Added negative_si option to create_config
to allow ancestries with negative serial intervals to be immediately
discarded.
Removed C++11 SystemRequirements specification (R 4.0+ defaults to
C++11)
outbreaker2 1.1.3
(2022-05-18)
Bug fixes
Email addresses fixed
Adegenet added to Suggests
outbreaker2 1.1.2
(2021-01-25)
New features
Custom likelihoods now support local likelihood calculations via the
optional i argument; this will speed up likelihood
calculations by avoiding global calculations where these are
unnecessary
Bug fixes
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
outbreaker2 1.1.1
(2020-01-31)
Bug fixes
Fixed uninitialized variable use
Updated email addresses
outbreaker2 1.1.0
(2019-06-06)
Bug fixes
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.
New features
outbreaker2 now accepts epicontacts objects
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' in
summary.outbreaker_chains
Added support for case-labelling in
plot.outbreaker_chains
Added progress bar
outbreaker2 1.0.1
(2018-03-06)
Minor bug fixes
Fixed convolution operator to keep values in log space with high
kappa (thanks to @gtonkinhill)
C++ garbage collection fix
outbreaker2 1.0.0
(2017-11-24)
First version of outbreaker2!
This package re-implements and generalises the package outbreaker
It provides various functions to process input data, specify
settings of the method, and even specify custom priors, likelihoods, or
movement functions.
Outputs of the main function outbreaker have a
dedicated class extending the regular data.frame, with
print, summary and plot
methods.
Its engine is written in C++, interfaced via Rcpp.
Its C++ API is accessible via the function
get_cpp_api().