smacpod: kdest – R documentation

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kdest

Difference of estimated K functions

Description

kdest determines the difference in estimated K functions for a set of cases and controls. Non-rejection envelopes can also be produced.

Usage

kdest(
  x,
  case = 2,
  nsim = 0,
  level = 0.95,
  r = NULL,
  rmax = NULL,
  breaks = NULL,
  correction = c("border", "isotropic", "Ripley", "translate"),
  nlarge = 3000,
  domain = NULL,
  var.approx = FALSE,
  ratio = FALSE
)

Arguments

`x`	A `ppp` object package with marks for the case and control groups.
`case`	The position of the name of the "case" group in `levels(x$marks)`. The default is 2. `x$marks` is assumed to be a factor. Automatic conversion is attempted if it is not.
`nsim`	An non-negative integer. Default is 0. The difference in estimated K functions will be calculated for `nsim` data sets generated under the random labeling hypothesis. These will be used to construct the non-rejection envelopes.
`level`	The level used for the non-rejection envelopes. Ignored if `nsim` is 0.
`r`	Optional. Vector of values for the argument r at which K(r) should be evaluated. Users are advised not to specify this argument; there is a sensible default. If necessary, specify `rmax`.
`rmax`	Optional. Maximum desired value of the argument r.
`breaks`	This argument is for internal use only.
`correction`	Optional. A character vector containing any selection of the options `"none"`, `"border"`, `"bord.modif"`, `"isotropic"`, `"Ripley"`, `"translate"`, `"translation"`, `"rigid"`, `"none"`, `"good"` or `"best"`. It specifies the edge correction(s) to be applied. Alternatively `correction="all"` selects all options.
`nlarge`	Optional. Efficiency threshold. If the number of points exceeds `nlarge`, then only the border correction will be computed (by default), using a fast algorithm.
`domain`	Optional. Calculations will be restricted to this subset of the window. See Details of `Kest`.
`var.approx`	Logical. If `TRUE`, the approximate variance of Kest(r) under CSR will also be computed.
`ratio`	Logical. If `TRUE`, the numerator and denominator of each edge-corrected estimate will also be saved, for use in analysing replicated point patterns.

Details

This function relies internally on the Kest and eval.fv functions from the spatstat package. The arguments are essentially the same as the Kest function, and the user is referred there for more details about the various arguments.

Value

Returns a kdenv object. See documentation for spatstat::Kest.

Author(s)

Joshua French

References

Waller, L.A. and Gotway, C.A. (2005). Applied Spatial Statistics for Public Health Data. Hoboken, NJ: Wiley.

Examples

data(grave)
kd1 = kdest(grave)
plot(kd1, iso ~ r, ylab = "difference", legend = FALSE, main = "")
kd2 = kdest(grave, nsim = 9, level = 0.8)
plot(kd2)

smacpod

Statistical Methods for the Analysis of Case-Control Point Data

v2.1.1

GPL (>= 2)

Authors

Joshua French [aut, cre] (<https://orcid.org/0000-0002-9708-3353>)

Initial release