# relrisk.ppp

##### Nonparametric Estimate of Spatially-Varying Relative Risk

Given a multitype point pattern, this function estimates the spatially-varying probability of each type of point, or the ratios of such probabilities, using kernel smoothing. The default smoothing bandwidth is selected by cross-validation.

##### Usage

```
# S3 method for ppp
relrisk(X, sigma = NULL, ..., varcov = NULL,
at = c("pixels", "points"),
relative=FALSE,
adjust=1, edge=TRUE, diggle=FALSE, se=FALSE,
casecontrol=TRUE, control=1, case)
```

##### Arguments

- X
A multitype point pattern (object of class

`"ppp"`

which has factor valued marks).- sigma
Optional. The numeric value of the smoothing bandwidth (the standard deviation of isotropic Gaussian smoothing kernel). Alternatively

`sigma`

may be a function which can be used to select a different bandwidth for each type of point. See Details.- …
Arguments passed to

`bw.relrisk`

to select the bandwidth, or passed to`density.ppp`

to control the pixel resolution.- varcov
Optional. Variance-covariance matrix of anisotopic Gaussian smoothing kernel. Incompatible with

`sigma`

.- at
Character string specifying whether to compute the probability values at a grid of pixel locations (

`at="pixels"`

) or only at the points of`X`

(`at="points"`

).- relative
Logical. If

`FALSE`

(the default) the algorithm computes the probabilities of each type of point. If`TRUE`

, it computes the*relative risk*, the ratio of probabilities of each type relative to the probability of a control.- adjust
Optional. Adjustment factor for the bandwidth

`sigma`

.- edge
Logical value indicating whether to apply edge correction.

- diggle
Logical. If

`TRUE`

, use the Jones-Diggle improved edge correction, which is more accurate but slower to compute than the default correction.- se
Logical value indicating whether to compute standard errors as well.

- casecontrol
Logical. Whether to treat a bivariate point pattern as consisting of cases and controls, and return only the probability or relative risk of a case. Ignored if there are more than 2 types of points. See Details.

- control
Integer, or character string, identifying which mark value corresponds to a control.

- case
Integer, or character string, identifying which mark value corresponds to a case (rather than a control) in a bivariate point pattern. This is an alternative to the argument

`control`

in a bivariate point pattern. Ignored if there are more than 2 types of points.

##### Details

The command `relrisk`

is generic and can be used to
estimate relative risk in different ways.

This function `relrisk.ppp`

is the method for point pattern
datasets. It computes *nonparametric* estimates of relative risk
by kernel smoothing.

If `X`

is a bivariate point pattern
(a multitype point pattern consisting of two types of points)
then by default,
the points of the first type (the first level of `marks(X)`

)
are treated as controls or non-events, and points of the second type
are treated as cases or events. Then by default this command computes
the spatially-varying *probability* of a case,
i.e. the probability \(p(u)\)
that a point at spatial location \(u\)
will be a case. If `relative=TRUE`

, it computes the
spatially-varying *relative risk* of a case relative to a
control, \(r(u) = p(u)/(1- p(u))\).

If `X`

is a multitype point pattern with \(m > 2\) types,
or if `X`

is a bivariate point pattern
and `casecontrol=FALSE`

,
then by default this command computes, for each type \(j\),
a nonparametric estimate of
the spatially-varying *probability* of an event of type \(j\).
This is the probability \(p_j(u)\)
that a point at spatial location \(u\)
will belong to type \(j\).
If `relative=TRUE`

, the command computes the
*relative risk* of an event of type \(j\)
relative to a control,
\(r_j(u) = p_j(u)/p_k(u)\),
where events of type \(k\) are treated as controls.
The argument `control`

determines which type \(k\)
is treated as a control.

If `at = "pixels"`

the calculation is performed for
every spatial location \(u\) on a fine pixel grid, and the result
is a pixel image representing the function \(p(u)\)
or a list of pixel images representing the functions
\(p_j(u)\) or \(r_j(u)\)
for \(j = 1,\ldots,m\).
An infinite value of relative risk (arising because the
probability of a control is zero) will be returned as `NA`

.

If `at = "points"`

the calculation is performed
only at the data points \(x_i\). By default
the result is a vector of values
\(p(x_i)\) giving the estimated probability of a case
at each data point, or a matrix of values
\(p_j(x_i)\) giving the estimated probability of
each possible type \(j\) at each data point.
If `relative=TRUE`

then the relative risks
\(r(x_i)\) or \(r_j(x_i)\) are
returned.
An infinite value of relative risk (arising because the
probability of a control is zero) will be returned as `Inf`

.

Estimation is performed by a simple Nadaraja-Watson type kernel smoother (Diggle, 2003). The smoothing bandwidth can be specified in any of the following ways:

`sigma`

is a single numeric value, giving the standard deviation of the isotropic Gaussian kernel.`sigma`

is a numeric vector of length 2, giving the standard deviations in the \(x\) and \(y\) directions of a Gaussian kernel.`varcov`

is a 2 by 2 matrix giving the variance-covariance matrix of the Gaussian kernel.`sigma`

is a`function`

which selects the bandwidth. Bandwidth selection will be applied**separately to each type of point**. An example of such a function is`bw.diggle`

.`sigma`

and`varcov`

are both missing or null. Then a**common**smoothing bandwidth`sigma`

will be selected by cross-validation using`bw.relrisk`

.An infinite smoothing bandwidth,

`sigma=Inf`

, is permitted and yields a constant estimate of relative risk.

If `se=TRUE`

then standard errors will also be computed,
based on asymptotic theory, *assuming a Poisson process*.

##### Value

If `se=FALSE`

(the default), the format is described below.
If `se=TRUE`

, the result is a list of two entries,
`estimate`

and `SE`

, each having the format described below.

If `X`

consists of only two types of points,
and if `casecontrol=TRUE`

,
the result is a pixel image (if `at="pixels"`

)
or a vector (if `at="points"`

).
The pixel values or vector values
are the probabilities of a case if `relative=FALSE`

,
or the relative risk of a case (probability of a case divided by the
probability of a control) if `relative=TRUE`

.

If `X`

consists of more than two types of points,
or if `casecontrol=FALSE`

, the result is:

(if

`at="pixels"`

) a list of pixel images, with one image for each possible type of point. The result also belongs to the class`"solist"`

so that it can be printed and plotted.(if

`at="points"`

) a matrix of probabilities, with rows corresponding to data points \(x_i\), and columns corresponding to types \(j\).

The pixel values or matrix entries
are the probabilities of each type of point if `relative=FALSE`

,
or the relative risk of each type (probability of each type divided by the
probability of a control) if `relative=TRUE`

.

If `relative=FALSE`

, the resulting values always lie between 0
and 1. If `relative=TRUE`

, the results are either non-negative
numbers, or the values `Inf`

or `NA`

.

##### References

Diggle, P.J. (2003)
*Statistical analysis of spatial point patterns*,
Second edition. Arnold.

##### See Also

There is another method `relrisk.ppm`

for point process
models which computes *parametric*
estimates of relative risk, using the fitted model.

See also
`bw.relrisk`

,
`density.ppp`

,
`Smooth.ppp`

,
`eval.im`

##### Examples

```
# NOT RUN {
p.oak <- relrisk(urkiola, 20)
if(interactive()) {
plot(p.oak, main="proportion of oak")
plot(eval.im(p.oak > 0.3), main="More than 30 percent oak")
plot(split(lansing), main="Lansing Woods")
p.lan <- relrisk(lansing, 0.05, se=TRUE)
plot(p.lan$estimate, main="Lansing Woods species probability")
plot(p.lan$SE, main="Lansing Woods standard error")
wh <- im.apply(p.lan$estimate, which.max)
types <- levels(marks(lansing))
wh <- eval.im(types[wh])
plot(wh, main="Most common species")
}
# }
```

*Documentation reproduced from package spatstat, version 1.57-1, License: GPL (>= 2)*