R: Studentised Permutation Test

studpermu.test {spatstat} | R Documentation

## Studentised Permutation Test

### Description

Perform a studentised permutation test for a difference between groups of point patterns.

### Usage

       studpermu.test(X, formula, summaryfunction = Kest,
           ..., rinterval = NULL, nperm = 999,
            use.Tbar = FALSE, minpoints = 20, rsteps = 128,
            r = NULL, arguments.in.data = FALSE)

### Arguments

`X` | Data. Either a `hyperframe` or a list of lists of point patterns.
`formula` | Formula describing the grouping, when `X` is a hyperframe. The left side of the formula identifies which column of `X` contains the point patterns. The right side identifies the grouping factor. If the formula is missing, the grouping variable is taken to be the first column of `X` that contains a factor, and the point patterns are taken from the first column that contains point patterns.
`summaryfunction` | Summary function applicable to point patterns.
`...` | Additional arguments passed to `summaryfunction`.
`rinterval` | Interval of distance values r over which the summary function should be evaluated and over which the test statistic will be integrated. If `NULL`, the default range of the summary statistic is used (taking the intersection of these ranges over all patterns).
`nperm` | Number of random permutations for the test.
`use.Tbar` | Logical value indicating choice of test statistic. If `TRUE`, use the alternative test statistic, which is appropriate for summary functions with roughly constant variance, such as K(r)/r or L(r).
`minpoints` | Minimum permissible number of points in a point pattern for inclusion in the test calculation.
`rsteps` | Number of discretisation steps in the `rinterval`.
`r` | Optional vector of distance values as the argument for `summaryfunction`. Should not usually be given. There is a sensible default.
`arguments.in.data` | Logical. If `TRUE`, individual extra arguments to `summaryfunction` will be taken from `X` (which must be a hyperframe). This assumes that the first argument of `summaryfunction` is the point pattern dataset.

### Details

This function performs the studentized permutation test of Hahn (2012) for a difference between groups of point patterns.

The first argument `X` should be either

a list of lists of point patterns.

  Each element of `X` will be interpreted as a group of point patterns, assumed to be replicates of the same point process.

a hyperframe:

  One column of the hyperframe should contain point patterns, and another column should contain a factor indicating the grouping. The argument `formula` should be a formula in the R language specifying the grouping: it should be of the form `P ~ G` where `P` is the name of the column of point patterns, and `G` is the name of the factor.

A group needs to contain at least two point patterns with at least `minpoints` points in each pattern.

The function returns an object of class `"htest"` and `"studpermutest"` that can be printed and plotted. The printout shows the test result and p-value. The plot shows the summary functions for the groups (and the group means if requested).

### Value

Object of class `"studpermutest"`.

### Author(s)

Ute Hahn.

Modified for `spatstat` by Adrian Baddeley Adrian.Baddeley@curtin.edu.au

Rolf Turner r.turner@auckland.ac.nz

and Ege Rubak rubak@math.aau.dk

### References

Hahn, U. (2012) A studentized permutation test for the comparison of spatial point patterns. Journal of the American Statistical Association 107 (498), 754–764.

### Examples

      np <- if(interactive()) 99 else 19
      testpyramidal <- studpermu.test(pyramidal, Neurons ~ group, nperm=np)
      testpyramidal

[Package spatstat version 1.54-0 Index]