--- a
+++ b/man/outbreaker_chains.Rd
@@ -0,0 +1,93 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outbreaker_chains_methods.R
+\name{print.outbreaker_chains}
+\alias{print.outbreaker_chains}
+\alias{outbreaker_chains}
+\alias{plot.outbreaker_chains}
+\alias{summary.outbreaker_chains}
+\title{Basic methods for processing outbreaker results}
+\usage{
+\method{print}{outbreaker_chains}(x, n_row = 3, n_col = 8, ...)
+
+\method{plot}{outbreaker_chains}(
+  x,
+  y = "post",
+  type = c("trace", "hist", "density", "alpha", "t_inf", "kappa", "network"),
+  group = NULL,
+  burnin = 0,
+  min_support = 0.1,
+  labels = NULL,
+  ...
+)
+
+\method{summary}{outbreaker_chains}(object, burnin = 0, method = c("mpa", "decycle"), ...)
+}
+\arguments{
+\item{x}{an \code{outbreaker_chains} object as returned by \code{outbreaker}.}
+
+\item{n_row}{the number of rows to display in head and tail; defaults to 3.}
+
+\item{n_col}{the number of columns to display; defaults to 8.}
+
+\item{...}{further arguments to be passed to other methods}
+
+\item{y}{a character string indicating which element of an
+\code{outbreaker_chains} object to plot}
+
+\item{type}{a character string indicating the kind of plot to be used (see details)}
+
+\item{group}{a vector of character strings indicating the parameters to display, 
+or "all" to display all global parameters (non node-specific parameters).}
+
+\item{burnin}{the number of iterations to be discarded as burnin}
+
+\item{min_support}{a number between 0 and 1 indicating the minimum support of
+ancestries to be plotted; only used if 'type' is 'network'}
+
+\item{labels}{a vector of length N indicating the case labels (must be
+provided in the same order used for dates of symptom onset)}
+
+\item{object}{an \code{outbreaker_chains} object as returned by \code{outbreaker}.}
+
+\item{method}{the method used to determine consensus ancestries. 'mpa'
+(maximum posterior ancestry) simply returns the posterior ancestry with the
+highest posterior support for each case, even if this includes
+cycles. 'decycle' will return the maximum posterior ancestry, except when
+cycles are detected, in which case the link in the cycle with the lowest
+support is pruned and the tree recalculated.}
+}
+\description{
+Several methods are defined for instances of the class
+\code{outbreaker_chains}, returned by \code{\link{outbreaker}}, including:
+\code{print}, \code{plot}, \code{summary}
+}
+\details{
+\code{type} indicates the type of graphic to plot:
+
+\itemize{
+
+\item \code{trace} to visualise MCMC traces for parameters or augmented data (plots the
+log-likelihood by default)
+
+\item \code{hist} to plot histograms of quantitative values
+
+\item \code{density} to plot kernel density estimations of quantitative values
+
+\item \code{alpha} to visualise the posterior frequency of ancestries
+
+\item \code{network} to visualise the transmission tree; note that
+ this opens up an interactive plot and requires a web browser with
+ Javascript enabled; the argument `min_support` is useful to select only the
+ most supported ancestries and avoid displaying too many links
+
+\item \code{kappa} to visualise the distributions generations between cases and their
+ancestor/infector
+
+}
+}
+\seealso{
+See \href{http://www.repidemicsconsortium.org/outbreaker2/articles/introduction.html#graphics}{introduction vignette} for detailed examples on how to visualise \code{outbreaker_chains} objects.
+}
+\author{
+Thibaut Jombart (\email{thibautjombart@gmail.com})
+}