--- a
+++ b/man/custom_moves.Rd
@@ -0,0 +1,87 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_moves.R
+\name{custom_moves}
+\alias{custom_moves}
+\alias{print.outbreaker_moves}
+\title{Customise samplers for outbreaker}
+\usage{
+custom_moves(...)
+
+\method{print}{outbreaker_moves}(x, ...)
+}
+\arguments{
+\item{...}{A list or a series of named, comma-separated functions
+implementing movements of parameters or augmented data.}
+
+\item{x}{an \code{outbreaker_moves} object as returned by \code{create_moves}.}
+}
+\value{
+A list of movement functions with a single argument 'param', with
+    class \code{outbreaker_moves}.
+}
+\description{
+This function is used to specify customised movement functions
+(a.k.a. samplers) for outbreaker. Custom functions are specified as a named
+list or series of comma-separated, named arguments, indicating which type of
+movement they implement. Values currently available are:
+}
+\details{
+\itemize{
+
+\item \code{mu}: movement of the mutation rate; by default, the function
+\code{cpp_move_mu} is used.
+
+\item \code{pi}: movement of the reporting probability; by default, the function
+\code{cpp_move_pi} is used.
+
+\item \code{eps}: movement of the contact reporting coverage; by default, the
+function \code{cpp_move_eps} is used.
+
+\item \code{lambda}: the movement of the non-infectious contact rate; the
+function \code{cpp_move_lambda} is used.
+
+\item \code{alpha}: movement of the transmission tree, by randomly proposing
+infectors in the pool of cases infected before; by default, the function
+\code{cpp_move_alpha} is used.
+
+\item \code{swap_cases}: movement of the transmission tree, by swapping
+infectors and infected cases; by default, the function
+\code{cpp_move_swap_cases} is used.
+
+\item \code{t_inf}: movement of the date of infection; by default, the
+function \code{cpp_move_t_inf} is used.
+
+\item \code{kappa}: movement of the number generations between cases; by
+default, the function \code{cpp_move_kappa} is used.
+
+}
+
+
+Movement functions must have an argument \code{param}, which is a list of
+parameters and augmented data of the class \code{\link{create_param}}.
+Each movement function will be enclosed with its other arguments, so that the
+resulting function will have a single argument 'param'. For non-standard
+movements (i.e. none of the names specified above), the closure will contain:
+
+\itemize{
+
+\item \code{data}: a list of named items containing input data as returned by
+\code{\link{outbreaker_data}}
+
+\item \code{config}:  a list of named items containing input data as returned by
+\code{\link{create_config}}
+
+\item \code{likelihoods}: a list of named custom likelihood functions as returned by
+\code{\link{custom_likelihoods}}
+
+\item \code{priors}: a list of named custom prior functions as returned by
+\code{\link{custom_priors}}
+
+}
+}
+\seealso{
+See \href{http://www.repidemicsconsortium.org/outbreaker2/articles/customisation.html#customising-movements}{customization vignette} for detailed examples on how to customise movement functions.
+}
+\author{
+Thibaut Jombart (\email{thibautjombart@gmail.com}).
+}