outbreaker2: main function for reconstructing disease outbreaks

The function outbreaker is the main function of the package. It runs processes various inputs (data, configuration settings, custom priors, likelihoods and movement functions) and explores the space of plausible transmission trees of a densely sampled outbreaks.

outbreaker(
  data = outbreaker_data(),
  config = create_config(),
  priors = custom_priors(),
  likelihoods = custom_likelihoods(),
  moves = custom_moves()
)

Arguments

data	a list of named items containing input data as returned by outbreaker_data
config	a set of settings as returned by create_config
priors	a set of log-prior functions as returned by custom_priors
likelihoods	a set of log-likelihood functions as returned by custom_likelihoods
moves	a set of movement functions as returned by custom_moves

Details

The emphasis of 'outbreaker2' is on modularity, which enables customisation of priors, likelihoods and even movements of parameters and augmented data by the user. This the dedicated vignette on this topic vignette("outbreaker2_custom").

References

Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N (2014). Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Computational Biology.

See also

outbreaker_data to process input data, and create_config to process/set up parameters

• outbreaker_data: function to process input data

• create_config: function to create default and customise configuration settings

• custom_priors: function to specify customised prior functions

• custom_likelihoods: function to specify customised likelihoods functions

• custom_moves: function to create default and customise movement functions

Author

Thibaut Jombart (thibautjombart@gmail.com)

Examples

## get data
data(fake_outbreak)
dat <- fake_outbreak

if (FALSE) {
## run outbreaker
out <- outbreaker(data = list(dna = dat$dna, dates = dat$onset, w_dens = dat$w),
config = list(n_iter = 2e4, sample_every = 200))
plot(out)
as.data.frame(out)

## run outbreaker, no DNA sequences
out2 <- outbreaker(data = list(dates = dat$onset, w_dens = w),
config = list(n_iter = 2e4, sample_every = 200))
plot(out2)
as.data.frame(out2)

}