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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/package.R |
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\name{outbreaker_package} |
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\alias{outbreaker_package} |
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\title{outbreaker2: a platform for disease outbreak reconstruction} |
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\description{ |
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This package provides a statistical platform for reconstructing transmission |
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trees ('who infects whom') in densely sampled disease outbreaks. It |
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reimplements, as a particular case, the model of 'outbreaker' (see |
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references). 'outbreaker2' extends and replaces 'outbreaker'. \cr |
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} |
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\details{ |
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The emphasis of 'outbreaker2' is on modularity, which enables customisation |
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of priors, likelihoods and even movements of parameters and augmented data by |
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the user. This the dedicated vignette on this topic |
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\code{vignette("outbreaker2_custom")}.\cr |
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The main functions of the package are: |
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\itemize{ |
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\item \code{\link{outbreaker}}: main function to run analyses |
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\item \code{\link{outbreaker_data}}: function to process input data |
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\item \code{\link{create_config}}: function to create default and customise |
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configuration settings |
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\item \code{\link{custom_priors}}: function to specify customised prior |
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functions |
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\item \code{\link{custom_likelihoods}}: function to specify customised likelihoods |
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functions |
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\item \code{\link{custom_moves}}: function to create default and customise movement |
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functions |
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} |
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} |
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\author{ |
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Thibaut Jombart \email{thibautjombart@gmail.com} |
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} |