R: Simulate Neyman-Scott Point Process with Variance Gamma...

rVarGamma {spatstat.core} | R Documentation

## Simulate Neyman-Scott Point Process with Variance Gamma cluster kernel

### Description

Generate a random point pattern, a simulated realisation of the Neyman-Scott process with Variance Gamma (Bessel) cluster kernel.

### Usage

     rVarGamma(kappa, nu, scale, mu, win = owin(),
               thresh = 0.001, nsim=1, drop=TRUE,
               saveLambda=FALSE, expand = NULL, ...,
               poisthresh=1e-6, saveparents=TRUE)

### Arguments

`kappa` | Intensity of the Poisson process of cluster centres. A single positive number, a function, or a pixel image.
`nu` | Shape parameter for the cluster kernel. A number greater than -1.
`scale` | Scale parameter for cluster kernel. Determines the size of clusters. A positive number in the same units as the spatial coordinates.
`mu` | Mean number of points per cluster (a single positive number) or reference intensity for the cluster points (a function or a pixel image).
`win` | Window in which to simulate the pattern. An object of class `"owin"` or something acceptable to `as.owin`.
`thresh` | Threshold relative to the cluster kernel value at the origin (parent location) determining when the cluster kernel will be treated as zero for simulation purposes. Will be overridden by argument `expand` if that is given.
`nsim` | Number of simulated realisations to be generated.
`drop` | Logical. If `nsim=1` and `drop=TRUE` (the default), the result will be a point pattern, rather than a list containing a point pattern.
`saveLambda` | Logical. If `TRUE` then the random intensity corresponding to the simulated parent points will also be calculated and saved, and returns as an attribute of the point pattern.
`expand` | Numeric. Size of window expansion for generation of parent points. By default determined by calling `clusterradius` with the numeric threshold value given in `thresh`.
`...` | Passed to `clusterfield` to control the image resolution when `saveLambda=TRUE` and to `clusterradius` when `expand` is missing or `NULL`.
`poisthresh` | Numerical threshold below which the model will be treated as a Poisson process. See Details.
`saveparents` | Logical value indicating whether to save the locations of the parent points as an attribute.

### Details

This algorithm generates a realisation of the Neyman-Scott process with Variance Gamma (Bessel) cluster kernel, inside the window `win`.

The process is constructed by first generating a Poisson point process of “parent” points with intensity `kappa`. Then each parent point is replaced by a random cluster of points, the number of points in each cluster being random with a Poisson (`mu`) distribution, and the points being placed independently and uniformly according to a Variance Gamma kernel.

The shape of the kernel is determined by the dimensionless index `nu`. This is the parameter nu' = alpha/2 - 1 appearing in equation (12) on page 126 of Jalilian et al (2013).

The scale of the kernel is determined by the argument `scale`, which is the parameter eta appearing in equations (12) and (13) of Jalilian et al (2013). It is expressed in units of length (the same as the unit of length for the window `win`).

In this implementation, parent points are not restricted to lie in the window; the parent process is effectively the uniform Poisson process on the infinite plane.

This model can be fitted to data by the method of minimum contrast, maximum composite likelihood or Palm likelihood using `kppm`.

The algorithm can also generate spatially inhomogeneous versions of the cluster process:

- The parent points can be spatially inhomogeneous. If the argument `kappa` is a `function(x,y)` or a pixel image (object of class `"im"`), then it is taken as specifying the intensity function of an inhomogeneous Poisson process that generates the parent points.

- The offspring points can be inhomogeneous. If the argument `mu` is a `function(x,y)` or a pixel image (object of class `"im"`), then it is interpreted as the reference density for offspring points, in the sense of Waagepetersen (2006).

When the parents are homogeneous (`kappa` is a single number) and the offspring are inhomogeneous (`mu` is a function or pixel image), the model can be fitted to data using `kppm`, or using `vargamma.estK` or `vargamma.estpcf` applied to the inhomogeneous K function.

If the pair correlation function of the model is very close to that of a Poisson process, deviating by less than `poisthresh`, then the model is approximately a Poisson process, and will be simulated as a Poisson process with intensity `kappa * mu`, using `rpoispp`. This avoids computations that would otherwise require huge amounts of memory.

### Value

A point pattern (an object of class `"ppp"`) if `nsim=1`, or a list of point patterns if `nsim > 1`.

Additionally, some intermediate results of the simulation are returned as attributes of this point pattern (see `rNeymanScott`). Furthermore, the simulated intensity function is returned as an attribute `"Lambda"`, if `saveLambda=TRUE`.

### Author(s)

Abdollah Jalilian and Rasmus Waagepetersen. Adapted for spatstat by Adrian Baddeley Adrian.Baddeley@curtin.edu.au

### References

Jalilian, A., Guan, Y. and Waagepetersen, R. (2013) Decomposition of variance for spatial Cox processes. Scandinavian Journal of Statistics 40, 119-137.

Waagepetersen, R. (2007) An estimating function approach to inference for inhomogeneous Neyman-Scott processes. Biometrics 63, 252–258.

### See Also

`rpoispp`, `rNeymanScott`, `kppm`.

`vargamma.estK`, `vargamma.estpcf`.

### Examples

     # homogeneous
     X <- rVarGamma(30, 2, 0.02, 5)
     # inhomogeneous
     ff <- function(x,y){ exp(2 - 3 * abs(x)) }
     Z <- as.im(ff, W= owin())
     Y <- rVarGamma(30, 2, 0.02, Z)
     YY <- rVarGamma(ff, 2, 0.02, 3)

[Package spatstat.core version 2.3-1 Index]