# kppm

##### Fit Cluster or Cox Point Process Model

Fit a homogeneous or inhomogeneous cluster process or Cox point process model to a point pattern.

##### Usage

`kppm(X, ...)` ## S3 method for class 'formula':
kppm(X,
clusters = c("Thomas","MatClust","Cauchy","VarGamma","LGCP"),
...,
data=NULL)

## S3 method for class 'ppp':
kppm(X,
trend = ~1,
clusters = c("Thomas","MatClust","Cauchy","VarGamma","LGCP"),
data = NULL,
...,
covariates=data,
method = c("mincon", "clik2", "palm"),
improve.type = c("none", "clik1", "wclik1", "quasi"),
improve.args = list(),
weightfun=NULL,
control=list(),
algorithm="Nelder-Mead",
statistic="K",
statargs=list(),
rmax = NULL,
covfunargs=NULL,
use.gam=FALSE,
nd=NULL, eps=NULL)

## S3 method for class 'quad':
kppm(X,
trend = ~1,
clusters = c("Thomas","MatClust","Cauchy","VarGamma","LGCP"),
data = NULL,
...,
covariates=data,
method = c("mincon", "clik2", "palm"),
improve.type = c("none", "clik1", "wclik1", "quasi"),
improve.args = list(),
weightfun=NULL,
control=list(),
algorithm="Nelder-Mead",
statistic="K",
statargs=list(),
rmax = NULL,
covfunargs=NULL,
use.gam=FALSE,
nd=NULL, eps=NULL)

##### Arguments

- X
- A point pattern dataset (object of class
`"ppp"`

or`"quad"`

) to which the model should be fitted, or a`formula`

in the Rlanguage defining the model. See Details. - trend
- An Rformula, with no left hand side, specifying the form of the log intensity.
- clusters
- Character string determining the cluster model.
Partially matched.
Options are
`"Thomas"`

,`"MatClust"`

,`"Cauchy"`

,`"VarGamma"`

and`"LGCP"`

. - data,covariates
- The values of spatial covariates (other than the Cartesian coordinates) required by the model. A named list of pixel images, functions, windows, tessellations or numeric constants.
- ...
- Additional arguments. See Details.
- method
- The fitting method. Either
`"mincon"`

for minimum contrast,`"clik2"`

for second order composite likelihood, or`"palm"`

for Palm likelihood. Partially matched. - improve.type
- Method for updating the initial estimate of the trend.
Initially the trend is estimated as if the process
is an inhomogeneous Poisson process.
The default,
`improve.type = "none"`

, is to use this initial estimate. Otherwise, the - improve.args
- Additional arguments passed to
`improve.kppm`

when`improve.type != "none"`

. See Details. - weightfun
- Optional weighting function $w$
in the composite likelihood or Palm likelihood.
A
`function`

in the Rlanguage. See Details. - control
- List of control parameters passed to the optimization function
`optim`

. - algorithm
- Character string determining the mathematical optimisation algorithm
to be used by
`optim`

. See the argument`method`

of`optim`

. - statistic
- Name of the summary statistic to be used
for minimum contrast estimation: either
`"K"`

or`"pcf"`

. - statargs
- Optional list of arguments to be used when calculating
the
`statistic`

. See Details. - rmax
- Maximum value of interpoint distance to use in the composite likelihood.
- covfunargs,use.gam,nd,eps
- Arguments passed to
`ppm`

when fitting the intensity.

##### Details

This function fits a clustered point process model to the
point pattern dataset `X`

.

The model may be either a *Neyman-Scott cluster process*
or another *Cox process*.
The type of model is determined by the argument `clusters`

.
Currently the options
are `clusters="Thomas"`

for the Thomas process,
`clusters="MatClust"`

for the Matern cluster process,
`clusters="Cauchy"`

for the Neyman-Scott cluster process
with Cauchy kernel,
`clusters="VarGamma"`

for the Neyman-Scott cluster process
with Variance Gamma kernel (requires an additional argument `nu`

to be passed through the dots; see `rVarGamma`

for details),
and `clusters="LGCP"`

for the log-Gaussian Cox process (may
require additional arguments passed through `...`

; see
`rLGCP`

for details on argument names).
The first four models are Neyman-Scott cluster processes.

The algorithm first estimates the intensity function
of the point process using `ppm`

.
The argument `X`

may be a point pattern
(object of class `"ppp"`

) or a quadrature scheme
(object of class `"quad"`

). The intensity is specified by
the `trend`

argument.
If the trend formula is `~1`

(the default)
then the model is *homogeneous*. The algorithm begins by
estimating the intensity as the number of points divided by
the area of the window.
Otherwise, the model is *inhomogeneous*.
The algorithm begins by fitting a Poisson process with log intensity
of the form specified by the formula `trend`

.
(See `ppm`

for further explanation).

The argument `X`

may also be a `formula`

in the
Rlanguage. The right hand side of the formula gives the
`trend`

as described above. The left hand side of the formula
gives the point pattern dataset to which the model should be fitted.

If `improve.type="none"`

this is the final estimate of the
intensity. Otherwise, the intensity estimate is updated, as explained in
`improve.kppm`

. Additional arguments to
`improve.kppm`

are passed as a named list in
`improve.args`

.
The clustering parameters of the model are then fitted
either by minimum contrast estimation, or by maximum
composite likelihood.

[object Object],[object Object],[object Object]
In all three methods, the optimisation is performed by the generic
optimisation algorithm `optim`

.
The behaviour of this algorithm can be modified using the
argument `control`

.
Useful control arguments include
`trace`

, `maxit`

and `abstol`

(documented in the help for `optim`

).

##### Value

- An object of class
`"kppm"`

representing the fitted model. There are methods for printing, plotting, predicting, simulating and updating objects of this class.

##### References

Guan, Y. (2006)
A composite likelihood approach in fitting spatial point process
models.
*Journal of the American Statistical Association*
**101**, 1502--1512.

Jalilian, A., Guan, Y. and Waagepetersen, R. (2012)
Decomposition of variance for spatial Cox processes.
*Scandinavian Journal of Statistics*, in press.

Tanaka, U. and Ogata, Y. and Stoyan, D. (2008)
Parameter estimation and model selection for
Neyman-Scott point processes.
*Biometrical Journal* **50**, 43--57.

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

##### See Also

methods for `kppm`

objects:
`plot.kppm`

,
`fitted.kppm`

,
`predict.kppm`

,
`simulate.kppm`

,
`update.kppm`

,
`vcov.kppm`

,
`methods.kppm`

,
`as.ppm.kppm`

,
`Kmodel.kppm`

,
`pcfmodel.kppm`

.

Minimum contrast fitting algorithm:
`mincontrast`

.

Alternative fitting algorithms:
`thomas.estK`

,
`matclust.estK`

,
`lgcp.estK`

,
`cauchy.estK`

,
`vargamma.estK`

,
`thomas.estpcf`

,
`matclust.estpcf`

,
`lgcp.estpcf`

,
`cauchy.estpcf`

,
`vargamma.estpcf`

,

Summary statistics:
`Kest`

,
`Kinhom`

,
`pcf`

,
`pcfinhom`

.

See also `ppm`

##### Examples

```
# method for point patterns
kppm(redwood, ~1, "Thomas")
# method for formulas
kppm(redwood ~ 1, "Thomas")
kppm(redwood ~ 1, "Thomas", method="c")
kppm(redwood ~ 1, "Thomas", method="p")
kppm(redwood ~ x, "MatClust")
kppm(redwood ~ x, "MatClust", statistic="pcf", statargs=list(stoyan=0.2))
kppm(redwood ~ 1, "LGCP", statistic="pcf")
kppm(redwood ~ x, cluster="Cauchy", statistic="K")
kppm(redwood, cluster="VarGamma", nu = 0.5, statistic="pcf")
if(require(RandomFields)) {
kppm(redwood ~ x, "LGCP", statistic="pcf",
model="matern", nu=0.3,
control=list(maxit=10))
}
# fit intensity with quasi-likelihood method
kppm(redwood ~ x, "Thomas", improve.type = "quasi")
```

*Documentation reproduced from package spatstat, version 1.42-2, License: GPL (>= 2)*