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outbreaker

Summary
The R-package outbreaker implements a Bayesian approach for reconstructing outbreak data from pathogen genome sequences (link to paper). It also implements a tool for outbreak simulation. 

Features
  • implementation of the approach of Jombart et al. (2014) for reconstructing densely sampled disease outbreaks
  • estimates the transmission tree, dates of infections, mutation rates, unobserved and imported cases
  • parallelized implementation allows for several MCMC to be run simultaneously on different processors / cores
  • graphics to visualize outputs
  • estimation of incidence based on the transmission trees
  • estimation of effective reproduction numbers based on the transmission trees
  • tool to simulate disease outbreaks, including genomic evolution of the pathogen
  • [under development] spatial module allowing for dispersal process to be modelled

Screenshots
Reconstructed transmission tree

Trace of log-posterior values
Incidence inferred from posterior trees
More screenshots are available here.


Download/installation
The current version of outbreaker is 1.1-4 for R 3.1.2. outbreaker can be installed from R as other packages by typing:
install.packages("outbreaker", dependencies=TRUE)

See CRAN for manual downloads.

The development of outbreaker is currently hosted on Github:

See the the Github page for installation guidelines, bug reports, feature requests, etc.

Documentation
outbreaker is distributed with the following documentation:

Feature request / bug report
If there is a feature you would like to suggest, or a bug you would like to report, use the ticket system on sourceforge.


Authors/contributors
outbreaker is developed by Thibaut Jombart. 
The original method has been developed by Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser and Neil Ferguson. 


References
Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C & Ferguson N (2014) Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. PLoS Comput Biol 10(1): e1003457. doi:10.1371/journal.pcbi.1003457


Subpages (1): outbreaker screenshots
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