o2geosocial: Reconstruction of Transmission Chains from Surveillance Data

Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).

Version: 1.1.3
Depends: R (≥ 3.5.0)
Imports: Rcpp, methods, stats, grDevices, geosphere, ggplot2, visNetwork, data.table, outbreaker2
LinkingTo: Rcpp
Suggests: testthat, tigris, sf, knitr, socialmixr, rmarkdown
Published: 2024-06-21
DOI: 10.32614/CRAN.package.o2geosocial
Author: Alexis Robert ORCID iD [aut, cre, cph], Sebastian Funk ORCID iD [aut], Adam J Kucharski ORCID iD [aut], Thibaut Jombart [ctb]
Maintainer: Alexis Robert <alexis.robert at lshtm.ac.uk>
BugReports: https://github.com/alxsrobert/o2geosocial/issues
License: MIT + file LICENSE
URL: https://github.com/alxsrobert/o2geosocial
NeedsCompilation: yes
Materials: README NEWS
In views: Epidemiology
CRAN checks: o2geosocial results


Reference manual: o2geosocial.pdf
Vignettes: o2geosocial


Package source: o2geosocial_1.1.3.tar.gz
Windows binaries: r-devel: o2geosocial_1.1.3.zip, r-release: o2geosocial_1.1.3.zip, r-oldrel: o2geosocial_1.1.3.zip
macOS binaries: r-release (arm64): o2geosocial_1.1.3.tgz, r-oldrel (arm64): o2geosocial_1.1.2.tgz, r-release (x86_64): o2geosocial_1.1.3.tgz, r-oldrel (x86_64): o2geosocial_1.1.2.tgz
Old sources: o2geosocial archive


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