R: Inhomogeneous Marked K-Function

Kmulti.inhom {spatstat.explore}

R Documentation

Inhomogeneous Marked K-Function

Description

For a marked point pattern, estimate the inhomogeneous version of the multitype K function which counts the expected number of points of subset J within a given distance from a typical point in subset I, adjusted for spatially varying intensity.

Usage

  Kmulti.inhom(X, I, J, lambdaI=NULL, lambdaJ=NULL,
          ...,
          r=NULL, breaks=NULL,
          correction=c("border", "isotropic", "Ripley", "translate"),
          lambdaIJ=NULL,
          sigma=NULL, varcov=NULL,
          lambdaX=NULL, update=TRUE, leaveoneout=TRUE)

Arguments

`X`	The observed point pattern, from which an estimate of the inhomogeneous multitype `K` function `K_{IJ}(r)` will be computed. It must be a marked point pattern. See under Details.
`I`	Subset index specifying the points of `X` from which distances are measured. See Details.
`J`	Subset index specifying the points in `X` to which distances are measured. See Details.
`lambdaI`	Optional. Values of the estimated intensity of the sub-process `X[I]`. Either a pixel image (object of class `"im"`), a numeric vector containing the intensity values at each of the points in `X[I]`, a fitted point process model (object of class `"ppm"` or `"kppm"` or `"dppm"`), or a `function(x,y)` which can be evaluated to give the intensity value at any location.
`lambdaJ`	Optional. Values of the estimated intensity of the sub-process `X[J]`. Either a pixel image (object of class `"im"`), a numeric vector containing the intensity values at each of the points in `X[J]`, a fitted point process model (object of class `"ppm"` or `"kppm"` or `"dppm"`), or a `function(x,y)` which can be evaluated to give the intensity value at any location.
`...`	Ignored.
`r`	Optional. Numeric vector. The values of the argument `r` at which the multitype `K` function `K_{IJ}(r)` should be evaluated. There is a sensible default. First-time users are strongly advised not to specify this argument. See below for important conditions on `r`.
`breaks`	This argument is for internal use only.
`correction`	A character vector containing any selection of the options `"border"`, `"bord.modif"`, `"isotropic"`, `"Ripley"`, `"translate"`, `"none"` or `"best"`. It specifies the edge correction(s) to be applied. Alternatively `correction="all"` selects all options.
`lambdaIJ`	Optional. A matrix containing estimates of the product of the intensities `lambdaI` and `lambdaJ` for each pair of points, the first point belonging to subset `I` and the second point to subset `J`.
`sigma`, `varcov`	Optional arguments passed to `density.ppp` to control the smoothing bandwidth, when `lambda` is estimated by kernel smoothing.
`lambdaX`	Optional. Values of the intensity for all points of `X`. Either a pixel image (object of class `"im"`), a numeric vector containing the intensity values at each of the points in `X`, a fitted point process model (object of class `"ppm"` or `"kppm"` or `"dppm"`), or a `function(x,y)` which can be evaluated to give the intensity value at any location. If present, this argument overrides both `lambdaI` and `lambdaJ`.
`update`	Logical value indicating what to do when `lambdaI`, `lambdaJ` or `lambdaX` is a fitted point process model (class `"ppm"`, `"kppm"` or `"dppm"`). If `update=TRUE` (the default), the model will first be refitted to the data `X` (using `update.ppm` or `update.kppm`) before the fitted intensity is computed. If `update=FALSE`, the fitted intensity of the model will be computed without re-fitting it to `X`.
`leaveoneout`	Logical value (passed to `density.ppp` or `fitted.ppm`) specifying whether to use a leave-one-out rule when calculating the intensity.

Details

The function Kmulti.inhom is the counterpart, for spatially-inhomogeneous marked point patterns, of the multitype K function Kmulti.

Suppose X is a marked point process, with marks of any kind. Suppose X_I, X_J are two sub-processes, possibly overlapping. Typically X_I would consist of those points of X whose marks lie in a specified range of mark values, and similarly for X_J. Suppose that \lambda_I(u), \lambda_J(u) are the spatially-varying intensity functions of X_I and X_J respectively. Consider all the pairs of points (u,v) in the point process X such that the first point u belongs to X_I, the second point v belongs to X_J, and the distance between u and v is less than a specified distance r. Give this pair (u,v) the numerical weight 1/(\lambda_I(u)\lambda_J(u)). Calculate the sum of these weights over all pairs of points as described. This sum (after appropriate edge-correction and normalisation) is the estimated inhomogeneous multitype K function.

The argument X must be a point pattern (object of class "ppp") or any data that are acceptable to as.ppp.

The arguments I and J specify two subsets of the point pattern. They may be any type of subset indices, for example, logical vectors of length equal to npoints(X), or integer vectors with entries in the range 1 to npoints(X), or negative integer vectors.

Alternatively, I and J may be functions that will be applied to the point pattern X to obtain index vectors. If I is a function, then evaluating I(X) should yield a valid subset index. This option is useful when generating simulation envelopes using envelope.

The argument lambdaI supplies the values of the intensity of the sub-process identified by index I. It may be either

a pixel image: (object of class "im") which gives the values of the intensity of X[I] at all locations in the window containing X;
a numeric vector: containing the values of the intensity of X[I] evaluated only at the data points of X[I]. The length of this vector must equal the number of points in X[I].
a function: of the form function(x,y) which can be evaluated to give values of the intensity at any locations.
a fitted point process model: (object of class "ppm", "kppm" or "dppm") whose fitted trend can be used as the fitted intensity. (If update=TRUE the model will first be refitted to the data X before the trend is computed.)
omitted:: if lambdaI is omitted then it will be estimated using a leave-one-out kernel smoother.

If lambdaI is omitted, then it will be estimated using a ‘leave-one-out’ kernel smoother, as described in Baddeley, Moller and Waagepetersen (2000). The estimate of lambdaI for a given point is computed by removing the point from the point pattern, applying kernel smoothing to the remaining points using density.ppp, and evaluating the smoothed intensity at the point in question. The smoothing kernel bandwidth is controlled by the arguments sigma and varcov, which are passed to density.ppp along with any extra arguments.

Similarly lambdaJ supplies the values of the intensity of the sub-process identified by index J.

Alternatively if the argument lambdaX is given, then it specifies the intensity values for all points of X, and the arguments lambdaI, lambdaJ will be ignored.

The argument r is the vector of values for the distance r at which K_{IJ}(r) should be evaluated. It is also used to determine the breakpoints (in the sense of hist) for the computation of histograms of distances.

First-time users would be strongly advised not to specify r. However, if it is specified, r must satisfy r[1] = 0, and max(r) must be larger than the radius of the largest disc contained in the window.

Biases due to edge effects are treated in the same manner as in Kinhom. The edge corrections implemented here are

border: the border method or “reduced sample” estimator (see Ripley, 1988). This is the least efficient (statistically) and the fastest to compute. It can be computed for a window of arbitrary shape.
isotropic/Ripley: Ripley's isotropic correction (see Ripley, 1988; Ohser, 1983). This is currently implemented only for rectangular windows.
translate: Translation correction (Ohser, 1983). Implemented for all window geometries.

The pair correlation function pcf can also be applied to the result of Kmulti.inhom.

Value

An object of class "fv" (see fv.object).

Essentially a data frame containing numeric columns

`r`	the values of the argument `r` at which the function `K_{IJ}(r)` has been estimated
`theo`	the theoretical value of `K_{IJ}(r)` for a marked Poisson process, namely `\pi r^2`

together with a column or columns named "border", "bord.modif", "iso" and/or "trans", according to the selected edge corrections. These columns contain estimates of the function K_{IJ}(r) obtained by the edge corrections named.

Author(s)

Adrian Baddeley Adrian.Baddeley@curtin.edu.au

and Rolf Turner rolfturner@posteo.net

References

Baddeley, A., Moller, J. and Waagepetersen, R. (2000) Non- and semiparametric estimation of interaction in inhomogeneous point patterns. Statistica Neerlandica 54, 329–350.

Examples

    # Finnish Pines data: marked by diameter and height
    plot(finpines, which.marks="height")
    II <- (marks(finpines)$height <= 2)
    JJ <- (marks(finpines)$height > 3)
    K <- Kmulti.inhom(finpines, II, JJ)
    plot(K)
    # functions determining subsets
    f1 <- function(X) { marks(X)$height <= 2 }
    f2 <- function(X) { marks(X)$height > 3 }
    K <- Kmulti.inhom(finpines, f1, f2)

[Package spatstat.explore version 3.3-1 Index]