create_param: Initializes outputs for outbreaker

Description

This function creates initial outputs and parameter states for outbreaker.

Usage

create_param(data = outbreaker_data(), config = create_config())

Value

A list containing two components $store and $current. store is a list with the class outbreaker_store, used for storing 'saved' states of the MCMC. current is a list with the class outbreaker_param, used for storing 'current' states of the MCMC.

outbreaker_store class content:

size: The length of the list, corresponding to the number of samples saved from the MCMC.
step: A vector of integers of length size, storing the steps of the MCMC corresponding to the saved samples.
post: A numeric vector of length size, storing log-posterior values.
like: A numeric vector of length size, storing log-likelihood values.
prior: A numeric vector of length size, storing log-prior values.
alpha: A list of length size. Each item of the list is an integer vector of length data$N, storing indices (from 1 to N) of infectors for each case.
t_inf: A list of length size. Each item of the list is an integer vector of length data$N, storing dates of infections for each case.
mu: A numeric vector of length size, storing values of the mutation rate.
kappa: A list of length size. Each item of the list is an integer vector of length data$N, storing the number of generations before the last sampled ancestor for each case.
pi: A numeric vector of length size, storing values of the reporting probability.
eps: A numeric vector of length size, storing values of the contact reporting coverage.
lambda: A numeric vector of length size, storing values of the non-infectious contact rate.
counter: A counter used to keep track of the current iteration of the MCMC (used internally).

outbreaker_param class content:

alpha: An integer vector of length data$N, storing indices (from 1 to N) of infectors for each case.
t_inf: An integer vector of length data$N, storing dates of infections for each case.
mu: The value of the mutation rate.
kappa: An integer vector of length data$N, storing the number of generations before the last sampled ancestor for each case.
pi: The value of the reporting probability.
eps: The value of the contact reporting coverage.
lambda: The value of the non-infectious contact rate.

Arguments

data: A list of data items as returned by outbreaker_data, or arguments passed to this function.
config: A list of settings as returned by create_config, or arguments passed to this function.

Author

Thibaut Jombart (thibautjombart@gmail.com).

Examples

Run this code


## load data
x <- fake_outbreak
data <- outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w)

## modify config settings
config <- create_config(move_alpha = FALSE, n_iter = 2e5, sample_every = 1000)

## create param object
param <- create_param(data = data, config = config)

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