Tools to process the results of
outbreaker2.
Install the package from CRAN:
install.packages("o2ools")
library(o2ools)Or the development version from GitHub:
devtools::install_github("cygei/o2ools")The inference of transmission chains from genomic, epidemiological and
contact data is central to outbreak investigations.
outbreaker2 and other
popular models use Bayesian inference to reconstruct who infected whom.
However, the results of these models are difficult to interpret and
visualise. o2ools provides tools to analyse and visualise the results
of outbreaker2. To get started, check the package
vignette.