Background:
Reconstructing individual transmission events in an infectious disease outbreak can provide
valuable information and help inform infection control po
licy. Recent years have seen
considerable progress in the development of methodologies for reconstructing transmission
chains using both epidemiological and genetic data. However, only a few of these methods
have been implemented in software packages, and
with little consideration for
customisability and interoperability. Users are therefore limited to a small number of
alternatives, incompatible tools with fixed functionality, or forced to develop their own
algorithms at considerable personal effort.
Results:
Here we present
outbreaker2
, a flexible framework for outbreak reconstruction. This R
package re
-
implements and extends the original model introduced with
outbreaker
, but most
importantly also provides a modular platform allowing users to specify c
ustom models within
an optimised inferential framework. As a proof of concept, we implement the within
-
host
evolutionary model introduced with
TransPhylo
, which is very distinct from the original
genetic model in
outbreaker
, and demonstrate how even comple
x model results can be
successfully included with minimal effort.
Conclusions:
outbreaker2
provides a valuable starting point for future outbreak reconstruction tools, and
represents a unifying platform that promotes customisability and interoperability.
Im
plemented in the R software,
outbreaker2
joins a growing body of tools for outbreak
analysis