--- a
+++ b/man/create_param.Rd
@@ -0,0 +1,113 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_param.R
+\name{create_param}
+\alias{create_param}
+\alias{outbreaker_store}
+\alias{outbreaker_param}
+\title{Initializes outputs for outbreaker}
+\usage{
+create_param(data = outbreaker_data(), config = create_config())
+}
+\arguments{
+\item{data}{A list of data items as returned by \code{outbreaker_data}, or
+arguments passed to this function.}
+
+\item{config}{A list of settings as returned by \code{create_config}, or
+arguments passed to this function.}
+}
+\value{
+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.
+
+}
+}
+\description{
+This function creates initial outputs and parameter states for outbreaker.
+}
+\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)
+
+}
+\author{
+Thibaut Jombart (\email{thibautjombart@gmail.com})
+}