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Outbreak reconstruction with sequence data

The package implements the method described in Klinkenberg et al (2016), doi:


  • enter data and priors by constructing an object of S3-class 'phybreak', with function 'phybreak'

  • do mcmc-updates with functions 'burnin_phybreak' and 'sample_phybreak'; remove samples with 'thin.phybreak'

  • access the 'phybreak'-object by get_phybreak-functions such as 'get_transtree', 'get_data', 'get_parameters'

  • summarize the mcmc-chain with the functions 'ESS', 'transtree', 'infectorsets', 'phylotree', 'get_mcmc', 'get_phylo'

  • plotting with 'plot', 'plotTrans', and 'plotPhylo'

  • it is possible to simulate data with 'sim_phybreak'