#' Initializes outputs for outbreaker

#'

#' This function creates initial outputs and parameter states for outbreaker.

#'

#' @author Thibaut Jombart (\email{thibautjombart@@gmail.com}).

#'

#' @param data A list of data items as returned by \code{outbreaker_data}, or

#' arguments passed to this function.

#'

#' @param config A list of settings as returned by \code{create_config}, or

#' arguments passed to this function.

#'

#' @export

#'

#' @aliases outbreaker_store

#'

#' @aliases outbreaker_param

#'

#' @return

#'

#' A list containing two components \code{$store} and

#' \code{$current}. \code{store} is a list with the class

#' \code{outbreaker_store}, used for storing 'saved' states of the

#' MCMC. \code{current} is a list with the class \code{outbreaker_param}, used

#' for storing 'current' states of the MCMC. \cr \cr

#'

#' \code{outbreaker_store} class content:

#' \itemize{

#'

#'  \item \code{size}: The length of the list, corresponding to the number of

#' samples saved from the MCMC.

#'

#'  \item \code{step}: A vector of integers of length \code{size}, storing the

#' steps of the MCMC corresponding to the saved samples.

#'

#'  \item \code{post}: A numeric vector of length \code{size}, storing

#' log-posterior values.

#'

#'  \item \code{like}: A numeric vector of length \code{size}, storing

#' log-likelihood values.

#'

#'  \item \code{prior}: A numeric vector of length \code{size},

#' storing log-prior values.

#'

#'  \item \code{alpha}: A list of length \code{size}. Each item of the list is

#' an integer vector of length \code{data$N}, storing indices (from 1 to N) of

#' infectors for each case.

#'

#'  \item \code{t_inf}: A list of length \code{size}. Each item of the list is

#' an integer vector of length \code{data$N}, storing dates of infections for

#' each case.

#'

#'  \item \code{mu}: A numeric vector of length \code{size}, storing values of

#' the mutation rate.

#'

#'  \item \code{kappa}: A list of length \code{size}. Each item of the list is

#' an integer vector of length \code{data$N}, storing the number of generations

#' before the last sampled ancestor for each case.

#'

#'  \item \code{pi}: A numeric vector of length \code{size}, storing values of

#' the reporting probability.

#'

#'  \item \code{eps}: A numeric vector of length \code{size}, storing values of

#' the contact reporting coverage.

#'

#'  \item \code{lambda}: A numeric vector of length \code{size}, storing values of

#' the non-infectious contact rate.

#'

#'  \item \code{counter}: A counter used to keep track of the current iteration

#' of the MCMC (used internally).

#'

#' }

#'

#'

#' \code{outbreaker_param} class content:

#' \itemize{

#'

#'  \item \code{alpha}: An integer vector of length \code{data$N}, storing

#' indices (from 1 to N) of infectors for each case.

#'

#'  \item \code{t_inf}: An integer vector of length \code{data$N}, storing dates

#' of infections for each case.

#'

#'  \item \code{mu}: The value of the mutation rate.

#'

#'  \item \code{kappa}: An integer vector of length \code{data$N}, storing the

#' number of generations before the last sampled ancestor for each case.

#'

#'  \item \code{pi}: The value of the reporting probability.

#'

#'  \item \code{eps}: The value of the contact reporting coverage.

#'

#'  \item \code{lambda}: The value of the non-infectious contact rate.

#'

#' }

#'

#' @examples

#'

#' ## 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)

#'

create_param <- function(data = outbreaker_data(),

                         config = create_config()) {

    ## CREATE EMPTY OUTPUT VECTORS ##

    size <- round(config$n_iter/config$sample_every)

    step <- integer(size)

    post <- prior <- like <- mu <- pi <- eps <- lambda <- double(size)

    alpha <- as.list(integer(size))

    t_inf <- as.list(integer(size))

    kappa <- as.list(integer(size))

    ## SET CURRENT VALUES AND COUNTER ##

    step[1] <- 1L

    current_mu <- mu[1] <- config$init_mu

    current_alpha <- alpha[[1]] <- config$init_alpha

    current_kappa <- kappa[[1]] <- config$init_kappa

    current_pi <- pi[1] <- config$init_pi

    current_eps <- eps[1] <- config$init_eps

    current_lambda <- lambda[1] <- config$init_lambda

    if (is.null(config$init_t_inf)) {

        current_t_inf <- t_inf[[1]] <- data$dates - which.max(data$f_dens) + 1L

    } else {

        current_t_inf <- t_inf[[1]] <- config$init_t_inf

    }

    counter <- 1L

    store <- list(

                size = size, step = step,

                post = post, like = like, prior = prior,

                alpha = alpha, t_inf = t_inf, mu = mu, kappa = kappa, pi = pi,

                eps = eps, lambda = lambda,

                counter = counter

                )

    class(store) <- c("outbreaker_store", "list")

    current  <- list(

        alpha = current_alpha, t_inf = current_t_inf, mu = current_mu,

        kappa = current_kappa, pi = current_pi, eps = current_eps,

        lambda = current_lambda

    )

    class(current) <- c("outbreaker_param", "list")

    ## SHAPE CHAIN ##

    out <- list(store = store,

                current = current)

    return(out)

}