https://github.com/cran/spatstat
Tip revision: 67dcdbb60550df766626a228cb0f0f3af568ceab authored by Adrian Baddeley on 15 August 2014, 17:39:22 UTC
version 1.38-0
version 1.38-0
Tip revision: 67dcdbb
options.R
#
# options.R
#
# Spatstat options and other internal states
#
# $Revision: 1.54 $ $Date: 2014/05/18 01:47:48 $
#
#
.spEnv <- new.env()
putSpatstatVariable <- function(name, value) {
assign(name, value, envir=.spEnv)
}
getSpatstatVariable <- function(name) {
get(name, envir=.spEnv)
}
putSpatstatVariable("Spatstat.Options", list())
putSpatstatVariable("Spatstat.ProgressBar", NULL)
putSpatstatVariable("Spatstat.ProgressData", NULL)
putSpatstatVariable("warnedkeys", character(0))
warn.once <- function(key, ...) {
warned <- getSpatstatVariable("warnedkeys")
if(!(key %in% warned)) {
warning(paste(...), call.=FALSE)
putSpatstatVariable("warnedkeys", c(warned, key))
}
return(invisible(NULL))
}
".Spat.Stat.Opt.Table" <-
list(
allow.logi.influence=list(
## whether leverage/influence calculations are permitted
## on a fitted model with method='logi'
default=FALSE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
checkpolygons = list(
## superseded
default=FALSE,
check=function(x) {
warning("spatstat.options('checkpolygons') will be ignored in future versions of spatstat", call.=FALSE)
return(is.logical(x) && length(x) == 1)
},
valid="a single logical value"
),
checksegments = list(
## default value of 'check' for psp objects
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1},
valid="a single logical value"
),
closepairs.newcode=list(
## use new code for 'closepairs'
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
crossing.psp.useCall=list(
## use new code for 'crossing.psp'
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
crosspairs.newcode=list(
## use new code for 'crosspairs'
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
densityC=list(
## use C routines for 'density.ppp'
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
dupC = list(
## value of 'DUP' for .C calls
default=FALSE,
check=function(x) { is.logical(x) && length(x) == 1},
valid="a single logical value"
),
exactdt.checks.data=list(
## whether 'exactdt' checks validity of return value
default=FALSE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
expand=list(
## default area expansion factor
default=2,
check=function(x) {
is.numeric(x) && length(x) == 1 && x > 1
},
valid="a single numeric value, greater than 1"
),
expand.polynom=list(
## whether to expand polynom() in ppm formulae
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
fasteval=list(
## whether to use 'fasteval' code if available
default="on",
check=function(x) { x %in% c("off", "on", "test") },
valid="one of the strings \'off\', \'on\' or \'test\'"
),
fastK.lgcp=list(
## whether to cut a few corners in 'lgcp.estK'
default=FALSE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
fixpolygons = list(
## whether to repair polygons automatically
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1},
valid="a single logical value"
),
gpclib=list(
## defunct!
default=FALSE,
check=function(x) {
message("gpclib is no longer needed")
return(TRUE)
},
valid="a single logical value"
),
huge.npoints=list(
## threshold to trigger a warning from rpoispp
default=1e6,
check=function(x) {
is.numeric(x) && length(x) == 1 && (x == ceiling(x)) && x > 1024
},
valid="a single integer, greater than 1024"
),
image.colfun=list(
## default colour scheme for plot.im
default=function(n){topo.colors(n)},
check=function(x) {
if(!is.function(x) || length(formals(x)) == 0) return(FALSE)
y <- x(42)
if(length(y) != 42 || !is.character(y)) return(FALSE)
z <- try(col2rgb(y), silent=TRUE)
return(!inherits(z, "try-error"))
},
valid="a function f(n) that returns character strings, interpretable as colours"
),
Kcom.remove.zeroes=list(
## whether Kcom removes zero distances
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
maxedgewt=list(
## maximum edge correction weight
default=100,
check=function(x){
is.numeric(x) && length(x) == 1 && is.finite(x) && x >= 1
},
valid="a finite numeric value, not less than 1"
),
maxmatrix=list(
## maximum size of matrix of pairs of points in mpl.R
default=2^24, # 16,777,216
check=function(x) {
is.numeric(x) && length(x) == 1 && (x == ceiling(x)) && x > 1024
},
valid="a single integer, greater than 1024"
),
monochrome = list(
## switch for monochrome colour scheme
default=FALSE,
check=function(x) { is.logical(x) && length(x) == 1},
valid="a single logical value"
),
n.bandwidth=list(
## number of values of bandwidth to try in bandwidth selection
default=32,
check=function(x) {
is.numeric(x) && (length(x) == 1) && (x == ceiling(x)) && (x > 2)
},
valid="a single integer, greater than 2"
),
ndummy.min=list(
## minimum grid size for dummy points
default=32,
check=function(x) {
is.numeric(x) && length(x) <= 2 && all(x == ceiling(x)) && all(x > 1)
},
valid="a single integer or a pair of integers, greater than 1"
),
ngrid.disc=list(
## number of grid points used to calculate area in area-interaction
default=128,
check=function(x) {
is.numeric(x) && length(x) == 1 && (x == ceiling(x)) && x > 1
},
valid="a single integer, greater than 1"
),
npixel=list(
## default pixel dimensions
default=128,
check=function(x){
is.numeric(x) && (length(x) %in% c(1,2)) && is.finite(x) &&
all(x == ceiling(x)) && all(x > 1)
},
valid="an integer, or a pair of integers, greater than 1"
),
nvoxel=list(
## default total number of voxels
default=2^22,
check=function(x) {
is.numeric(x) && length(x) == 1 && (x == ceiling(x)) && x > 2^12
},
valid="a single integer, greater than 2^12"
),
old.morpho.psp=list(
## use old code for morphological operations
default=FALSE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
par.binary=list(
## default graphics parameters for masks
default=list(),
check=is.list,
valid="a list"
),
par.contour=list(
## default graphics parameters for 'contour'
default=list(),
check=is.list,
valid="a list"
),
par.fv=list(
## default graphics parameters for 'plot.fv'
default=list(),
check=is.list,
valid="a list"
),
par.persp=list(
## default graphics parameters for 'persp' plots
default=list(),
check=is.list,
valid="a list"
),
par.points=list(
## default graphics parameters for 'points'
default=list(),
check=is.list,
valid="a list"
),
print.ppm.SE=list(
## under what conditions to print estimated SE in print.ppm
default="poisson",
check=function(x) { is.character(x) && length(x) == 1 &&
x %in% c("always", "poisson", "never") },
valid="one of the strings \'always\', \'poisson\' or \'never\'"
),
progress = list(
## how to display progress reports
default="tty",
check=function(x){ x %in% c("tty", "txtbar") },
valid=paste("one of the strings", dQuote("tty"),
"or", dQuote("txtbar"))
),
project.fast=list(
## whether to cut corners when projecting an invalid ppm object
default=FALSE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
psstA.ngrid=list(
## size of point grid for computing areas in psstA
default=32,
check=function(x) {
is.numeric(x) && length(x) == 1 && (x == ceiling(x)) && x >= 8
},
valid="a single integer, greater than or equal to 8"
),
psstA.nr=list(
## number of 'r' values to consider in psstA
default=30,
check=function(x) {
is.numeric(x) && length(x) == 1 && (x == ceiling(x)) && x >= 4
},
valid="a single integer, greater than or equal to 4"
),
psstG.remove.zeroes=list(
## whether to remove zero distances in psstG
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
rmh.nrep=list(
## default value of parameter 'nrep' in rmh
default=5e5,
check=function(x) {
is.numeric(x) && length(x) == 1 && (x == ceiling(x)) && x > 0
},
valid="a single integer, greater than 0"
),
rmh.p=list(
## default value of parameter 'p' in rmh
default=0.9,
check=function(x) { is.numeric(x) && length(x) == 1 &&
x >= 0 && x <= 1 },
valid="a single numerical value, between 0 and 1"
),
rmh.q=list(
## default value of parameter 'q' in rmh
default=0.9,
check=function(x) { is.numeric(x) && length(x) == 1 &&
x > 0 && x < 1 },
valid="a single numerical value, strictly between 0 and 1"
),
scalable = list(
## whether certain calculations in ppm should be scalable
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1},
valid="a single logical value"
),
selfcrossing.psp.useCall=list(
## whether to use new code in selfcrossing.psp
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
terse = list(
## Level of terseness in printed output (higher => more terse)
default=0,
check=function(x) { length(x) == 1 && (x %in% 0:4) },
valid="an integer between 0 and 4"
),
use.Krect=list(
## whether to use function Krect in Kest(X) when window is rectangle
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
),
Cwhist=list(
## whether to use C code for whist
default=TRUE,
check=function(x) { is.logical(x) && length(x) == 1 },
valid="a single logical value"
)
)
# end of options list
reset.spatstat.options <- function() {
Spatstat.Options <- lapply(.Spat.Stat.Opt.Table,
function(z) { z$default })
putSpatstatVariable("Spatstat.Options", Spatstat.Options)
invisible(Spatstat.Options)
}
reset.spatstat.options()
"spatstat.options" <-
function (...)
{
Spatstat.Options <- getSpatstatVariable("Spatstat.Options")
called <- list(...)
if(length(called) == 0)
return(Spatstat.Options)
if(is.null(names(called)) && length(called)==1) {
# spatstat.options(x)
x <- called[[1]]
if(is.null(x))
return(Spatstat.Options) # spatstat.options(NULL)
if(is.list(x))
called <- x
}
if(is.null(names(called))) {
# spatstat.options("par1", "par2", ...)
ischar <- unlist(lapply(called, is.character))
if(all(ischar)) {
choices <- unlist(called)
ok <- choices %in% names(Spatstat.Options)
if(!all(ok))
stop(paste("Unrecognised option(s):", called[!ok]))
if(length(called) == 1)
return(Spatstat.Options[[choices]])
else
return(Spatstat.Options[choices])
} else {
wrong <- called[!ischar]
offending <- unlist(lapply(wrong,
function(x) { y <- x;
short.deparse(substitute(y)) }))
offending <- paste(offending, collapse=",")
stop(paste("Unrecognised mode of argument(s) [",
offending,
"]: should be character string or name=value pair"))
}
}
# spatstat.options(name=value, name2=value2,...)
assignto <- names(called)
if (is.null(assignto) || !all(nzchar(assignto)))
stop("options must all be identified by name=value")
recog <- assignto %in% names(.Spat.Stat.Opt.Table)
if(!all(recog))
stop(paste("Unrecognised option(s):", assignto[!recog]))
# validate new values
for(i in seq_along(assignto)) {
nama <- assignto[i]
valo <- called[[i]]
entry <- .Spat.Stat.Opt.Table[[nama]]
ok <- entry$check(valo)
if(!ok)
stop(paste("Parameter", dQuote(nama), "should be",
entry$valid))
}
# reassign
changed <- Spatstat.Options[assignto]
Spatstat.Options[assignto] <- called
putSpatstatVariable("Spatstat.Options", Spatstat.Options)
# return
invisible(changed)
}