% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/outbreaker_data.R

\name{outbreaker_data}

\alias{outbreaker_data}

\title{Process input data for outbreaker}

\usage{

outbreaker_data(..., data = list(...))

}

\arguments{

\item{...}{a list of data items to be processed (see description)}

\item{data}{optionally, an existing list of data item as returned by \code{outbreaker_data}.}

}

\description{

This function performs various checks on input data given to outbreaker.  It

takes a list of named items as input, performs various checks, set defaults

where arguments are missing, and return a correct list of data input. If no

input is given, it returns the default settings.

}

\details{

Acceptables arguments for ... are:

\describe{

\item{dates}{dates a vector indicating the collection dates, provided either as

integer numbers or in a usual date format such as \code{Date} or

\code{POSIXct} format. By convention, zero will indicate the oldest date. If

the vector is named, the vector names will be used for matching cases to

contact tracing data and labelled DNA sequences.}

\item{dna}{the DNA sequences in \code{DNAbin} format (see

\code{\link[ape]{read.dna}} in the ape package); this can be imported from a

fasta file (extension .fa, .fas, or .fasta) using \code{adegenet}'s function

\link[adegenet]{fasta2DNAbin}.}

\item{ctd}{the contact tracing data provided as a matrix/dataframe of two

columns, indicating a reported contact between the two individuals whose ids

are provided in a given row of the data, or an epicontacts object. In the case

of the latter, linelist IDs will be used for matching dates and DNA

sequences}

\item{w_dens}{a vector of numeric values indicating the generation time

distribution, reflecting the infectious potential of a case t = 1, 2, ...

time steps after infection. By convention, it is assumed that

newly infected patients cannot see new infections on the same time step. If not

standardized, this distribution is rescaled to sum to 1.}

\item{f_dens}{similar to \code{w_dens}, except that this is the distribution

of the colonization time, i_e. time interval during which the pathogen can

be sampled from the patient.}}

}

\examples{

x <- fake_outbreak

outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w)

}

\author{

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

}