outbreaker21.1.3 package

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

bind_to_function

Encloses argument in a function's environment

create_config

Set and check parameter settings of outbreaker

create_param

Initializes outputs for outbreaker

custom_likelihoods

Customise likelihood functions for outbreaker

custom_moves

Customise samplers for outbreaker

custom_priors

Customise priors for outbreaker

get_cpp_api

Access internal C++ rountines used in outbreaker2

outbreaker

outbreaker2: main function for reconstructing disease outbreaks

outbreaker_chains

Basic methods for processing outbreaker results

outbreaker_data

Process input data for outbreaker

outbreaker_package

outbreaker2: a platform for disease outbreak reconstruction

palettes

Color palettes used in outbreaker

sim_ctd

Simulate contact data from a transmission tree

Download source packageRead PDF manual

Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.

  • Maintainer: Finlay Campbell
  • License: MIT + file LICENSE
  • Last published: 2022-05-23