S7 Fig -
<p>Comparison of EpiFusion and BDSky likelihoods on the same datasets for varying values of (a) beta, (b) gamma and (c) psi around the true values (marked by the blue vertical line). The stochastic and approximate nature of the EpiFusion likelihood means the values are not identical, though th...
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2024
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| _version_ | 1852025271087005696 |
|---|---|
| author | Ciara Judge (20161514) |
| author2 | Timothy Vaughan (5654278) Timothy Russell (20161517) Sam Abbott (9548946) Louis du Plessis (3264087) Tanja Stadler (118822) Oliver Brady (5331668) Sarah Hill (101064) |
| author2_role | author author author author author author author |
| author_facet | Ciara Judge (20161514) Timothy Vaughan (5654278) Timothy Russell (20161517) Sam Abbott (9548946) Louis du Plessis (3264087) Tanja Stadler (118822) Oliver Brady (5331668) Sarah Hill (101064) |
| author_role | author |
| dc.creator.none.fl_str_mv | Ciara Judge (20161514) Timothy Vaughan (5654278) Timothy Russell (20161517) Sam Abbott (9548946) Louis du Plessis (3264087) Tanja Stadler (118822) Oliver Brady (5331668) Sarah Hill (101064) |
| dc.date.none.fl_str_mv | 2024-11-11T18:47:47Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pcbi.1012528.s010 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/S7_Fig_-/27658931 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Genetics Biotechnology Evolutionary Biology Cancer Infectious Diseases Computational Biology Mathematical Sciences not elsewhere classified surveillance rapidly changes scaled trees estimated remain largely distinct poorly sampled epidemics effective reproduction number accommodate future extensions respiratory virus outbreaks approach scales efficiently 2014 ebola outbreak phylodynamic observation models div >< p </ sub >) </ sub simulated outbreaks outbreak dynamics joint approach xlink "> weighted according sierra leone retrospective analysis phylogenetic uncertainty pathogen phylodynamics joint inference integrating phylodynamic infectious disease increases certainty genetic sequences fundamental challenge existing methods demonstrate advances dataset size complementary strengths circulating pathogen case incidence accurately estimating |
| dc.title.none.fl_str_mv | S7 Fig - |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>Comparison of EpiFusion and BDSky likelihoods on the same datasets for varying values of (a) beta, (b) gamma and (c) psi around the true values (marked by the blue vertical line). The stochastic and approximate nature of the EpiFusion likelihood means the values are not identical, though they do show good agreement in awarding the true value with the highest likelihood. As the model values of each parameter become further from the true value, the EpiFusion likelihood shows a tendency to drop sharply due to the parameters values implying very unlikely or impossible trajectories. The EpiFusion models appear to demonstrate a marginal overestimation of the sampling parameter psi here, however this was not seen in the simulation based calibration.</p> <p>(TIFF)</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_bfdf6d017cfe692b180e40c195713645 |
| identifier_str_mv | 10.1371/journal.pcbi.1012528.s010 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/27658931 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | S7 Fig - Ciara Judge (20161514)Timothy Vaughan (5654278)Timothy Russell (20161517)Sam Abbott (9548946)Louis du Plessis (3264087)Tanja Stadler (118822)Oliver Brady (5331668)Sarah Hill (101064)GeneticsBiotechnologyEvolutionary BiologyCancerInfectious DiseasesComputational BiologyMathematical Sciences not elsewhere classifiedsurveillance rapidly changesscaled trees estimatedremain largely distinctpoorly sampled epidemicseffective reproduction numberaccommodate future extensionsrespiratory virus outbreaksapproach scales efficiently2014 ebola outbreakphylodynamic observation modelsdiv >< p</ sub >)</ subsimulated outbreaksoutbreak dynamicsjoint approachxlink ">weighted accordingsierra leoneretrospective analysisphylogenetic uncertaintypathogen phylodynamicsjoint inferenceintegrating phylodynamicinfectious diseaseincreases certaintygenetic sequencesfundamental challengeexisting methodsdemonstrate advancesdataset sizecomplementary strengthscirculating pathogencase incidenceaccurately estimating<p>Comparison of EpiFusion and BDSky likelihoods on the same datasets for varying values of (a) beta, (b) gamma and (c) psi around the true values (marked by the blue vertical line). The stochastic and approximate nature of the EpiFusion likelihood means the values are not identical, though they do show good agreement in awarding the true value with the highest likelihood. As the model values of each parameter become further from the true value, the EpiFusion likelihood shows a tendency to drop sharply due to the parameters values implying very unlikely or impossible trajectories. The EpiFusion models appear to demonstrate a marginal overestimation of the sampling parameter psi here, however this was not seen in the simulation based calibration.</p> <p>(TIFF)</p>2024-11-11T18:47:47ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pcbi.1012528.s010https://figshare.com/articles/figure/S7_Fig_-/27658931CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/276589312024-11-11T18:47:47Z |
| spellingShingle | S7 Fig - Ciara Judge (20161514) Genetics Biotechnology Evolutionary Biology Cancer Infectious Diseases Computational Biology Mathematical Sciences not elsewhere classified surveillance rapidly changes scaled trees estimated remain largely distinct poorly sampled epidemics effective reproduction number accommodate future extensions respiratory virus outbreaks approach scales efficiently 2014 ebola outbreak phylodynamic observation models div >< p </ sub >) </ sub simulated outbreaks outbreak dynamics joint approach xlink "> weighted according sierra leone retrospective analysis phylogenetic uncertainty pathogen phylodynamics joint inference integrating phylodynamic infectious disease increases certainty genetic sequences fundamental challenge existing methods demonstrate advances dataset size complementary strengths circulating pathogen case incidence accurately estimating |
| status_str | publishedVersion |
| title | S7 Fig - |
| title_full | S7 Fig - |
| title_fullStr | S7 Fig - |
| title_full_unstemmed | S7 Fig - |
| title_short | S7 Fig - |
| title_sort | S7 Fig - |
| topic | Genetics Biotechnology Evolutionary Biology Cancer Infectious Diseases Computational Biology Mathematical Sciences not elsewhere classified surveillance rapidly changes scaled trees estimated remain largely distinct poorly sampled epidemics effective reproduction number accommodate future extensions respiratory virus outbreaks approach scales efficiently 2014 ebola outbreak phylodynamic observation models div >< p </ sub >) </ sub simulated outbreaks outbreak dynamics joint approach xlink "> weighted according sierra leone retrospective analysis phylogenetic uncertainty pathogen phylodynamics joint inference integrating phylodynamic infectious disease increases certainty genetic sequences fundamental challenge existing methods demonstrate advances dataset size complementary strengths circulating pathogen case incidence accurately estimating |