envelope.spp: Envelope for Point Patterns on Sphere

In rubak/spatstatsphere: Point patterns on the sphere for spatstat package

Description

Enables envelopes to be computed for point patterns on a sphere.

Usage

## S3 method for class 'spp'
envelope(Y, fun = Kspp, nsim = 99, nrank = 1, ...,
  funargs = list(), 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, do.pwrong = FALSE,
  envir.simul = NULL)

Arguments

Y	A point pattern on a spherical domain (object of class "spp")
fun	Function that is to be computed for each simulated pattern.
nsim	Number of simulations to perform.
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.
funargs	A list, containing extra arguments to be passed to fun.
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 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 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.
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.
...	Extra arguments passed to fun.

Details

This is a method for the generic function envelope applicable to point patterns on a sphere.

The argument Y should be a point pattern on a sphere. The function fun will be evaluated for the data and also for nsim simulated point patterns on the same spherical domain. The upper and lower envelopes of these evaluated functions will be computed as described in envelope.

The type of simulation is determined as follows.

• simulate is missing or NULL, then random point patterns will be generated according to a Poisson point process on the spherical domain on which Y is defined, with intensity estimated from Y.

• If simulate is present, it should be an expression that can be evaluated to yield random point patterns on the same spherical domain as Y.

The function fun should accept as its first argument a point pattern on a spherical domain (object of class "spp") and should have another argument called r or a ...{} argument.

Value

Function value table (object of class "fv") with additional information, as described in envelope.

See Also

envelope, Kspp

Examples

   if(interactive()) {
     ns <- 39
     np <- 40
   } else { ns <- np <- 3 }
   X <- runifspp(np)
   # uniform Poisson
   envelope(X, nsim=ns)

rubak/spatstatsphere documentation built on May 28, 2019, 9:56 a.m.