https://github.com/cran/spatstat
Tip revision: 32c7daeb36b6e48fd0356bdcec9580ae124fee5e authored by Adrian Baddeley on 29 December 2015, 22:08:27 UTC
version 1.44-1
version 1.44-1
Tip revision: 32c7dae
applynbd.Rd
\name{applynbd}
\alias{applynbd}
\title{Apply Function to Every Neighbourhood in a Point Pattern}
\description{
Visit each point in a point pattern, find the neighbouring points,
and apply a given function to them.
}
\usage{
applynbd(X, FUN, N=NULL, R=NULL, criterion=NULL, exclude=FALSE, \dots)
}
\arguments{
\item{X}{
Point pattern.
An object of class \code{"ppp"},
or data which can be converted into
this format by \code{\link{as.ppp}}.
}
\item{FUN}{
Function to be applied to each neighbourhood.
The arguments of \code{FUN} are described under \bold{Details}.
}
\item{N}{
Integer. If this argument is present,
the neighbourhood of a point of \code{X} is defined to consist of the
\code{N} points of \code{X} which are closest to it.
}
\item{R}{
Nonnegative numeric value. If this argument is present,
the neighbourhood of a point of \code{X} is defined to consist of
all points of \code{X} which lie within a distance \code{R}
of it.
}
\item{criterion}{
Function. If this argument is present,
the neighbourhood of a point of \code{X} is determined by
evaluating this function. See under \bold{Details}.
}
\item{exclude}{
Logical. If \code{TRUE} then the point currently being visited
is excluded from its own neighbourhood.
}
\item{\dots}{
extra arguments passed to the function \code{FUN}.
They must be given in the form \code{name=value}.
}
}
\value{
Similar to the result of \code{\link{apply}}.
If each call to \code{FUN} returns a single numeric value,
the result is a vector of dimension \code{X$n}, the number of points
in \code{X}.
If each call to \code{FUN} returns a vector of the same length
\code{m}, then the result is a matrix of dimensions \code{c(m,n)};
note the transposition of the indices, as usual for the family of
\code{apply} functions.
If the calls to \code{FUN} return vectors of different lengths,
the result is a list of length \code{X$n}.
}
\details{
This is an analogue of \code{\link{apply}}
for point patterns. It visits each point in the point pattern \code{X},
determines which points of \code{X} are ``neighbours'' of the current
point, applies the function \code{FUN} to this neighbourhood,
and collects the values returned by \code{FUN}.
The definition of ``neighbours'' depends on the arguments
\code{N}, \code{R} and \code{criterion}.
Also the argument \code{exclude} determines whether
the current point is excluded from its own neighbourhood.
\itemize{
\item
If \code{N} is given, then the neighbours of the current
point are the \code{N} points of \code{X} which are closest to
the current point (including the current point itself
unless \code{exclude=TRUE}).
\item
If \code{R} is given, then the neighbourhood of the current point
consists of all points of \code{X} which lie closer than a distance \code{R}
from the current point.
\item
If \code{criterion} is given, then it must be a function
with two arguments \code{dist} and \code{drank} which will be
vectors of equal length.
The interpretation is that \code{dist[i]} will be the
distance of a point from the current point, and
\code{drank[i]} will be the rank of that distance (the three points
closest to the current point will have rank 1, 2 and 3).
This function must return a logical vector of the same length
as \code{dist} and \code{drank} whose \code{i}-th entry is
\code{TRUE} if the corresponding point should be included in
the neighbourhood. See the examples below.
\item
If more than one of the arguments \code{N}, \code{R} and
\code{criterion} is given, the neighbourhood is defined as
the \emph{intersection} of the neighbourhoods specified by these arguments.
For example if \code{N=3} and \code{R=5} then the neighbourhood
is formed by finding the 3 nearest neighbours of current point,
and retaining only those neighbours which lie closer than 5 units
from the current point.
}
When \code{applynbd} is executed,
each point of \code{X} is visited, and the following happens
for each point:
\itemize{
\item
the neighbourhood of the current point is determined according
to the chosen rule, and stored as a point pattern \code{Y};
\item
the function \code{FUN} is called as:
\code{FUN(Y=Y, current=current, dists=dists, dranks=dranks, \dots)}
where \code{current} is the location of the current point
(in a format explained below),
\code{dists} is a vector of distances from the current
point to each of the points in \code{Y},
\code{dranks} is a vector of the ranks of these distances
with respect to the full point pattern \code{X},
and \code{\dots} are the arguments passed from the call to
\code{applynbd};
\item
The result of the call to \code{FUN} is stored.
}
The results of each call to \code{FUN} are collected and returned
according to the usual rules for \code{\link{apply}} and its
relatives. See the \bold{Value} section of this help file.
The format of the argument \code{current} is as follows.
If \code{X} is an unmarked point pattern, then \code{current} is a
vector of length 2 containing the coordinates of the current point.
If \code{X} is marked, then \code{current} is a point pattern
containing exactly one point, so that \code{current$x} is its
\eqn{x}-coordinate and \code{current$marks} is its mark value.
In either case, the coordinates of the current point can be referred to as
\code{current$x} and \code{current$y}.
Note that \code{FUN} will be called exactly as described above,
with each argument named explicitly. Care is required when writing the
function \code{FUN} to ensure that
the arguments will match up. See the Examples.
See \code{\link{markstat}} for a common use of this function.
To simply tabulate the marks in every \code{R}-neighbourhood, use
\code{\link{marktable}}.
}
\seealso{
\code{\link{ppp.object}},
\code{\link{apply}},
\code{\link{markstat}},
\code{\link{marktable}}
}
\examples{
data(redwood)
# count the number of points within radius 0.2 of each point of X
nneighbours <- applynbd(redwood, R=0.2, function(Y, ...){Y$n-1})
# equivalent to:
nneighbours <- applynbd(redwood, R=0.2, function(Y, ...){Y$n}, exclude=TRUE)
# compute the distance to the second nearest neighbour of each point
secondnndist <- applynbd(redwood, N = 2,
function(dists, ...){max(dists)},
exclude=TRUE)
# marked point pattern
data(longleaf)
\testonly{
# smaller dataset
longleaf <- longleaf[seq(1, longleaf$n, by=80)]
}
# compute the median of the marks of all neighbours of a point
# (see also 'markstat')
dbh.med <- applynbd(longleaf, R=90, exclude=TRUE,
function(Y, ...) { median(Y$marks)})
# ANIMATION explaining the definition of the K function
# (arguments `fullpicture' and 'rad' are passed to FUN)
\dontrun{
showoffK <- function(Y, current, dists, dranks, fullpicture,rad) {
plot(fullpicture, main="")
points(Y, cex=2)
u <- current
points(u$x,u$y,pch="+",cex=3)
theta <- seq(0,2*pi,length=100)
polygon(u$x+ rad * cos(theta),u$y+rad*sin(theta))
text(u$x+rad/3,u$y+rad/2,Y$n,cex=3)
Sys.sleep(if(runif(1) < 0.1) 1.5 else 0.3)
return(Y$n - 1)
}
applynbd(redwood, R=0.2, showoffK, fullpicture=redwood, rad=0.2, exclude=TRUE)
# animation explaining the definition of the G function
showoffG <- function(Y, current, dists, dranks, fullpicture) {
plot(fullpicture, main="")
points(Y, cex=2)
u <- current
points(u[1],u[2],pch="+",cex=3)
v <- c(Y$x[1],Y$y[1])
segments(u[1],u[2],v[1],v[2],lwd=2)
w <- (u + v)/2
nnd <- dists[1]
text(w[1],w[2],round(nnd,3),cex=2)
Sys.sleep(if(runif(1) < 0.1) 1.5 else 0.3)
return(nnd)
}
data(cells)
applynbd(cells, N=1, showoffG, exclude=TRUE, fullpicture=cells)
}
}
\author{Adrian Baddeley \email{Adrian.Baddeley@curtin.edu.au}
and Rolf Turner \email{r.turner@auckland.ac.nz}
}
\keyword{spatial}
\keyword{programming}
\keyword{iteration}