Data from: Two-phase importance sampling for inference about transmission trees

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dc.contributor.affiliationUniversity of Helsinki - Numminen, Elina
dc.contributor.affiliationWellcome Trust - Chewapreecha, Claire
dc.contributor.affiliationUniversity of Helsinki - Sirén, Jukka
dc.contributor.affiliationMahidol University - Turner, Claudia
dc.contributor.affiliationMahidol University - Turner, Paul
dc.contributor.affiliationWellcome Trust - Bentley, Stephen D.
dc.contributor.affiliationUniversity of Helsinki - Corander, Jukka
dc.contributor.affiliationUniversity of Helsinki - Siren, J.
dc.contributor.authorNumminen, Elina
dc.contributor.authorChewapreecha, Claire
dc.contributor.authorSirén, Jukka
dc.contributor.authorTurner, Claudia
dc.contributor.authorTurner, Paul
dc.contributor.authorBentley, Stephen D.
dc.contributor.authorCorander, Jukka
dc.contributor.authorSiren, J.
dc.coverage.spatialNorthwestern Thailand
dc.date.accessioned2025-03-24T15:11:27Z
dc.date.issued2014-08-29
dc.date.issued2014-08-29
dc.descriptionThere has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary to many earlier proposed methods. We illustrate the scheme by analysing transmissions of Streptococcus pneumoniae from household to household within a refugee camp, using data in which only a fraction of hosts is observed, but which is still rich enough to unravel the within-household transmission dynamics and pairs of households between whom transmission is plausible. We observe that while probability of direct transmission is low even for the most prominent cases of transmission, still those pairs of households are geographically much closer to each other than expected under random proximity.
dc.identifierhttps://doi.org/10.5061/dryad.8d2f6
dc.identifier.urihttps://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/9184
dc.rightsOpen
dc.rights.licensecc-zero
dc.subjectmolecular epidemiology
dc.subjectparsimony trees
dc.subjectSNP trees
dc.subjectTransmission tree
dc.subjectStreptococcus pneumoniae
dc.titleData from: Two-phase importance sampling for inference about transmission trees
dc.typedataset
dc.typedataset

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