Outbreak reconstruction with sequence data
The package implements the method described in Klinkenberg et al (2016), doi: http://dx.doi.org/10.1101/069195
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'
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