{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T11:38:40Z","timestamp":1767181120625,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006955","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,17]],"date-time":"2019-04-17T00:00:00Z","timestamp":1555459200000}}],"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2019,4,5]],"date-time":"2019-04-05T00:00:00Z","timestamp":1554422400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006955","type":"journal-article","created":{"date-parts":[[2019,4,5]],"date-time":"2019-04-05T13:31:40Z","timestamp":1554471100000},"page":"e1006955","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Model diagnostics and refinement for phylodynamic models"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0420-9736","authenticated-orcid":true,"given":"Max S. Y.","family":"Lau","sequence":"first","affiliation":[]},{"given":"Bryan T.","family":"Grenfell","sequence":"additional","affiliation":[]},{"given":"Colin J.","family":"Worby","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8203-0083","authenticated-orcid":true,"given":"Gavin J.","family":"Gibson","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,4,5]]},"reference":[{"issue":"5656","key":"ref1","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1126\/science.1090727","article-title":"Unifying the epidemiological and evolutionary dynamics of pathogens","volume":"303","author":"BT Grenfell","year":"2004","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2012.0193","article-title":"Evolutionary epidemiology: preparing for an age of genomic plenty","author":"O Pybus","year":"2013"},{"issue":"11","key":"ref3","doi-asserted-by":"crossref","first-page":"e1004633","DOI":"10.1371\/journal.pcbi.1004633","article-title":"A systematic Bayesian integration of epidemiological and genetic data","volume":"11","author":"MS Lau","year":"2015","journal-title":"PLoS computational biology"},{"issue":"1","key":"ref4","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1214\/15-AOAS898","article-title":"Reconstructing transmission trees for communicable diseases using densely sampled genetic data","volume":"10","author":"CJ Worby","year":"2016","journal-title":"The annals of applied statistics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e1002768","DOI":"10.1371\/journal.pcbi.1002768","article-title":"A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data","volume":"8","author":"MJ Morelli","year":"2012","journal-title":"PLoS Computational Biology"},{"issue":"4","key":"ref6","doi-asserted-by":"crossref","first-page":"e1004869","DOI":"10.1371\/journal.pcbi.1004869","article-title":"Molecular infectious disease epidemiology: survival analysis and algorithms linking phylogenies to transmission trees","volume":"12","author":"E Kenah","year":"2016","journal-title":"PLoS computational biology"},{"issue":"1782","key":"ref7","doi-asserted-by":"crossref","first-page":"20133251","DOI":"10.1098\/rspb.2013.3251","article-title":"A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data","volume":"281","author":"N Mollentze","year":"2014","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"issue":"1728","key":"ref8","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1098\/rspb.2011.0913","article-title":"Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data","volume":"279","author":"R Ypma","year":"2012","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"issue":"1","key":"ref9","doi-asserted-by":"crossref","first-page":"e1003457","DOI":"10.1371\/journal.pcbi.1003457","article-title":"Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data","volume":"10","author":"T Jombart","year":"2014","journal-title":"PLoS Computational Biology"},{"key":"ref10","article-title":"Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees","author":"M Kendall","year":"2017","journal-title":"Statistical Science"},{"issue":"4","key":"ref11","first-page":"997","article-title":"Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks","volume":"34","author":"X Didelot","year":"2017","journal-title":"Molecular biology and evolution"},{"issue":"9","key":"ref12","doi-asserted-by":"crossref","first-page":"e1005130","DOI":"10.1371\/journal.pcbi.1005130","article-title":"SCOTTI: efficient reconstruction of transmission within outbreaks with the structured coalescent","volume":"12","author":"N De Maio","year":"2016","journal-title":"PLoS computational biology"},{"issue":"1637","key":"ref13","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1098\/rspb.2007.1442","article-title":"Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus","volume":"275","author":"EM Cottam","year":"2008","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"issue":"1794","key":"ref14","doi-asserted-by":"crossref","first-page":"20141324","DOI":"10.1098\/rspb.2014.1324","article-title":"Two-phase importance sampling for inference about transmission trees","volume":"281","author":"E Numminen","year":"2014","journal-title":"Proceedings of the Royal Society of London B: Biological Sciences"},{"issue":"1","key":"ref15","first-page":"129","article-title":"Construction of semi-Markov genetic-space-time SEIR models and inference","volume":"157","author":"S Soubeyrand","year":"2016","journal-title":"Journal de la Soci\u00e9t\u00e9 Fran\u00e7aise de Statistique"},{"issue":"1614","key":"ref16","doi-asserted-by":"crossref","first-page":"20120198","DOI":"10.1098\/rstb.2012.0198","article-title":"Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods","volume":"368","author":"T Stadler","year":"2013","journal-title":"Philosophical Transactions of the Royal Society B: Biological Sciences"},{"issue":"10","key":"ref17","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1093\/aje\/kwx182","article-title":"Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data","volume":"186","author":"CJ Worby","year":"2017","journal-title":"American journal of epidemiology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.meegid.2016.07.010","article-title":"Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus","volume":"44","author":"DJ King","year":"2016","journal-title":"Infection, Genetics and Evolution"},{"issue":"1","key":"ref19","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1742-4690-10-49","article-title":"Within-host and between-host evolutionary rates across the HIV-1 genome","volume":"10","author":"S Alizon","year":"2013","journal-title":"Retrovirology"},{"issue":"7","key":"ref20","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1016\/j.cell.2015.06.007","article-title":"Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone","volume":"161","author":"DJ Park","year":"2015","journal-title":"Cell"},{"issue":"5","key":"ref21","doi-asserted-by":"crossref","first-page":"e1002730","DOI":"10.1371\/journal.ppat.1002730","article-title":"Evolution of an Eurasian avian-like influenza virus in naive and vaccinated pigs","volume":"8","author":"PR Murcia","year":"2012","journal-title":"PLoS Pathogens"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"20131093","DOI":"10.1098\/rsif.2013.1093","article-title":"New model diagnostics for spatio-temporal systems in epidemiology and ecology","volume":"11","author":"MSY Lau","year":"2014","journal-title":"J R Soc Interface"},{"issue":"4","key":"ref23","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1007\/s11222-006-0019-z","article-title":"Bayesian estimation for percolation models of disease spread in plant populations","volume":"16","author":"GJ Gibson","year":"2006","journal-title":"Statistics and Computing"},{"issue":"4","key":"ref24","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1111\/1467-9868.00353","article-title":"Bayesian measures of model complexity and fit","volume":"64","author":"DJ Spiegelhalter","year":"2002","journal-title":"Journal of the Royal Statistical Society: Series B (Statistical Methodology)"},{"key":"ref25","doi-asserted-by":"crossref","DOI":"10.3389\/fvets.2017.00016","article-title":"Data-Driven risk assessment from small scale epidemics: estimation and Model choice for spatio-Temporal Data with application to a classical swine Fever Outbreak","volume":"4","author":"K Gamado","year":"2017","journal-title":"Frontiers in Veterinary Science"},{"issue":"9","key":"ref26","doi-asserted-by":"crossref","first-page":"2337","DOI":"10.1073\/pnas.1614595114","article-title":"Spatial and temporal dynamics of superspreading events in the 2014\u20132015 West Africa Ebola epidemic","volume":"114","author":"MS Lau","year":"2017","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"17","key":"ref27","doi-asserted-by":"crossref","first-page":"6258","DOI":"10.1073\/pnas.1310997111","article-title":"Bayesian inference for an emerging arboreal epidemic in the presence of control","volume":"111","author":"M Parry","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref28","article-title":"Computational molecular evolution","volume":"vol. 284","author":"Z Yang","year":"2006"},{"issue":"3","key":"ref29","doi-asserted-by":"crossref","first-page":"e1003549","DOI":"10.1371\/journal.pcbi.1003549","article-title":"Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data","volume":"10","author":"CJ Worby","year":"2014","journal-title":"PLoS computational biology"},{"issue":"4","key":"ref30","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1534\/genetics.114.171538","article-title":"The distribution of pairwise genetic distances: a tool for investigating disease transmission","volume":"198","author":"CJ Worby","year":"2014","journal-title":"Genetics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1214\/aos\/1176345970","article-title":"The functional-model basis of fiducial inference","author":"AP Dawid","year":"1982","journal-title":"The Annals of Statistics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1111\/j.2517-6161.1968.tb00724.x","article-title":"A general definition of residuals","author":"DR Cox","year":"1968","journal-title":"Journal of the Royal Statistical Society Series B (Methodological)"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1214\/aoms\/1177704850","article-title":"Distribution of the Anderson-Darling statistic","author":"PA Lewis","year":"1961","journal-title":"The Annals of Mathematical Statistics"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1214\/17-STS615","article-title":"Comparison and Assessment of Epidemic Models","volume":"33","author":"GJ Gibson","year":"2018","journal-title":"Statistical Science"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1214\/aos\/1176325622","article-title":"Posterior predictive p-values","volume":"22","author":"X-L Meng","year":"1994","journal-title":"Ann. Stat"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1093\/sysbio\/syx076","article-title":"Analysis of Phylogenomic trees space resolves relationships among marsupial families","volume":"67","author":"DA Duchene","year":"2018","journal-title":"Syst. Biol"},{"issue":"7066","key":"ref37","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nature04153","article-title":"Superspreading and the effect of individual variation on disease emergence","volume":"438","author":"JO Lloyd-Smith","year":"2005","journal-title":"Nature"},{"issue":"430","key":"ref38","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1080\/01621459.1995.10476572","article-title":"Bayes factors","volume":"90","author":"RE Kass","year":"1995","journal-title":"Journal of the American Statistical Association"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006955","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,17]],"date-time":"2019-04-17T00:00:00Z","timestamp":1555459200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006955","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T01:45:04Z","timestamp":1588988704000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006955"}},"subtitle":[],"editor":[{"given":"David A","family":"Rasmussen","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,4,5]]},"references-count":38,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,4,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006955","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,5]]}}}