spatstat.options {spatstat}R Documentation

Internal Options in Spatstat Package

Description

Allows the user to examine and reset the values of global parameters which control actions in the spatstat package.

Usage

  spatstat.options(...)
  reset.spatstat.options()

Arguments

...

Either empty, or a succession of parameter names in quotes, or a succession of name=value pairs. See below for the parameter names.

Details

The function spatstat.options allows the user to examine and reset the values of global parameters which control actions in the spatstat package. It is analogous to the system function options.

The function reset.spatstat.options resets all the global parameters in spatstat to their original, default values.

The global parameters are:

scalable

Logical flag indicating whether the new code in rmh.default which makes the results scalable (invariant to change of units) should be used. In order to recover former behaviour (so that previous results can be reproduced) set this option equal to FALSE. See the “Warning” section in the help for rmh() for more detail.

npixel

Default number of pixels in a binary mask or pixel image. Either an integer, or a pair of integers, giving the number of pixels in the x and y directions respectively.

maxedgewt

Edge correction weights will be trimmed so as not to exceed this value. This applies to the weights computed by edge.Trans or edge.Ripley and used in Kest and its relatives.

par.binary

List of arguments to be passed to the function image when displaying a binary image mask (in plot.owin or plot.ppp). Typically used to reset the colours of foreground and background.

par.persp

List of arguments to be passed to the function persp when displaying a real-valued image, such as the fitted surfaces in plot.ppm.

par.points

List of arguments controlling the plotting of point patterns by plot.ppp.

par.contour

List of arguments controlling contour plots of pixel images by contour.im.

par.fv

List of arguments controlling the plotting of functions by plot.fv and its relatives.

ndummy.min

The minimum number of dummy points in a quadrature scheme created by default.dummy. Either an integer or a pair of integers giving the minimum number of dummy points in the x and y directions respectively.

ngrid.disc

Number of points in the square grid used to compute a discrete approximation to the areas of discs in areaLoss and areaGain when exact calculation is not available. A single integer.

image.colfun

Function determining the default colour map for plot.im. When called with one integer argument n, this function should return a character vector of length n specifying n different colours.

progress

Character string determining the style of progress reports printed by progressreport. Either "tty" or "txtbar".

checkpolygons

Logical flag indicating whether the functions owin and as.owin should check the validity of polygon data. It is advisable to leave this set to TRUE. If you set checkpolygons=FALSE, no checking will be performed, making it possible to create window objects whose topology is garbled. This can be useful for inspecting spatial data that contain errors, for example, when converting data from shapefiles. However, other functions in spatstat may return incorrect answers on these data.

checksegments

Logical flag indicating whether the functions psp and as.psp should check the validity of line segment data (in particular, checking that the endpoints of the line segments are inside the specified window). It is advisable to leave this flag set to TRUE.

gpclib

Logical flag indicating whether the polygon clipping library gpclib can be used. The default is FALSE, which means that the package gpclib is not loaded, and certain polygon operations (such as the intersection and union of polygons) will be approximated by raster operations. If this option is re-set to TRUE, then the package gpclib will be loaded, and polygon operations such as the union and intersection of polygons will result in a polygon. The licence for gpclib is not Free Open Source and explicitly forbids commercial use. See library(help=gpclib). If you are using spatstat for commercial purposes, this option should remain set to FALSE.

maxmatrix

The maximum permitted size (rows times columns) of matrices generated by spatstat's internal code. Used by ppm and predict.ppm (for example) to decide when to split a large calculation into blocks. Defaults to 2^24=16777216.

huge.npoints

The maximum value of n for which runif(n) will not generate an error (possible errors include failure to allocate sufficient memory, and integer overflow of n). An attempt to generate more than this number of random points triggers a warning from runifpoint and other functions. Defaults to 1e6.

expand

The default expansion factor (area inflation factor) for expansion of the simulation window in rmh (see rmhcontrol). Initialised to 2.

fasteval

One of the strings 'off', 'on' or 'test' determining whether to use accelerated C code to evaluate the conditional intensity of a Gibbs model. Initialised to 'on'.

density

Logical. Indicates whether to use accelerated C code to evaluate density.ppp(X, at="points") Initialised to TRUE.

n.bandwidth

Integer. Number of trial values of smoothing bandwidth to use for cross-validation in bw.relrisk and similar functions.

psstG.remove.zeroes

Logical value, determining whether the algorithm in psstG removes or retains the contributions to the function from pairs of points that are identical. If these are retained then the function has a jump at r=0. Initialised to TRUE.

Kcom.remove.zeroes

Logical value, determining whether the algorithm in Kcom and Kres removes or retains the contributions to the function from pairs of points that are identical. If these are retained then the function has a jump at r=0. Initialised to TRUE.

psstA.ngrid

Single integer, controlling the accuracy of the discrete approximation of areas computed in the function psstA. The area of a disc is approximated by counting points on an n * n grid. Initialised to 32.

psstA.nr

Single integer, determining the number of distances r at which the function psstA will be evaluated (in the default case where argument r is absent). Initialised to 30.

project.fast

Logical. If TRUE, the algorithm of project.ppm will be accelerated using a shorcut. Initialised to FALSE.

exactdt.checks.data,closepairs.newcode

Logical. For software development purposes only. Do not change these values, unless you are Adrian Baddeley.

rmh.p, rmh.q, rmh.nrep

New default values for the parameters p, q and nrep in the Metropolis-Hastings simulation algorithm. These override the defaults in rmhcontrol.default.

If no arguments are given, the current values of all parameters are returned, in a list.

If one parameter name is given, the current value of this parameter is returned (not in a list, just the value).

If several parameter names are given, the current values of these parameters are returned, in a list.

If name=value pairs are given, the named parameters are reset to the given values, and the previous values of these parameters are returned, in a list.

Value

Either a list of parameters and their values, or a single value. See Details.

Author(s)

Adrian Baddeley Adrian.Baddeley@csiro.au http://www.maths.uwa.edu.au/~adrian/ and Rolf Turner r.turner@auckland.ac.nz

See Also

options

Examples

  # save current values
  oldopt <- spatstat.options()

  spatstat.options("npixel")
  spatstat.options(npixel=150)
  spatstat.options(npixel=c(100,200))

  spatstat.options(par.binary=list(col=grey(c(0.5,1))))

  spatstat.options(par.persp=list(theta=-30,phi=40,d=4))
  # see help(persp.default) for other options

  # revert
  spatstat.options(oldopt)


[Package spatstat version 1.25-3 Index]