https://github.com/cran/spatstat
Tip revision: b5ed1f414c22095e6b9b7da0cdc1fc1112d495d1 authored by Adrian Baddeley on 24 October 2014, 10:52:35 UTC
version 1.39-1
version 1.39-1
Tip revision: b5ed1f4
rmhcontrol.R
#
#
# rmhcontrol.R
#
# $Revision: 1.25 $ $Date: 2014/10/24 00:22:30 $
#
#
rmhcontrol <- function(...) {
UseMethod("rmhcontrol")
}
rmhcontrol.rmhcontrol <- function(...) {
argz <- list(...)
if(length(argz) == 1)
return(argz[[1]])
stop("Arguments not understood")
}
rmhcontrol.list <- function(...) {
argz <- list(...)
nama <- names(argz)
if(length(argz) == 1 && !any(nzchar(nama)))
do.call("rmhcontrol.default", argz[[1]])
else
do.call.matched("rmhcontrol.default", argz)
}
rmhcontrol.default <- function(..., p=0.9, q=0.5, nrep=5e5,
expand=NULL, periodic=NULL, ptypes=NULL,
x.cond=NULL, fixall=FALSE, nverb=0,
nsave=NULL, nburn=nsave, track=FALSE)
{
argh <- list(...)
nargh <- length(argh)
if(nargh > 0) {
# allow rmhcontrol(NULL), otherwise flag an error
if(!(nargh == 1 && is.null(argh[[1]])))
stop(paste("Unrecognised arguments to rmhcontrol;",
"valid arguments are listed in help(rmhcontrol.default)"))
}
# impose default values
if(missing(p)) p <- spatstat.options("rmh.p")
if(missing(q)) q <- spatstat.options("rmh.q")
if(missing(nrep)) nrep <- spatstat.options("rmh.nrep")
# validate arguments
if(!is.numeric(p) || length(p) != 1
|| p < 0 || p > 1)
stop("p should be a number in [0,1]")
if(!is.numeric(q) || length(q) != 1
|| q < 0 || q > 1)
stop("q should be a number in [0,1]")
if(!is.numeric(nrep) || length(nrep) != 1
|| nrep < 1)
stop("nrep should be an integer >= 1")
nrep <- as.integer(nrep)
if(!is.numeric(nverb) || length(nverb) != 1
|| nverb < 0 || nverb > nrep)
stop("nverb should be an integer <= nrep")
nverb <- as.integer(nverb)
if(!is.logical(fixall) || length(fixall) != 1)
stop("fixall should be a logical value")
if(!is.null(periodic) && (!is.logical(periodic) || length(periodic) != 1))
stop(paste(sQuote("periodic"), "should be a logical value or NULL"))
if(saving <- !is.null(nsave)) {
if(!is.numeric(nsave) || length(nsave) != 1
|| nsave < 0 || nsave >= nrep)
stop("nsave should be an integer < nrep")
if(is.null(nburn)) nburn <- min(nsave, nrep-nsave)
if(!is.null(nburn)) stopifnot(nburn + nsave <= nrep)
}
stopifnot(is.logical(track))
#################################################################
# Conditioning on point configuration
#
# condtype = "none": no conditioning
# condtype = "Palm": conditioning on the presence of specified points
# condtype = "window": conditioning on the configuration in a subwindow
#
if(is.null(x.cond)) {
condtype <- "none"
n.cond <- NULL
} else if(is.ppp(x.cond)) {
condtype <- "window"
n.cond <- x.cond$n
} else if(is.data.frame(x.cond)) {
if(ncol(x.cond) %in% c(2,3)) {
condtype <- "Palm"
n.cond <- nrow(x.cond)
} else stop("Wrong number of columns in data frame x.cond")
} else if(is.list(x.cond)) {
if(length(x.cond) %in% c(2,3)) {
x.cond <- as.data.frame(x.cond)
condtype <- "Palm"
n.cond <- nrow(x.cond)
} else stop("Wrong number of components in list x.cond")
} else stop("Unrecognised format for x.cond")
if(condtype == "Palm" && n.cond == 0) {
warning(paste("Ignored empty configuration x.cond;",
"conditional (Palm) simulation given an empty point pattern",
"is equivalent to unconditional simulation"))
condtype <- "none"
x.cond <- NULL
n.cond <- NULL
}
#################################################################
# Fixing the number of points?
#
# fixcode = 1 <--> no conditioning
# fixcode = 2 <--> conditioning on n = number of points
# fixcode = 3 <--> conditioning on the number of points of each type.
fixcode <- 2 - (p<1) + fixall - fixall*(p<1)
fixing <- switch(fixcode, "none", "n.total", "n.each.type")
# Warn about silly combination
if(fixall && p < 1)
warning("fixall = TRUE conflicts with p < 1. Ignored.\n")
###############################################################
# `expand' determines expansion of the simulation window
expand <- rmhexpand(expand)
# No expansion is permitted if we are conditioning on the
# number of points
if(fixing != "none") {
if(expand$force.exp)
stop(paste("When conditioning on the number of points,",
"no expansion may be done.\n"), call.=FALSE)
# no expansion
expand <- .no.expansion
}
###################################################################
# return augmented list
out <- list(p=p, q=q,
nrep=nrep, nverb=nverb,
expand=expand,
periodic=periodic,
ptypes=ptypes,
fixall=fixall,
fixcode=fixcode,
fixing=fixing,
condtype=condtype,
x.cond=x.cond,
saving=saving, nsave=nsave, nburn=nburn,
track=track)
class(out) <- c("rmhcontrol", class(out))
return(out)
}
print.rmhcontrol <- function(x, ...) {
verifyclass(x, "rmhcontrol")
cat("Metropolis-Hastings algorithm control parameters\n")
cat(paste("Probability of shift proposal: p =", x$p, "\n"))
if(x$fixing == "none") {
cat(paste("Conditional probability of death proposal: q =", x$q, "\n"))
if(!is.null(x$ptypes)) {
cat("Birth proposal probabilities for each type of point:\n")
print(x$ptypes)
}
}
switch(x$fixing,
none={},
n.total=cat("The total number of points is fixed\n"),
n.each.type=cat("The number of points of each type is fixed\n"))
switch(x$condtype,
none={},
window={
cat(paste("Conditional simulation given the",
"configuration in a subwindow\n"))
print(x$x.cond$window)
},
Palm={
cat("Conditional simulation of Palm type\n")
})
cat(paste("Number of M-H iterations: nrep =", x$nrep, "\n"))
if(x$saving)
cat(paste("Save point pattern every", x$nsave, "iterations",
"after a burn-in of", x$nburn, "iterations\n"))
cat(paste("Track proposal type and acceptance/rejection?",
if(x$track) "yes" else "no", "\n"))
if(x$nverb > 0)
cat(paste("Progress report every nverb=", x$nverb, "iterations\n"))
else
cat("No progress reports (nverb = 0).\n")
# invoke print.rmhexpand
print(x$expand)
cat("Periodic edge correction? ")
if(is.null(x$periodic)) cat("Not yet determined.\n") else
if(x$periodic) cat("Yes.\n") else cat("No.\n")
#
return(invisible(NULL))
}
default.rmhcontrol <- function(model) {
# set default for 'expand'
return(rmhcontrol(expand=default.expand(model)))
}
update.rmhcontrol <- function(object, ...) {
do.call.matched("rmhcontrol.default",
resolve.defaults(list(...), as.list(object),
.StripNull=TRUE))
}
rmhResolveControl <- function(control, model) {
# adjust control information once the model is known
stopifnot(inherits(control, "rmhcontrol"))
# change *default* expansion rule to something appropriate for model
# (applies only if expansion rule is undecided)
control$expand <- change.default.expand(control$expand, default.expand(model))
return(control)
}