Revision c9b2c621c3bff55aaa77646dc1ba7316765cd7e4 authored by Adrian Baddeley on 25 April 2013, 00:00:00 UTC, committed by Gabor Csardi on 25 April 2013, 00:00:00 UTC
1 parent f86606a
markconnect.Rd
\name{markconnect}
\alias{markconnect}
\title{
Mark Connection Function
}
\description{
Estimate the marked connection function
of a multitype point pattern.
}
\usage{
markconnect(X, i, j, r=NULL,
correction=c("isotropic", "Ripley", "translate"),
method="density", \dots, normalise=FALSE)
}
\arguments{
\item{X}{The observed point pattern.
An object of class \code{"ppp"} or something acceptable to
\code{\link{as.ppp}}.
}
\item{i}{Number or character string identifying the type (mark value)
of the points in \code{X} from which distances are measured.
}
\item{j}{Number or character string identifying the type (mark value)
of the points in \code{X} to which distances are measured.
}
\item{r}{numeric vector. The values of the argument \eqn{r}
at which the mark connection function \eqn{p_{ij}(r)}{p[ij](r)}
should be evaluated. There is a sensible default.
}
\item{correction}{
A character vector containing any selection of the
options \code{"isotropic"}, \code{"Ripley"} or \code{"translate"}.
It specifies the edge correction(s) to be applied.
}
\item{method}{
A character vector indicating the user's choice of
density estimation technique to be used. Options are
\code{"density"},
\code{"loess"},
\code{"sm"} and \code{"smrep"}.
}
\item{\dots}{
Arguments passed to the density estimation routine
(\code{\link{density}}, \code{\link{loess}} or \code{sm.density})
selected by \code{method}.
}
\item{normalise}{
If \code{TRUE}, normalise the pair connection function by
dividing it by \eqn{p_i p_j}{p[i]*p[j]}, the estimated probability
that randomly-selected points will have marks \eqn{i} and \eqn{j}.
}
}
\value{
An object of class \code{"fv"} (see \code{\link{fv.object}}).
Essentially a data frame containing numeric columns
\item{r}{the values of the argument \eqn{r}
at which the mark connection function \eqn{p_{ij}(r)}{p[i,j](r)}
has been estimated
}
\item{theo}{the theoretical value of \eqn{p_{ij}(r)}{p[i,j](r)}
when the marks attached to different points are independent
}
together with a column or columns named
\code{"iso"} and/or \code{"trans"},
according to the selected edge corrections. These columns contain
estimates of the function \eqn{p_{ij}(r)}{p[i,j](r)}
obtained by the edge corrections named.
}
\details{
The mark connection function \eqn{p_{ij}(r)}{p[i,j](r)}
of a multitype point process \eqn{X}
is a measure of the dependence between the types of two
points of the process a distance \eqn{r} apart.
Informally \eqn{p_{ij}(r)}{p[i,j](r)} is defined
as the conditional probability,
given that there is a point of the process at a location \eqn{u}
and another point of the process at a location \eqn{v}
separated by a distance \eqn{||u-v|| = r}, that the first point
is of type \eqn{i} and the second point is of type \eqn{j}.
See Stoyan and Stoyan (1994).
If the marks attached to the points of \code{X} are independent
and identically distributed, then
\eqn{p_{ij}(r) \equiv p_i p_j}{p[i,j](r) = p[i]p[j]} where
\eqn{p_i}{p[i]} denotes the probability that a point is of type
\eqn{i}. Values larger than this,
\eqn{p_{ij}(r) > p_i p_j}{p[i,j](r) > p[i]p[j]},
indicate positive association between the two types,
while smaller values indicate negative association.
The argument \code{X} must be a point pattern (object of class
\code{"ppp"}) or any data that are acceptable to \code{\link{as.ppp}}.
It must be a multitype point pattern (a marked point pattern
with factor-valued marks).
The argument \code{r} is the vector of values for the
distance \eqn{r} at which \eqn{p_{ij}(r)}{p[i,j](r)} is estimated.
There is a sensible default.
This algorithm assumes that \code{X} can be treated
as a realisation of a stationary (spatially homogeneous)
random spatial point process in the plane, observed through
a bounded window.
The window (which is specified in \code{X} as \code{X$window})
may have arbitrary shape.
Biases due to edge effects are
treated in the same manner as in \code{\link{Kest}}.
The edge corrections implemented here are
\describe{
\item{isotropic/Ripley}{Ripley's isotropic correction
(see Ripley, 1988; Ohser, 1983).
This is implemented only for rectangular and polygonal windows
(not for binary masks).
}
\item{translate}{Translation correction (Ohser, 1983).
Implemented for all window geometries, but slow for
complex windows.
}
}
Note that the estimator assumes the process is stationary (spatially
homogeneous).
The mark connection function is estimated using density estimation
techniques. The user can choose between
\describe{
\item{\code{"density"}}{
which uses the standard kernel
density estimation routine \code{\link{density}}, and
works only for evenly-spaced \code{r} values;
}
\item{\code{"loess"}}{
which uses the function \code{loess} in the
package \pkg{modreg};
}
\item{\code{"sm"}}{
which uses the function \code{sm.density} in the
package \pkg{sm} and is extremely slow;
}
\item{\code{"smrep"}}{
which uses the function \code{sm.density} in the
package \pkg{sm} and is relatively fast, but may require manual
control of the smoothing parameter \code{hmult}.
}
}
}
\references{
Stoyan, D. and Stoyan, H. (1994)
Fractals, random shapes and point fields:
methods of geometrical statistics.
John Wiley and Sons.
}
\seealso{
Multitype pair correlation \code{\link{pcfcross}}
and multitype K-functions \code{\link{Kcross}}, \code{\link{Kdot}}.
Use \code{\link{alltypes}} to compute the mark connection functions
between all pairs of types.
Mark correlation \code{\link{markcorr}} and
mark variogram \code{\link{markvario}}
for numeric-valued marks.
}
\examples{
# Hughes' amacrine data
# Cells marked as 'on'/'off'
data(amacrine)
M <- markconnect(amacrine, "on", "off")
plot(M)
# Compute for all pairs of types at once
plot(alltypes(amacrine, markconnect))
}
\author{Adrian Baddeley
\email{Adrian.Baddeley@csiro.au}
\url{http://www.maths.uwa.edu.au/~adrian/}
and Rolf Turner
\email{r.turner@auckland.ac.nz}
}
\keyword{spatial}
\keyword{nonparametric}
Computing file changes ...