- Email addresses fixed
- Adegenet added to Suggests
- Custom likelihoods now support local likelihood calculations via the optional
iargument; this will speed up likelihood calculations by avoiding global calculations where these are unnecessary
- Random index shuffling in cpp_move_swap_cases to ensure correct mixing
- Negative serial intervals now allowed in can_be_ances
- ID labels fix in plotting functions
- Fixed uninitialized variable use
- Updated email addresses
- The genetic likelihood of the original outbreaker paper was found to contain a minor mistake in accounting for unobserved generations of infection. As of June 7th 2019, outbreaker2 will use the correct genetic likelihood published here.
- outbreaker2 now accepts
epicontactsobjects for contact data - Contact tracing data can be directed or not by toggling
ctd_directed - Cyclical consensus trees can now be avoided by using
method = 'decyle'insummary.outbreaker_chains - Added support for case-labelling in
plot.outbreaker_chains - Added progress bar
- Fixed convolution operator to keep values in log space with high kappa (thanks to @gtonkinhill)
- C++ garbage collection fix
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This package re-implements and generalises the package outbreaker
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It provides various functions to process input data, specify settings of the method, and even specify custom priors, likelihoods, or movement functions.
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Outputs of the main function
outbreakerhave a dedicated class extending the regulardata.frame, withprint,summaryandplotmethods. -
Its engine is written in C++, interfaced via Rcpp.
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Its C++ API is accessible via the function
get_cpp_api(). -
Functionalities are documented in 4 vignettes.