--- a
+++ b/man/outbreaker_data.Rd
@@ -0,0 +1,58 @@
+% 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})
+}