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#
# $Revision: 1.59 $ $Date: 2022/01/04 05:30:06 $
#
# ppm()
# Fit a point process model to a two-dimensional point pattern
#
#
ppm <- function(Q, ...) {
UseMethod("ppm")
}
ppm.formula <- function(Q, interaction=NULL, ..., data=NULL, subset) {
## remember call
callstring <- short.deparse(sys.call())
cl <- match.call()
## trap a common error to give a more informative message
if(is.sob(data) || is.function(data))
stop(paste("The argument", sQuote("data"),
"should not be a spatial object;",
"it should be a list of spatial objects"),
call.=FALSE)
########### INTERPRET FORMULA ##############################
if(!inherits(Q, "formula"))
stop(paste("Argument 'Q' should be a formula"))
formula <- Q
## check formula has LHS and RHS. Extract them
if(length(formula) < 3)
stop(paste("Formula must have a left hand side"))
Yexpr <- formula[[2]]
trend <- formula[c(1,3)]
## FIT #######################################
thecall <- if(missing(subset)) {
call("ppm", Q=Yexpr, trend=trend, data=data, interaction=interaction)
} else {
call("ppm", Q=Yexpr, trend=trend, data=data, interaction=interaction,
subset=substitute(subset))
}
ncall <- length(thecall)
argh <- list(...)
nargh <- length(argh)
if(nargh > 0) {
thecall[ncall + 1:nargh] <- argh
names(thecall)[ncall + 1:nargh] <- names(argh)
}
callenv <- list2env(as.list(data), parent=parent.frame())
result <- eval(thecall, envir=callenv)
result$call <- cl
result$callstring <- callstring
result$callframe <- parent.frame()
return(result)
}
ppm.quad <- ppm.ppp <- ppm.default <-
function(Q,
trend = ~1,
interaction = Poisson(),
...,
covariates = data,
data = NULL,
covfunargs = list(),
subset,
clipwin,
correction="border",
rbord = reach(interaction),
use.gam=FALSE,
method = "mpl",
forcefit=FALSE,
emend=project,
project=FALSE,
prior.mean = NULL,
prior.var = NULL,
nd = NULL,
eps = NULL,
gcontrol=list(),
nsim=100,
nrmh=1e5,
start=NULL,
control=list(nrep=nrmh),
verb=TRUE,
callstring=NULL
) {
Qname <- short.deparse(substitute(Q))
subsetexpr <- if(!missing(subset)) substitute(subset) else NULL
clipwin <- if(!missing(clipwin)) clipwin else NULL
datalistname <- if(missing(covariates)) "data" else "covariates"
if(!(method %in% c("mpl", "ho", "logi", "VBlogi")))
stop(paste("Unrecognised fitting method", sQuote(method)))
if(!missing(emend) && !missing(project) && emend != project)
stop("Conflicting options: emend != project")
if(!is.null(prior.mean) | !is.null(prior.var)){
if(missing(method))
method <- "VBlogi"
if(method!="VBlogi")
stop("Prior specification only works with method ",
sQuote("VBlogi"))
}
if(method=="VBlogi"){
VB <- TRUE
method <- "logi"
} else{
VB <- FALSE
}
if(is.sob(covariates) || is.function(covariates))
stop(paste("The argument", sQuote(datalistname),
"should not be a spatial object;",
"it should be a list of spatial objects"),
call.=FALSE)
if(inherits(Q, "logiquad")){
if(missing(method))
method <- "logi"
if(method != "logi")
stop(paste("Only method =", sQuote("logi"),
"makes sense when Q is of type", sQuote("logiquad")))
}
cl <- match.call()
if(is.null(callstring))
callstring <- paste(short.deparse(sys.call()), collapse="")
if(is.ppp(Q) && is.marked(Q) && !is.multitype(Q))
stop(paste("ppm is not yet implemented for marked point patterns,",
"other than multitype patterns."))
if(!(is.ppp(Q) || is.quad(Q) || checkfields(Q, c("data", "dummy")))) {
stop("Argument Q must be a point pattern or a quadrature scheme")
}
X <- if(is.ppp(Q)) Q else Q$data
## Validate interaction
if(is.null(interaction)) {
interaction <- Poisson()
} else if(inherits(interaction, "intermaker")) {
## e.g. 'interaction=Hardcore': invoke it without arguments
interaction <- (f <- interaction)()
dont.complain.about(f)
} else if(!is.interact(interaction))
stop("Argument 'interaction' must be an object of class 'interact'")
## Ensure interaction is fully defined
if(!is.null(ss <- interaction$selfstart)) {
# invoke selfstart mechanism to fix all parameters
interaction <- ss(X, interaction)
}
if(inherits(trend, "formula")) {
## handle "." in formula, representing all variables in 'data'
if("." %in% variablesinformula(trend)) {
if(is.null(covariates))
stop("Cannot expand '.' since 'data' is not present", call.=FALSE)
rhs <- paste(names(covariates), collapse=" + ")
allmaineffects <- as.formula(paste("~", rhs))
environment(allmaineffects) <- environment(trend)
trend <- update(allmaineffects, trend)
}
## expand polynom() in formula
if(spatstat.options("expand.polynom"))
trend <- expand.polynom(trend)
}
# validate choice of edge correction
correction <- pickoption("correction", correction,
c(border="border",
periodic="periodic",
isotropic="isotropic",
Ripley="isotropic",
trans="translate",
translate="translate",
translation="translate",
none="none"))
# validate rbord
if(correction == "border") {
# rbord for border correction
rbord.given <- !missing(rbord) && !is.null(rbord)
if(is.null(rbord))
rbord <- reach(interaction)
infin <- is.infinite(rbord)
too.large <- infin || (eroded.areas(as.owin(X), rbord) == 0)
if(too.large) {
whinge <-
paste(if(rbord.given) "rbord" else "the reach of this interaction",
if(infin) "is infinite or unknown;"
else "is too large for this window;",
"please specify",
if(rbord.given) "a smaller value of",
"rbord, or use a different edge correction")
stop(whinge)
}
} else {
# rbord must be numeric to satisfy mpl.engine
if(is.null(rbord))
rbord <- 0
}
if(method == "logi") {
fitLOGI <- logi.engine(Q=Q, trend=trend,
interaction=interaction,
covariates=covariates,
covfunargs=covfunargs,
subsetexpr=subsetexpr,
clipwin=clipwin,
correction=correction,
rbord=rbord,
use.gam=use.gam,
forcefit=forcefit,
nd = nd,
gcontrol=gcontrol,
callstring=callstring,
prior.mean=prior.mean,
prior.var=prior.var,
VB=VB,
...)
fitLOGI$Qname <- Qname
fitLOGI$call <- cl
fitLOGI$callstring <- callstring
fitLOGI$callframe <- parent.frame()
if(emend && !valid.ppm(fitLOGI))
fitLOGI <- emend.ppm(fitLOGI)
return(fitLOGI)
}
# fit by maximum pseudolikelihood
fitMPL <- mpl.engine(Q=Q, trend=trend,
interaction=interaction,
covariates=covariates,
covfunargs=covfunargs,
subsetexpr=subsetexpr,
clipwin=clipwin,
correction=correction,
rbord=rbord,
use.gam=use.gam,
forcefit=forcefit,
nd = nd,
eps = eps,
gcontrol=gcontrol,
callstring=callstring,
...)
fitMPL$Qname <- Qname
if(!is.ppm(fitMPL)) {
# internal use only - returns some other data
return(fitMPL)
}
fitMPL$call <- cl
fitMPL$callstring <- callstring
fitMPL$callframe <- parent.frame()
if(emend && !valid.ppm(fitMPL))
fitMPL <- emend.ppm(fitMPL)
if(method == "mpl" || is.poisson.ppm(fitMPL))
return(fitMPL)
fitHO <- ho.engine(fitMPL, nsim=nsim, nrmh=nrmh, start=start,
control=control, verb=verb)
if(is.null(fitHO))
return(fitMPL)
if(emend && !valid.ppm(fitHO))
fitHO <- emend.ppm(fitHO)
return(fitHO)
}
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