HierHard.Rd
\name{HierHard}
\alias{HierHard}
\title{The Hierarchical Hard Core Point Process Model}
\description{
Creates an instance of the hierarchical hard core point process model
which can then be fitted to point pattern data.
}
\usage{
HierHard(hradii=NULL, types=NULL, archy=NULL)
}
\arguments{
\item{hradii}{Optional matrix of hard core distances}
\item{types}{Optional; vector of all possible types (i.e. the possible levels
of the \code{marks} variable in the data)}
\item{archy}{Optional: the hierarchical order. See Details.}
}
\value{
An object of class \code{"interact"}
describing the interpoint interaction
structure of the hierarchical hard core process with
hard core distances \eqn{hradii[i,j]}.
}
\details{
This is a hierarchical point process model
for a multitype point pattern
(\ifelse{latex}{\out{H{\"o}gmander}}{Hogmander} and
\ifelse{latex}{\out{S{\"a}rkk{\"a}}}{Sarkka}, 1999;
Grabarnik and \ifelse{latex}{\out{S\"{a}rkk\"{a}}}{Sarkka}, 2009).
It is appropriate for analysing multitype point pattern data
in which the types are ordered so that
the points of type \eqn{j} depend on the points of type
\eqn{1,2,\ldots,j-1}{1,2,...,j-1}.
The hierarchical version of the (stationary)
hard core process with \eqn{m} types, with
hard core distances \eqn{h_{ij}}{h[i,j]} and
parameters \eqn{\beta_j}{beta[j]}, is a point process
in which each point of type \eqn{j}
contributes a factor \eqn{\beta_j}{beta[j]} to the
probability density of the point pattern.
If any pair of points
of types \eqn{i} and \eqn{j} lies closer than \eqn{h_{ij}}{h[i,j]}
units apart, the configuration of points is impossible (probability
density zero).
The nonstationary hierarchical hard core
process is similar except that
the contribution of each individual point \eqn{x_i}{x[i]}
is a function \eqn{\beta(x_i)}{beta(x[i])}
of location and type, rather than a constant beta.
The function \code{\link{ppm}()},
which fits point process models to
point pattern data, requires an argument
of class \code{"interact"} describing the interpoint interaction
structure of the model to be fitted.
The appropriate description of the hierarchical
hard core process pairwise interaction is
yielded by the function \code{HierHard()}. See the examples below.
The argument \code{types} need not be specified in normal use.
It will be determined automatically from the point pattern data set
to which the HierHard interaction is applied,
when the user calls \code{\link{ppm}}.
However, the user should be confident that
the ordering of types in the dataset corresponds to the ordering of
rows and columns in the matrix \code{radii}.
The argument \code{archy} can be used to specify a hierarchical
ordering of the types. It can be either a vector of integers
or a character vector matching the possible types.
The default is the sequence
\eqn{1,2, \ldots, m}{1,2, ..., m} meaning that type \eqn{j}
depends on types \eqn{1,2, \ldots, j-1}{1,2, ..., j-1}.
The matrix \code{iradii} must be square, with entries
which are either positive numbers, or zero or \code{NA}.
A value of zero or \code{NA} indicates that no hard core interaction term
should be included for this combination of types.
Note that only the hard core distances are
specified in \code{HierHard}. The canonical
parameters \eqn{\log(\beta_j)}{log(beta[j])}
are estimated by
\code{\link{ppm}()}, not fixed in \code{HierHard()}.
}
\seealso{
\code{\link{MultiHard}} for the corresponding
symmetrical interaction.
\code{\link{HierStrauss}},
\code{\link{HierStraussHard}}.
}
\examples{
h <- matrix(c(4, NA, 10, 15), 2, 2)
HierHard(h)
# prints a sensible description of itself
ppm(ants ~1, HierHard(h))
# fit the stationary hierarchical hard core process to ants data
}
\author{\adrian
,
\rolf
and \ege.
}
\references{
Grabarnik, P. and \ifelse{latex}{\out{S\"{a}rkk\"{a}}}{Sarkka}, A. (2009)
Modelling the spatial structure of forest stands by
multivariate point processes with hierarchical interactions.
\emph{Ecological Modelling} \bold{220}, 1232--1240.
\ifelse{latex}{\out{H{\"o}gmander}}{Hogmander}, H. and
\ifelse{latex}{\out{S{\"a}rkk{\"a}}}{Sarkka}, A. (1999)
Multitype spatial point patterns with hierarchical interactions.
\emph{Biometrics} \bold{55}, 1051--1058.
}
\keyword{spatial}
\keyword{models}