of estimating the basic reproduction number, R0, focusing on the early stages of an epidemic, and assuming weekly reports of new infecteds. We study the situation when data is generated by one of three standard epidemiological compartmental models: SIR, SEIR, and S...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205483/?tool=EBI |
| _version_ | 1811343163858616320 |
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| author | Sawitree Boonpatcharanon Jane M. Heffernan Hanna Jankowski |
| author_facet | Sawitree Boonpatcharanon Jane M. Heffernan Hanna Jankowski |
| author_sort | Sawitree Boonpatcharanon |
| collection | DOAJ |
| description | We compare several popular methods of estimating the basic reproduction number, R0, focusing on the early stages of an epidemic, and assuming weekly reports of new infecteds. We study the situation when data is generated by one of three standard epidemiological compartmental models: SIR, SEIR, and SEAIR; and examine the sensitivity of the estimators to the model structure. As some methods are developed assuming specific epidemiological models, our work adds a study of their performance in both a well-specified (data generating model and method model are the same) and miss-specified (data generating model and method model differ) settings. We also study R0 estimation using Canadian COVID-19 case report data. In this study we focus on examples of influenza and COVID-19, though the general approach is easily extendable to other scenarios. Our simulation study reveals that some estimation methods tend to work better than others, however, no singular best method was clearly detected. In the discussion, we provide recommendations for practitioners based on our results. |
| first_indexed | 2024-04-13T19:24:51Z |
| format | Article |
| id | doaj.art-bbc79ae8372b4c2f82386f0d6e9f6f6a |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T19:24:51Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-bbc79ae8372b4c2f82386f0d6e9f6f6a2022-12-22T02:33:24ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01176Estimating the basic reproduction number at the beginning of an outbreakSawitree BoonpatcharanonJane M. HeffernanHanna JankowskiWe compare several popular methods of estimating the basic reproduction number, R0, focusing on the early stages of an epidemic, and assuming weekly reports of new infecteds. We study the situation when data is generated by one of three standard epidemiological compartmental models: SIR, SEIR, and SEAIR; and examine the sensitivity of the estimators to the model structure. As some methods are developed assuming specific epidemiological models, our work adds a study of their performance in both a well-specified (data generating model and method model are the same) and miss-specified (data generating model and method model differ) settings. We also study R0 estimation using Canadian COVID-19 case report data. In this study we focus on examples of influenza and COVID-19, though the general approach is easily extendable to other scenarios. Our simulation study reveals that some estimation methods tend to work better than others, however, no singular best method was clearly detected. In the discussion, we provide recommendations for practitioners based on our results.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205483/?tool=EBI |
| spellingShingle | Sawitree Boonpatcharanon Jane M. Heffernan Hanna Jankowski Estimating the basic reproduction number at the beginning of an outbreak PLoS ONE |
| title | Estimating the basic reproduction number at the beginning of an outbreak |
| title_full | Estimating the basic reproduction number at the beginning of an outbreak |
| title_fullStr | Estimating the basic reproduction number at the beginning of an outbreak |
| title_full_unstemmed | Estimating the basic reproduction number at the beginning of an outbreak |
| title_short | Estimating the basic reproduction number at the beginning of an outbreak |
| title_sort | estimating the basic reproduction number at the beginning of an outbreak |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205483/?tool=EBI |
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