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#
# alltypes.R
#
# $Revision: 1.38 $ $Date: 2022/01/04 05:30:06 $
#
#
alltypes <- function(X, fun="K", ...,
dataname=NULL,verb=FALSE,envelope=FALSE,reuse=TRUE) {
#
# Function 'alltypes' --- calculates a summary function for
# each type, or each pair of types, in a multitype point pattern
#
if(is.ppp(X)) classname <- "ppp" else
if(is.lpp(X)) classname <- "lpp" else
stop("X should be a ppp or lpp object")
if(is.null(dataname))
dataname <- short.deparse(substitute(X))
# --------------------------------------------------------------------
# First inspect marks
if(!is.marked(X)) {
nmarks <- 0
marklabels <- ""
} else {
if(!is.multitype(X))
stop("the marks must be a factor")
# ensure type names are parseable (for mathematical labels)
levels(marks(X)) <- make.parseable(levels(marks(X)))
mks <- marks(X)
ma <- levels(mks)
nmarks <- length(ma)
marklabels <- paste(ma)
}
# ---------------------------------------------------------------------
# determine function name
f.is.name <- is.name(substitute(fun))
fname <-
if(f.is.name)
paste(as.name(substitute(fun)))
else if(is.character(fun))
fun
else sQuote("fun")
# ---------------------------------------------------------------------
# determine function to be called
if(is.function(fun)) {
estimator <- fun
} else if(is.character(fun)) {
# First try matching one of the standard abbreviations K, G etc
estimator <- getSumFun(fun, classname, (nmarks > 0), fatal=FALSE)
if(is.null(estimator))
estimator <- get(fun, mode="function")
} else
stop(paste(sQuote("fun"), "should be a function or a character string"))
# ------------------------------------------------------------------
# determine how the function shall be called.
#
indices.expected <- sum(c("i", "j") %in% names(formals(estimator)))
apply.to.split <- (indices.expected == 0 && nmarks > 1)
if(apply.to.split)
ppsplit <- split(X)
# --------------------------------------------------------------------
# determine array dimensions and margin labels
witch <-
if(nmarks == 0)
matrix(1L, nrow=1L, ncol=1L, dimnames=list("",""))
else if (nmarks == 1)
matrix(1L, nrow=1L, ncol=1L, dimnames=list(marklabels, marklabels))
else if(indices.expected != 2)
matrix(1L:nmarks, nrow=nmarks, ncol=1L,
dimnames=list(marklabels, ""))
else
matrix(1L:(nmarks^2),ncol=nmarks,nrow=nmarks, byrow=TRUE,
dimnames=list(marklabels, marklabels))
# ------------ start computing -------------------------------
# if computing envelopes, first generate simulated patterns
# using undocumented feature of envelope()
if(envelope && reuse) {
L <- do.call(spatstat.core::envelope,
resolve.defaults(
list(quote(X), fun=estimator),
list(internal=list(eject="patterns")),
list(...),
switch(1L+indices.expected,
NULL,
list(i=ma[1L]),
list(i=ma[1L], j=ma[2L]),
NULL),
list(verbose=verb)))
intern <- attr(L, "internal")
} else intern <- L <- NULL
# compute function array and build up 'fasp' object
fns <- list()
k <- 0
maxerr.action <- if(verb) "warn" else "null"
for(i in 1L:nrow(witch)) {
Y <- if(apply.to.split) ppsplit[[i]] else X
for(j in 1L:ncol(witch)) {
if(verb) cat("i =",i,"j =",j,"\n")
currentfv <-
if(!envelope)
switch(1L+indices.expected,
estimator(Y, ...),
estimator(Y, i=ma[i], ...),
estimator(Y, i=ma[i], j=ma[j], ...))
else
do.call(spatstat.core::envelope,
resolve.defaults(
list(quote(Y), estimator),
list(simulate=L, internal=intern),
list(verbose=FALSE),
list(...),
list(Yname=dataname,
silent=TRUE,
maxerr.action=maxerr.action),
switch(1L+indices.expected,
NULL,
list(i=ma[i]),
list(i=ma[i], j=ma[j]),
NULL)))
k <- k+1
fns[[k]] <- as.fv(currentfv)
}
}
einfo <- lapply(fns, attr, which="einfo")
gaveup <- sapply(lapply(einfo, getElement, name="gaveup"), isTRUE)
if(any(gaveup)) {
ng <- sum(gaveup)
warning(paste(ng, "out of", length(fns), "envelopes",
ngettext(ng, "was", "were"),
"not computed, due to errors in evaluating",
"the summary functions for simulated patterns"))
}
# wrap up into 'fasp' object
title <- paste(if(nmarks > 1) "array of " else NULL,
if(envelope) "envelopes of " else NULL,
fname,
if(nmarks <= 1) " function " else " functions ",
"for ", dataname, ".", sep="")
rslt <- fasp(fns, which=witch,
formulae=NULL,
dataname=dataname,
title=title,
checkfv=FALSE)
return(rslt)
}
# Lookup table for standard abbreviations of functions
getSumFun <- local({
ftable <-
rbind(
data.frame(class="ppp", marked=FALSE,
abbrev=c("F", "G", "J", "K", "L", "pcf"),
full=c("Fest", "Gest", "Jest", "Kest", "Lest", "pcf"),
stringsAsFactors=FALSE),
data.frame(class="ppp", marked=TRUE,
abbrev=c("F", "G", "J", "K", "L", "pcf"),
full= c("Fest",
"Gcross", "Jcross", "Kcross", "Lcross",
"pcfcross"),
stringsAsFactors=FALSE),
data.frame(class="lpp", marked=FALSE,
abbrev=c("K", "pcf"),
full=c("linearK", "linearpcf"),
stringsAsFactors=FALSE),
data.frame(class="lpp", marked=TRUE,
abbrev=c("K", "pcf"),
full=c("linearKcross", "linearpcfcross"),
stringsAsFactors=FALSE)
)
getfun <- function(abbreviation, classname, ismarked, fatal=TRUE) {
matches <- with(ftable,
which(abbrev == abbreviation &
class == classname &
marked == ismarked))
if(length(matches) == 0) {
if(!fatal)
return(NULL)
stop(paste("No match to function abbreviation",
sQuote(abbreviation),
"for class",
sQuote(classname)))
}
if(length(matches) > 1)
stop("Ambiguous function name")
fullname <- ftable$full[matches]
get(fullname, mode="function")
}
getfun
})
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