spatstat.options {spatstat} | R Documentation |
Allows the user to examine and reset the values of global parameters which control actions in the spatstat package.
spatstat.options(...) reset.spatstat.options()
... |
Either empty,
or a succession of parameter names in quotes,
or a succession of |
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:
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.
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.
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.
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.
List of arguments to be passed to the function persp
when displaying a real-valued image, such as the fitted surfaces
in plot.ppm
.
List of arguments controlling the plotting of point patterns
by plot.ppp
.
List of arguments controlling contour plots of pixel images
by contour.im
.
List of arguments controlling the plotting of functions
by plot.fv
and its relatives.
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.
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.
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.
Character string determining the style of progress reports
printed by progressreport
. Either
"tty"
or "txtbar"
.
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.
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
.
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
.
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
.
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
.
The default expansion factor (area inflation factor)
for expansion of the simulation window in
rmh
(see rmhcontrol
).
Initialised to 2
.
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'
.
Logical. Indicates whether to use accelerated C code
to evaluate density.ppp(X, at="points")
Initialised to TRUE
.
Integer. Number of trial values of smoothing bandwidth to use for
cross-validation in bw.relrisk
and similar
functions.
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
.
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
.
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.
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.
Logical. If TRUE
, the algorithm of
project.ppm
will be accelerated using a shorcut.
Initialised to FALSE
.
Logical. For software development purposes only. Do not change these values, unless you are Adrian Baddeley.
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.
Either a list of parameters and their values, or a single value. See Details.
Adrian Baddeley Adrian.Baddeley@csiro.au http://www.maths.uwa.edu.au/~adrian/ and Rolf Turner r.turner@auckland.ac.nz
# 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)