markcorr {spatstat}R Documentation

Mark Correlation Function

Description

Estimate the marked correlation function of a marked point pattern.

Usage

markcorr(X, f = function(m1,m2) { m1 * m2 }, r=NULL,
         slow=FALSE, correction=c("border", "isotropic", "Ripley", "translate"),
         method="density", ...)

Arguments

X The observed point pattern. An object of class "ppp" or something acceptable to as.ppp.
f Function f used in the definition of the mark correlation function.
r numeric vector. The values of the argument r at which the mark correlation function rho_f(r) should be evaluated. There is a sensible default.
correction A character vector containing any selection of the options "border", "isotropic", "Ripley" or "translate". It specifies the edge correction(s) to be applied.
method A character vector indicating the user's choice of density estimation technique to be used. Options are "density", "loess", "sm" and "smrep".
slow Logical vector indicating whether to use exact analytic geometry to calculate the edge correction weights for the translation correction in the case where the window of observation of X is polygonal. These calculations are extremely slow and should be avoided unless you are a developer investigating the package.
... Arguments passed to the density estimation routine (density, loess or sm.density) selected by method.

Details

The mark correlation function rho_f(r) of a marked point process X is a measure of the dependence between the marks of two points of the process a distance r apart. It is informally defined as

rho_f(r) = E[f(M1,M2)]/E[f(M,M')]

where E[ ] denotes expectation and M1,M2 are the marks attached to two points of the process separated by a distance r, while M,M' are independent realisations of the marginal distribution of marks.

Here f is any function f(m1,m2) with two arguments which are possible marks of the pattern, and which returns a nonnegative real value. Common choices of f are: for continuous real-valued marks,

f(m1,m2)= m1 * m2

for discrete marks (multitype point patterns),

f(m1,m2)= (m1 == m2)

and for marks taking values in [0,2 * pi),

f(m1,m2) = sin(m1-m2)

.

Note that rho_f(r) is not a ``correlation'' in the usual statistical sense. It can take any nonnegative real value. The value 1 suggests ``lack of correlation'': if the marks attached to the points of X are independent and identically distributed, then rho_f(r) = 1. The interpretation of values larger or smaller than 1 depends on the choice of function f.

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

The argument f must be a function, accepting two arguments m1 and m2 which are vectors of equal length containing mark values (of the same type as the marks of X). It must return a vector of numeric values of the same length as m1 and m2. The values must be non-negative.

The argument r is the vector of values for the distance r at which rho_f(r) is estimated.

This algorithm assumes that 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 X as X$window) may have arbitrary shape.

Biases due to edge effects are treated in the same manner as in Kest. 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, but slow for complex windows.

Note that the estimator assumes the process is stationary (spatially homogeneous).

The numerator and denominator of the mark correlation function (in the expression above) are estimated using density estimation techniques. The user can choose between

"density"
which uses the standard kernel density estimation routine density, and works only for evenly-spaced r values;
"loess"
which uses the function loess in the package modreg;
"sm"
which uses the function sm.density in the package sm and is extremely slow;
"smrep"
which uses the function sm.density in the package sm and is relatively fast.

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 mark correlation function rho_f(r) has been estimated
theo the theoretical value of rho_f(r) when the marks attached to different points are independent, namely 1

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

Author(s)

Adrian Baddeley adrian@maths.uwa.edu.au http://www.maths.uwa.edu.au/~adrian/ and Rolf Turner rolf@math.unb.ca http://www.math.unb.ca/~rolf

References

Stoyan, D. and Stoyan, H. (1994) Fractals, random shapes and point fields: methods of geometrical statistics. John Wiley and Sons.

See Also

Kest, Kmulti

Examples

    # CONTINUOUS-VALUED MARKS:
    # (1) Longleaf Pine data
    # marks represent tree diameter
    data(longleaf)
    # Subset of this large pattern
    swcorner <- owin(c(0,100),c(0,100))
    sub <- longleaf[ , swcorner]
    # mark correlation function
    mc <- markcorr(sub)
    plot(mc)

    # (2) simulated data with independent marks
    X <- rpoispp(100)
    X <- X %mark% runif(X$n)
    Xc <- markcorr(X)
    plot(Xc)
    
    # MULTITYPE DATA:
    # Hughes' amacrine data
    # Cells marked as 'on'/'off'
    data(amacrine)
    # (3) Kernel density estimate with Epanecnikov kernel
    # (as proposed by Stoyan & Stoyan)
    M <- markcorr(amacrine, function(m1,m2) {m1==m2},
                  correction="translate", method="density",
                  kernel="epanechnikov")
    plot(M)
    # Note: kernel="epanechnikov" comes from help(density)

    # (4) Same again with explicit control over bandwidth
    M <- markcorr(amacrine, function(m1,m2) {m1==m2},
                  correction="translate", method="density",
                  kernel="epanechnikov", bw=0.02)
    # see help(density) for correct interpretation of 'bw'

   

[Package spatstat version 1.6-9 Index]