outbreaker: outbreaker: main function for reconstructing disease...

In o2geosocial: Reconstruction of Transmission Chains from Surveillance Data

Description

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.

Usage

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

Value

A data frame of n_iter / sample_every rows (as defined in the functioncreate_config()). For each row, the data frame contains:

• post: The posterior value of the transmission tree at this iteration.

• like: The likelihood value of the transmission tree at this iteration.

• post: The posterior value of the transmission tree at this iteration.

• a: The estimate of the spatial parameter a at this iteration,

• a: The estimate of the spatial parameter b at this iteration,

• pi: The estimate of the conditional report ratio pi at this iteration,

• alpha_1 to alpha_N: The infector of each case at this iteration.

• t_inf_1 to t_inf_N: The infection date of each case at this iteration.

• kappa_1 to kappa_N: The number of generation between each case and their infector at this iteration.

Author(s)

Initial version by Thibaut Jombart, rewritten by Alexis Robert ([e-mail])

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

Examples

## get data
data(toy_outbreak_short)

## run outbreaker
dt_cases <- toy_outbreak_short$cases
dt_cases <- dt_cases[order(dt_cases$Date), ]
dt_regions <- toy_outbreak_short$dt_regions
all_dist <- geosphere::distGeo(matrix(c(rep(dt_regions$long, nrow(dt_regions)), 
                                        rep(dt_regions$lat, nrow(dt_regions))), 
                                      ncol = 2), 
                               matrix(c(rep(dt_regions$long, each = nrow(dt_regions)), 
                                        rep(dt_regions$lat, each = nrow(dt_regions))),
                                      ncol = 2))

dist_mat <- matrix(all_dist/1000, nrow = nrow(dt_regions))
pop_vect <- dt_regions$population
names(pop_vect) <- rownames(dist_mat) <- colnames(dist_mat) <- dt_regions$region

data <- outbreaker_data(dates = dt_cases$Date, age_group = dt_cases$age_group,
                        region = dt_cases$Cens_tract, population = pop_vect, 
                        distance = dist_mat, a_dens = toy_outbreak_short$age_contact,
                        f_dens = dgamma(x = 1:300, scale = 0.43, shape = 27),
                        w_dens = dnorm(x = 1:300, mean = 11.7, sd = 2.0))
out <- outbreaker(data = data, config = list(n_iter = 200, sample_every = 5,
                                             n_iter_import = 100, sample_every_import = 5,
                                             gamma = 100, delta = 30, burnin = 20))
plot(out)

o2geosocial documentation built on Sept. 11, 2021, 9:07 a.m.