R: Simulation Envelopes of Summary Function for 3D Point Pattern

envelope.pp3 {spatstat.core} | R Documentation

## Simulation Envelopes of Summary Function for 3D Point Pattern

### Description

Computes simulation envelopes of a summary function for a three-dimensional point pattern.

### Usage

      ## S3 method for class 'pp3'
    envelope(Y, fun=K3est, nsim=99, nrank=1, ...,
      funargs=list(), funYargs=funargs, simulate=NULL, verbose=TRUE,
      transform=NULL,global=FALSE,ginterval=NULL,use.theory=NULL,
      alternative=c("two.sided", "less", "greater"),
      scale=NULL, clamp=FALSE,
      savefuns=FALSE, savepatterns=FALSE,
      nsim2=nsim, VARIANCE=FALSE, nSD=2, Yname=NULL,
      maxnerr=nsim, rejectNA=FALSE, silent=FALSE,
      do.pwrong=FALSE, envir.simul=NULL)

### Arguments

`Y` | A three-dimensional point pattern (object of class `"pp3"`).
`fun` | Function that computes the desired summary statistic for a 3D point pattern.
`nsim` | Number of simulated point patterns to be generated when computing the envelopes.
`nrank` | Integer. Rank of the envelope value amongst the `nsim` simulated values. A rank of 1 means that the minimum and maximum simulated values will be used.
`...` | Extra arguments passed to `fun`.
`funargs` | A list, containing extra arguments to be passed to `fun`.
`funYargs` | Optional. A list, containing extra arguments to be passed to `fun` when applied to the original data `Y` only.
`simulate` | Optional. Specifies how to generate the simulated point patterns. If `simulate` is an expression in the R language, then this expression will be evaluated `nsim` times, to obtain `nsim` point patterns which are taken as the simulated patterns from which the envelopes are computed. If `simulate` is a function, then this function will be repeatedly applied to the data pattern `Y` to obtain `nsim` simulated patterns. If `simulate` is a list of point patterns, then the entries in this list will be treated as the simulated patterns from which the envelopes are computed. Alternatively `simulate` may be an object produced by the `envelope` command: see Details.
`verbose` | Logical flag indicating whether to print progress reports during the simulations.
`transform` | Optional. A transformation to be applied to the function values, before the envelopes are computed. An expression object (see Details).
`global` | Logical flag indicating whether envelopes should be pointwise (`global=FALSE`) or simultaneous (`global=TRUE`).
`ginterval` | Optional. A vector of length 2 specifying the interval of r values for the simultaneous critical envelopes. Only relevant if `global=TRUE`.
`use.theory` | Logical value indicating whether to use the theoretical value, computed by `fun`, as the reference value for simultaneous envelopes. Applicable only when `global=TRUE`.
`alternative` | Character string determining whether the envelope corresponds to a two-sided test (`side="two.sided"`, the default) or a one-sided test with a lower critical boundary (`side="less"`) or a one-sided test with an upper critical boundary (`side="greater"`).
`scale` | Optional. Scaling function for global envelopes. A function in the R language which determines the relative scale of deviations, as a function of distance r, when computing the global envelopes. Applicable only when `global=TRUE`. Summary function values for distance `r` will be divided by `scale(r)` before the maximum deviation is computed. The resulting global envelopes will have width proportional to `scale(r)`.
`clamp` | Logical value indicating how to compute envelopes when `alternative="less"` or `alternative="greater"`. Deviations of the observed summary function from the theoretical summary function are initially evaluated as signed real numbers, with large positive values indicating consistency with the alternative hypothesis. If `clamp=FALSE` (the default), these values are not changed. If `clamp=TRUE`, any negative values are replaced by zero.
`savefuns` | Logical flag indicating whether to save all the simulated function values.
`savepatterns` | Logical flag indicating whether to save all the simulated point patterns.
`nsim2` | Number of extra simulated point patterns to be generated if it is necessary to use simulation to estimate the theoretical mean of the summary function. Only relevant when `global=TRUE` and the simulations are not based on CSR.
`VARIANCE` | Logical. If `TRUE`, critical envelopes will be calculated as sample mean plus or minus `nSD` times sample standard deviation.
`nSD` | Number of estimated standard deviations used to determine the critical envelopes, if `VARIANCE=TRUE`.
`Yname` | Character string that should be used as the name of the data point pattern `Y` when printing or plotting the results.
`maxnerr` | Maximum number of rejected patterns. If `fun` yields a fatal error when applied to a simulated point pattern (for example, because the pattern is empty and `fun` requires at least one point), the pattern will be rejected and a new random point pattern will be generated. If this happens more than `maxnerr` times, the algorithm will give up.
`rejectNA` | Logical value specifying whether to reject a simulated pattern if the resulting values of `fun` are all equal to `NA`, `NaN` or infinite. If `FALSE` (the default), then simulated patterns are only rejected when `fun` gives a fatal error.
`silent` | Logical value specifying whether to print a report each time a simulated pattern is rejected.
`do.pwrong` | Logical. If `TRUE`, the algorithm will also estimate the true significance level of the “wrong” test (the test that declares the summary function for the data to be significant if it lies outside the pointwise critical boundary at any point). This estimate is printed when the result is printed.
`envir.simul` | Environment in which to evaluate the expression `simulate`, if not the current environment.

### Details

The `envelope` command performs simulations and computes envelopes of a summary statistic based on the simulations. The result is an object that can be plotted to display the envelopes. The envelopes can be used to assess the goodness-of-fit of a point process model to point pattern data.

The `envelope` function is generic, with methods for the classes `"ppp"`, `"ppm"` and `"kppm"` described in the help file for `envelope`. This function `envelope.pp3` is the method for three-dimensional point patterns (objects of class `"pp3"`).

For the most basic use, if you have a 3D point pattern `X` and you want to test Complete Spatial Randomness (CSR), type `plot(envelope(X, K3est,nsim=39))` to see the three-dimensional K function for `X` plotted together with the envelopes of the three-dimensional K function for 39 simulations of CSR.

To create simulation envelopes, the command `envelope(Y, ...)` first generates `nsim` random point patterns in one of the following ways.

- If `simulate=NULL`, then we generate `nsim` simulations of Complete Spatial Randomness (i.e. `nsim` simulated point patterns each being a realisation of the uniform Poisson point process) with the same intensity as the pattern `Y`.

- If `simulate` is supplied, then it determines how the simulated point patterns are generated. See `envelope` for details.

The summary statistic `fun` is applied to each of these simulated patterns. Typically `fun` is one of the functions `K3est`, `G3est`, `F3est` or `pcf3est`. It may also be a character string containing the name of one of these functions.

For further information, see the documentation for `envelope`.

### Value

A function value table (object of class `"fv"`) which can be plotted directly. See `envelope` for further details.

### Author(s)

Adrian Baddeley Adrian.Baddeley@curtin.edu.au

and Rolf Turner r.turner@auckland.ac.nz

### References

Baddeley, A.J, Moyeed, R.A., Howard, C.V. and Boyde, A. (1993) Analysis of a three-dimensional point pattern with replication. Applied Statistics 42, 641–668.

### See Also

`pp3`, `rpoispp3`, `K3est`, `G3est`, `F3est`, `pcf3est`.

### Examples

       X <- rpoispp3(20, box3())
     if(interactive()) {
     plot(envelope(X, nsim=39))
     }

[Package spatstat.core version 2.4-4 Index]