Internal Options in Spatstat Package

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Description

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

Usage

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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 of interest to the user are:

checkpolygons

Logical flag indicating whether the functions owin and as.owin should apply very strict checks on the validity of polygon data. These strict checks are no longer necessary, and the default is checkpolygons=FALSE. See also fixpolygons below.

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.

eroded.intensity

Logical flag affecting the behaviour of the score and pseudo-score residual functions Gcom, Gres Kcom, Kres, psstA, psstG, psst. The flag indicates whether to compute intensity estimates on an eroded window (eroded.intensity=TRUE) or on the original data window (eroded.intensity=FALSE, the default).

expand

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

expand.polynom

Logical. Whether expressions involving polynom in a model formula should be expanded, so that polynom(x,2) is replaced by x + I(x^2) and so on. Initialised to TRUE.

fastpois

Logical. Whether to use a fast algorithm (introduced in spatstat 1.42-3) for simulating the Poisson point process in rpoispp when the argument lambda is a pixel image. Initialised to TRUE. Should be set to FALSE if needed to guarantee repeatability of results computed using earlier versions of spatstat.

fastthin

Logical. Whether to use a fast C language algorithm (introduced in spatstat 1.42-3) for random thinning in rthin when the argument P is a single number. Initialised to TRUE. Should be set to FALSE if needed to guarantee repeatability of results computed using earlier versions of spatstat.

fastK.lgcp

Logical. Whether to use fast or slow algorithm to compute the (theoretical) K-function of a log-Gaussian Cox process for use in lgcp.estK or Kmodel. The slow algorithm uses accurate numerical integration; the fast algorithm uses Simpson's Rule for numerical integration, and is about two orders of magnitude faster. Initialised to FALSE.

fixpolygons

Logical flag indicating whether the functions owin and as.owin should repair errors in polygon data. For example, self-intersecting polygons and overlapping polygons will be repaired. The default is fixpolygons=TRUE.

gpclib

Defunct. This parameter was used to permit or forbid the use of the package gpclib, because of its restricted software licence. This package is no longer needed.

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.

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.

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.

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.

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.

monochrome

Logical flag indicating whether graphics should be plotted in grey scale (monochrome=TRUE) or in colour (monochrome=FALSE, the default).

n.bandwidth

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

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.

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.

nvoxel

Default number of voxels in a 3D image, typically for calculating the distance transform in F3est. Initialised to 4 megavoxels: nvoxel = 2^22 = 4194304.

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.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.

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.pp3

List of arguments controlling the plotting of three-dimensional point patterns by plot.pp3.

print.ppm.SE

Default rule used by print.ppm to decide whether to calculate and print standard errors of the estimated coefficients of the model. One of the strings "always", "never" or "poisson" (the latter indicating that standard errors will be calculated only for Poisson models). The default is "poisson" because the calculation for non-Poisson models can take a long time.

progress

Character string determining the style of progress reports printed by progressreport. Either "tty", "tk" or "txtbar". For explanation of these options, see progressreport.

project.fast

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

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.

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.

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.

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.

terse

Integer between 0 and 4. The level of terseness (brevity) in printed output from many functions in spatstat. Higher values mean shorter output. A rough guide is the following:

0 Full output
1 Avoid wasteful output
2 Remove space between paragraphs
3 Suppress extras such as standard errors
4 Compress text, suppress internal warnings

The value of terse is initialised to 0.

transparent

Logical value indicating whether default colour maps are allowed to include semi-transparent colours, where possible. Default is TRUE. Currently this only affects plot.ppp.

units.paren

The kind of parenthesis which encloses the text that explains a unitname. This text is seen in the text output of functions like print.ppp and in the graphics generated by plot.fv. The value should be one of the character strings '(', '[', '{' or ''. The default is '('.

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.

Internal parameters

The following parameters may also be specified to spatstat.options but are intended for software development or testing purposes.

allow.logi.influence

Logical. For software development purposes only: prevents spatstat from performing incorrect calculations in cases which are not yet supported. Initialised to FALSE.

closepairs.newcode

Logical. Whether to use new version of the code for closepairs. Initialised to TRUE.

crossing.psp.useCall

Logical. Whether to use new version of the code for crossing.psp. Initialised to TRUE.

crosspairs.newcode

Logical. Whether to use new version of the code for crosspairs. Initialised to TRUE.

densityC

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

exactdt.checks.data

Logical. Do not change this value, unless you are \adrian.

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'.

old.morpho.psp

Logical. Whether to use old R code for morphological operations. Initialise to FALSE.

selfcrossing.psp.useCall

Logical. Whether to use new version of the code for selfcrossing.psp. Initialised to TRUE.

use.Krect

Logical. Whether to use new code for the K-function in a rectangular window. Initialised to TRUE.

Author(s)

\adrian

and \rolf

See Also

options

Examples

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  # 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)

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