https://github.com/cran/spatstat
Tip revision: 128682d8d4cbaa1cea60af7ed901d17071160798 authored by Adrian Baddeley on 05 June 2015, 20:05:20 UTC
version 1.42-1
version 1.42-1
Tip revision: 128682d
mpl.R
# mpl.R
#
# $Revision: 5.190 $ $Date: 2015/01/22 06:14:14 $
#
# mpl.engine()
# Fit a point process model to a two-dimensional point pattern
# by maximum pseudolikelihood
#
# mpl.prepare()
# set up data for glm procedure
#
# -------------------------------------------------------------------
#
"mpl" <- function(Q,
trend = ~1,
interaction = NULL,
data = NULL,
correction="border",
rbord = 0,
use.gam=FALSE) {
.Deprecated("ppm", package="spatstat")
ppm(Q=Q, trend=trend, interaction=interaction,
covariates=data, correction=correction, rbord=rbord,
use.gam=use.gam, method="mpl")
}
mpl.engine <-
function(Q,
trend = ~1,
interaction = NULL,
...,
covariates = NULL,
subsetexpr = NULL,
covfunargs = list(),
correction="border",
rbord = 0,
use.gam=FALSE,
gcontrol=list(),
famille=NULL,
forcefit=FALSE,
nd = NULL,
eps = eps,
allcovar=FALSE,
callstring="",
precomputed=NULL,
savecomputed=FALSE,
preponly=FALSE,
rename.intercept=TRUE,
justQ = FALSE,
weightfactor = NULL)
{
## Extract precomputed data if available
if(!is.null(precomputed$Q)) {
Q <- precomputed$Q
X <- precomputed$X
P <- precomputed$U
} else {
## Determine quadrature scheme from argument Q
if(verifyclass(Q, "quad", fatal=FALSE)) {
## user-supplied quadrature scheme - validate it
validate.quad(Q, fatal=TRUE, repair=FALSE, announce=TRUE)
## Extract data points
X <- Q$data
} else if(verifyclass(Q, "ppp", fatal = FALSE)) {
## point pattern - create default quadrature scheme
X <- Q
Q <- quadscheme(X, nd=nd, eps=eps, check=FALSE)
} else
stop("First argument Q should be a point pattern or a quadrature scheme")
## Data and dummy points together
P <- union.quad(Q)
}
## secret exit
if(justQ) return(Q)
##
computed <- if(savecomputed) list(X=X, Q=Q, U=P) else NULL
##
## Validate main arguments
if(!is.null(trend) && !inherits(trend, "formula"))
stop(paste("Argument", sQuote("trend"), "must be a formula"))
if(!is.null(interaction) && !inherits(interaction, "interact"))
stop(paste("Argument", sQuote("interaction"), "has incorrect format"))
##
check.1.real(rbord, "In ppm")
explain.ifnot(rbord >= 0, "In ppm")
## rbord applies only to border correction
if(correction != "border") rbord <- 0
##
##
## Interpret the call
if(is.null(trend)) {
trend <- ~1
environment(trend) <- parent.frame()
}
want.trend <- !identical.formulae(trend, ~1)
want.inter <- !is.null(interaction) && !is.null(interaction$family)
## Stamp with spatstat version number
spv <- package_version(versionstring.spatstat())
the.version <- list(major=spv$major,
minor=spv$minor,
release=spv$patchlevel,
date="$Date: 2015/01/22 06:14:14 $")
if(want.inter) {
## ensure we're using the latest version of the interaction object
if(outdated.interact(interaction))
interaction <- update(interaction)
}
##
if(!want.trend && !want.inter &&
!forcefit && !allcovar && is.null(subsetexpr)) {
## the model is the uniform Poisson process
## The MPLE (= MLE) can be evaluated directly
npts <- npoints(X)
W <- as.owin(X)
if(correction == "border" && rbord > 0) {
npts <- sum(bdist.points(X) >= rbord)
areaW <- eroded.areas(W, rbord)
} else {
npts <- npoints(X)
areaW <- area(W)
}
volume <- areaW * markspace.integral(X)
lambda <- npts/volume
## fitted canonical coefficient
co <- log(lambda)
## asymptotic variance of canonical coefficient
varcov <- matrix(1/npts, 1, 1)
fisher <- matrix(npts, 1, 1)
se <- sqrt(1/npts)
## give names
tag <- if(rename.intercept) "log(lambda)" else "(Intercept)"
names(co) <- tag
dimnames(varcov) <- dimnames(fisher) <- list(tag, tag)
## maximised log likelihood
maxlogpl <- if(npts == 0) 0 else npts * (log(lambda) - 1)
##
rslt <- list(
method = "mpl",
fitter = "exact",
projected = FALSE,
coef = co,
trend = trend,
interaction = NULL,
fitin = fii(),
Q = Q,
maxlogpl = maxlogpl,
internal = list(computed=computed, se=se),
covariates = mpl.usable(covariates),
## covariates are still retained!
covfunargs = covfunargs,
subsetexpr = NULL,
correction = correction,
rbord = rbord,
terms = terms(trend),
fisher = fisher,
varcov = varcov,
version = the.version,
problems = list())
class(rslt) <- "ppm"
return(rslt)
}
################# P r e p a r e D a t a ######################
prep <- mpl.prepare(Q, X, P, trend, interaction,
covariates,
want.trend, want.inter, correction, rbord,
"quadrature points", callstring,
subsetexpr=subsetexpr,
allcovar=allcovar,
precomputed=precomputed, savecomputed=savecomputed,
covfunargs=covfunargs,
weightfactor=weightfactor,
...)
## back door
if(preponly) {
## exit now, returning prepared data frame and internal information
prep$info <- list(want.trend=want.trend,
want.inter=want.inter,
correction=correction,
rbord=rbord,
interaction=interaction)
return(prep)
}
fmla <- prep$fmla
glmdata <- prep$glmdata
problems <- prep$problems
likelihood.is.zero <- prep$likelihood.is.zero
is.identifiable <- prep$is.identifiable
computed <- resolve.defaults(prep$computed, computed)
IsOffset <- prep$IsOffset
## update covariates (if they were resolved from the environment)
if(!is.null(prep$covariates))
covariates <- prep$covariates
################# F i t i t ####################################
if(!is.identifiable)
stop(paste("in", callstring, ":", problems$unidentifiable$print),
call.=FALSE)
## to avoid problem with package checker
.mpl.W <- glmdata$.mpl.W
.mpl.SUBSET <- glmdata$.mpl.SUBSET
## determine algorithm control parameters
if(is.null(gcontrol)) gcontrol <- list() else stopifnot(is.list(gcontrol))
gc <- if(use.gam) "gam.control" else "glm.control"
gcontrol <- do.call(gc, gcontrol)
## Fit the generalized linear/additive model.
if(is.null(famille)) {
## the sanctioned technique, using `quasi' family
if(want.trend && use.gam)
FIT <- gam(fmla, family=quasi(link=log, variance=mu), weights=.mpl.W,
data=glmdata, subset=.mpl.SUBSET,
control=gcontrol)
else
FIT <- glm(fmla, family=quasi(link=log, variance=mu), weights=.mpl.W,
data=glmdata, subset=.mpl.SUBSET,
control=gcontrol, model=FALSE)
} else {
## for experimentation only!
if(is.function(famille))
famille <- famille()
stopifnot(inherits(famille, "family"))
if(want.trend && use.gam)
FIT <- gam(fmla, family=famille, weights=.mpl.W,
data=glmdata, subset=.mpl.SUBSET,
control=gcontrol)
else
FIT <- glm(fmla, family=famille, weights=.mpl.W,
data=glmdata, subset=.mpl.SUBSET,
control=gcontrol, model=FALSE)
}
environment(FIT$terms) <- sys.frame(sys.nframe())
################ I n t e r p r e t f i t #######################
## Fitted coefficients
co <- FIT$coef
## glm covariates
W <- glmdata$.mpl.W
SUBSET <- glmdata$.mpl.SUBSET
Z <- is.data(Q)
Vnames <- prep$Vnames
## attained value of max log pseudolikelihood
maxlogpl <-
if(likelihood.is.zero) { -Inf } else
-(deviance(FIT)/2 + sum(log(W[Z & SUBSET])) + sum(Z & SUBSET))
## fitted interaction object
fitin <- if(want.inter) fii(interaction, co, Vnames, IsOffset) else fii()
unitname(fitin) <- unitname(X)
######################################################################
## Clean up & return
rslt <-
list(
method = "mpl",
fitter = if(use.gam) "gam" else "glm",
projected = FALSE,
coef = co,
trend = trend,
interaction = if(want.inter) interaction else NULL,
fitin = fitin,
Q = Q,
maxlogpl = maxlogpl,
internal = list(glmfit=FIT, glmdata=glmdata, Vnames=Vnames,
IsOffset=IsOffset, fmla=fmla, computed=computed),
covariates = mpl.usable(covariates),
covfunargs = covfunargs,
subsetexpr = subsetexpr,
correction = correction,
rbord = rbord,
terms = terms(trend),
version = the.version,
problems = problems)
class(rslt) <- "ppm"
return(rslt)
}
##########################################################################
### /////////////////////////////////////////////////////////////////////
##########################################################################
mpl.prepare <- local({
mpl.prepare <- function(Q, X, P, trend, interaction, covariates,
want.trend, want.inter, correction, rbord,
Pname="quadrature points", callstring="",
...,
subsetexpr=NULL,
covfunargs=list(),
allcovar=FALSE,
precomputed=NULL, savecomputed=FALSE,
vnamebase=c("Interaction", "Interact."),
vnameprefix=NULL,
warn.illegal=TRUE,
warn.unidentifiable=TRUE,
weightfactor=NULL,
skip.border=FALSE) {
## Q: quadrature scheme
## X = data.quad(Q)
## P = union.quad(Q)
if(missing(want.trend))
want.trend <- !is.null(trend) && !identical.formulae(trend, ~1)
if(missing(want.inter))
want.inter <- !is.null(interaction) && !is.null(interaction$family)
want.subset <- !is.null(subsetexpr)
computed <- list()
problems <- list()
names.precomputed <- names(precomputed)
likelihood.is.zero <- FALSE
is.identifiable <- TRUE
if(!missing(vnamebase)) {
if(length(vnamebase) == 1)
vnamebase <- rep.int(vnamebase, 2)
if(!is.character(vnamebase) || length(vnamebase) != 2)
stop("Internal error: illegal format of vnamebase")
}
if(!is.null(vnameprefix)) {
if(!is.character(vnameprefix) || length(vnameprefix) != 1)
stop("Internal error: illegal format of vnameprefix")
}
################ C o m p u t e d a t a ####################
## Extract covariate values
updatecovariates <- FALSE
covariates.df <- NULL
if(allcovar || want.trend || want.subset) {
if("covariates.df" %in% names.precomputed) {
covariates.df <- precomputed$covariates.df
} else {
if(!is.data.frame(covariates)) {
## names of 'external' covariates to be found
covnames <- variablesinformula(trend)
if(want.subset)
covnames <- union(covnames, all.vars(subsetexpr))
if(allcovar)
covnames <- union(covnames, names(covariates))
covnames <- setdiff(covnames, c("x", "y", "marks"))
## resolve 'external' covariates
tenv <- environment(trend)
covariates <- getdataobjects(covnames, tenv, covariates, fatal=TRUE)
updatecovariates <- any(attr(covariates, "external"))
}
## extract values of covariates ('internal' and 'external')
covariates.df <- mpl.get.covariates(covariates, P, Pname, covfunargs)
}
if(savecomputed)
computed$covariates.df <- covariates.df
}
## Form the weights and the ``response variable''.
if("dotmplbase" %in% names.precomputed)
.mpl <- precomputed$dotmplbase
else {
nQ <- n.quad(Q)
wQ <- w.quad(Q)
mQ <- marks.quad(Q) ## is NULL for unmarked patterns
zQ <- is.data(Q)
yQ <- numeric(nQ)
yQ[zQ] <- 1/wQ[zQ]
zeroes <- attr(wQ, "zeroes")
sQ <- if(is.null(zeroes)) rep.int(TRUE, nQ) else !zeroes
## tweak weights ONLY
if(!is.null(weightfactor))
wQ <- wQ * weightfactor
## pack up
.mpl <- list(W = wQ,
Z = zQ,
Y = yQ,
MARKS = mQ,
SUBSET = sQ)
}
if(savecomputed)
computed$dotmplbase <- .mpl
glmdata <- data.frame(.mpl.W = .mpl$W,
.mpl.Y = .mpl$Y)
## count data and dummy points in specified subset
izdat <- .mpl$Z[.mpl$SUBSET]
ndata <- sum(izdat)
# ndummy <- sum(!izdat)
## Determine the domain of integration for the pseudolikelihood.
if(correction == "border") {
bdP <-
if("bdP" %in% names.precomputed)
precomputed$bdP
else
bdist.points(P)
if(savecomputed)
computed$bdP <- bdP
.mpl$DOMAIN <- (bdP >= rbord)
}
skip.border <- skip.border && (correction == "border")
####################### T r e n d ##############################
internal.names <- c(".mpl.W", ".mpl.Y", ".mpl.Z", ".mpl.SUBSET",
"SUBSET", ".mpl")
reserved.names <- c("x", "y", "marks", internal.names)
if(allcovar || want.trend || want.subset) {
trendvariables <- variablesinformula(trend)
## Check for use of internal names in trend
cc <- check.clashes(internal.names, trendvariables, "the model formula")
if(cc != "") stop(cc)
if(want.subset) {
subsetvariables <- all.vars(subsetexpr)
cc <- check.clashes(internal.names, trendvariables,
"the subset expression")
if(cc != "") stop(cc)
trendvariables <- union(trendvariables, subsetvariables)
}
## Standard variables
if(allcovar || "x" %in% trendvariables)
glmdata <- data.frame(glmdata, x=P$x)
if(allcovar || "y" %in% trendvariables)
glmdata <- data.frame(glmdata, y=P$y)
if(("marks" %in% trendvariables) || !is.null(.mpl$MARKS)) {
if(is.null(.mpl$MARKS))
stop("Model formula depends on marks, but data do not have marks",
call.=FALSE)
glmdata <- data.frame(glmdata, marks=.mpl$MARKS)
}
##
## Check covariates
if(!is.null(covariates.df)) {
## Check for duplication of reserved names
cc <- check.clashes(reserved.names, names(covariates),
sQuote("covariates"))
if(cc != "") stop(cc)
## Take only those covariates that are named in the trend formula
if(!allcovar)
needed <- names(covariates.df) %in% trendvariables
else
needed <- rep.int(TRUE, ncol(covariates.df))
if(any(needed)) {
covariates.needed <- covariates.df[, needed, drop=FALSE]
## Append to `glmdata'
glmdata <- data.frame(glmdata,covariates.needed)
## Ignore any quadrature points that have NA's in the covariates
nbg <- is.na(covariates.needed)
if(any(nbg)) {
offending <- matcolany(nbg)
covnames.na <- names(covariates.needed)[offending]
quadpoints.na <- matrowany(nbg)
n.na <- sum(quadpoints.na)
n.tot <- length(quadpoints.na)
errate <- n.na/n.tot
pcerror <- round(signif(100 * errate, 2), 2)
complaint <- paste("Values of the",
ngettext(length(covnames.na),
"covariate", "covariates"),
paste(sQuote(covnames.na), collapse=", "),
"were NA or undefined at",
paste(pcerror, "%",
" (",
n.na,
" out of ",
n.tot,
")",
sep=""),
"of the", Pname)
warning(paste(complaint,
". Occurred while executing: ",
callstring, sep=""),
call. = FALSE)
.mpl$SUBSET <- .mpl$SUBSET & !quadpoints.na
details <- list(covnames.na = covnames.na,
quadpoints.na = quadpoints.na,
print = complaint)
problems <- append(problems,
list(na.covariates=details))
}
}
}
}
###################### I n t e r a c t i o n ####################
Vnames <- NULL
IsOffset <- NULL
if(want.inter) {
## Form the matrix of "regression variables" V.
## The rows of V correspond to the rows of P (quadrature points)
## while the column(s) of V are the regression variables (log-potentials)
E <- precomputed$E %orifnull% equalpairs.quad(Q)
if(!skip.border) {
## usual case
V <- evalInteraction(X, P, E, interaction, correction,
...,
precomputed=precomputed,
savecomputed=savecomputed)
} else {
## evaluate only in eroded domain
if(all(c("Esub", "Usub", "Retain") %in% names.precomputed)) {
## use precomputed data
Psub <- precomputed$Usub
Esub <- precomputed$Esub
Retain <- precomputed$Retain
} else {
Retain <- .mpl$DOMAIN
Psub <- P[Retain]
## map serial numbers in 'P[Retain]' to serial numbers in 'Psub'
Pmap <- cumsum(Retain)
keepE <- Retain[ E[,2] ]
## adjust equal pairs matrix
Esub <- E[ keepE, , drop=FALSE]
Esub[,2] <- Pmap[Esub[,2]]
}
## call evaluator on reduced data
## with 'W=NULL' (currently detected only by AreaInter)
if(all(c("X", "Q", "U") %in% names.precomputed)) {
subcomputed <- resolve.defaults(list(E=Esub, U=Psub, Q=Q[Retain]),
precomputed)
} else subcomputed <- NULL
V <- evalInteraction(X, Psub, Esub, interaction, correction,
...,
W=NULL,
precomputed=subcomputed,
savecomputed=savecomputed)
if(savecomputed) {
computed$Usub <- Psub
computed$Esub <- Esub
computed$Retain <- Retain
}
}
if(!is.matrix(V))
stop("interaction evaluator did not return a matrix")
## extract information about offsets
IsOffset <- attr(V, "IsOffset")
if(is.null(IsOffset)) IsOffset <- FALSE
if(skip.border) {
## fill in the values in the border region with zeroes.
Vnew <- matrix(0, nrow=npoints(P), ncol=ncol(V))
colnames(Vnew) <- colnames(V)
Vnew[Retain, ] <- V
## retain attributes
attr(Vnew, "IsOffset") <- IsOffset
attr(Vnew, "computed") <- attr(V, "computed")
attr(Vnew, "POT") <- attr(V, "POT")
V <- Vnew
}
## extract intermediate computation results
if(savecomputed)
computed <- resolve.defaults(attr(V, "computed"), computed)
## Augment data frame by appending the regression variables
## for interactions.
##
## First determine the names of the variables
##
Vnames <- dimnames(V)[[2]]
if(is.null(Vnames)) {
## No names were provided for the columns of V.
## Give them default names.
## In ppm the names will be "Interaction"
## or "Interact.1", "Interact.2", ...
## In mppm an alternative tag will be specified by vnamebase.
nc <- ncol(V)
Vnames <- if(nc == 1) vnamebase[1] else paste0(vnamebase[2], 1:nc)
dimnames(V) <- list(dimnames(V)[[1]], Vnames)
} else if(!is.null(vnameprefix)) {
## Variable names were provided by the evaluator (e.g. MultiStrauss).
## Prefix the variable names by a string
## (typically required by mppm)
Vnames <- paste(vnameprefix, Vnames, sep="")
dimnames(V) <- list(dimnames(V)[[1]], Vnames)
}
## Check the names are valid as column names in a dataframe
okVnames <- make.names(Vnames, unique=TRUE)
if(any(Vnames != okVnames)) {
warning(paste("Names of interaction terms",
"contained illegal characters;",
"names have been repaired."))
Vnames <- okVnames
}
## Check for name clashes between the interaction variables
## and the formula
cc <- check.clashes(Vnames, termsinformula(trend), "model formula")
if(cc != "") stop(cc)
## and with the variables in 'covariates'
if(!is.null(covariates)) {
cc <- check.clashes(Vnames, names(covariates), sQuote("covariates"))
if(cc != "") stop(cc)
}
## OK. append variables.
glmdata <- data.frame(glmdata, V)
## check IsOffset matches Vnames
if(length(IsOffset) != length(Vnames)) {
if(length(IsOffset) == 1)
IsOffset <- rep.int(IsOffset, length(Vnames))
else
stop("Internal error: IsOffset has wrong length", call.=FALSE)
}
## Keep only those quadrature points for which the
## conditional intensity is nonzero.
##KEEP <- apply(V != -Inf, 1, all)
.mpl$KEEP <- matrowall(V != -Inf)
.mpl$SUBSET <- .mpl$SUBSET & .mpl$KEEP
## Check that there are at least some data and dummy points remaining
datremain <- .mpl$Z[.mpl$SUBSET]
somedat <- any(datremain)
somedum <- !all(datremain)
if(warn.unidentifiable && !(somedat && somedum)) {
## Model would be unidentifiable if it were fitted.
## Register problem
is.identifiable <- FALSE
if(ndata == 0) {
complaint <- "model is unidentifiable: data pattern is empty"
} else {
offending <- !c(somedat, somedum)
offending <- c("all data points", "all dummy points")[offending]
offending <- paste(offending, collapse=" and ")
complaint <- paste("model is unidentifiable:",
offending, "have zero conditional intensity")
}
details <- list(data=!somedat,
dummy=!somedum,
print=complaint)
problems <- append(problems, list(unidentifiable=details))
}
## check whether the model has zero likelihood:
## check whether ANY data points have zero conditional intensity
if(any(.mpl$Z & !.mpl$KEEP)) {
howmany <- sum(.mpl$Z & !.mpl$KEEP)
complaint <- paste(howmany,
"data point(s) are illegal",
"(zero conditional intensity under the model)")
details <- list(illegal=howmany,
print=complaint)
problems <- append(problems, list(zerolikelihood=details))
if(warn.illegal && is.identifiable)
warning(paste(complaint,
". Occurred while executing: ",
callstring, sep=""),
call. = FALSE)
likelihood.is.zero <- TRUE
}
}
################## S u b s e t ###################
if(correction == "border")
.mpl$SUBSET <- .mpl$SUBSET & .mpl$DOMAIN
if(!is.null(subsetexpr)) {
## user-defined subset expression
USER.SUBSET <- eval(subsetexpr, glmdata, environment(trend))
.mpl$SUBSET <- .mpl$SUBSET & USER.SUBSET
}
glmdata <- cbind(glmdata,
data.frame(.mpl.SUBSET=.mpl$SUBSET,
stringsAsFactors=FALSE))
################# F o r m u l a ##################################
if(!want.trend) trend <- ~1
trendpart <- paste(as.character(trend), collapse=" ")
if(!want.inter)
rhs <- trendpart
else {
VN <- Vnames
## enclose offset potentials in 'offset(.)'
if(any(IsOffset))
VN[IsOffset] <- paste("offset(", VN[IsOffset], ")", sep="")
rhs <- paste(c(trendpart, VN), collapse= "+")
}
fmla <- paste(".mpl.Y ", rhs)
fmla <- as.formula(fmla)
## character string of trend formula (without Vnames)
trendfmla <- paste(".mpl.Y ", trendpart)
####
result <- list(fmla=fmla, trendfmla=trendfmla,
covariates=if(updatecovariates) covariates else NULL,
glmdata=glmdata, Vnames=Vnames, IsOffset=IsOffset,
subsetexpr=subsetexpr,
problems=problems,
likelihood.is.zero=likelihood.is.zero,
is.identifiable=is.identifiable,
computed=computed)
return(result)
}
check.clashes <- function(forbidden, offered, where) {
name.match <- outer(forbidden, offered, "==")
if(any(name.match)) {
is.matched <- apply(name.match, 2, any)
matched.names <- (offered)[is.matched]
if(sum(is.matched) == 1) {
return(paste("The variable",sQuote(matched.names),
"in", where, "is a reserved name"))
} else {
return(paste("The variables",
paste(sQuote(matched.names), collapse=", "),
"in", where, "are reserved names"))
}
}
return("")
}
mpl.prepare
})
####################################################################
####################################################################
mpl.usable <- function(x) {
## silently remove covariates that don't have recognised format
if(length(x) == 0 || is.data.frame(x)) return(x)
isim <- unlist(lapply(x, is.im))
isfun <- unlist(lapply(x, is.function))
iswin <- unlist(lapply(x, is.owin))
istess <- unlist(lapply(x, is.tess))
isnum <- unlist(lapply(x, is.numeric)) & (unlist(lapply(x, length)) == 1)
recognised <- isim | isfun | iswin | istess | isnum
if(!all(recognised))
x <- x[recognised]
return(x)
}
mpl.get.covariates <- local({
mpl.get.covariates <- function(covariates, locations, type="locations",
covfunargs=list(),
need.deriv=FALSE) {
covargname <- sQuote(short.deparse(substitute(covariates)))
locargname <- sQuote(short.deparse(substitute(locations)))
if(is.null(covfunargs)) covfunargs <- list()
##
x <- locations$x
y <- locations$y
if(is.null(x) || is.null(y)) {
xy <- xy.coords(locations)
x <- xy$x
y <- xy$y
}
if(is.null(x) || is.null(y))
stop(paste("Can't interpret", locargname, "as x,y coordinates"))
n <- length(x)
if(is.data.frame(covariates)) {
if(nrow(covariates) != n)
stop(paste("Number of rows in", covargname,
"does not equal the number of", type))
return(covariates)
} else if(is.list(covariates)) {
if(length(covariates) == 0)
return(as.data.frame(matrix(, n, 0)))
isim <- unlist(lapply(covariates, is.im))
isfun <- unlist(lapply(covariates, is.function))
iswin <- unlist(lapply(covariates, is.owin))
istess <- unlist(lapply(covariates, is.tess))
isnum <- unlist(lapply(covariates, is.number))
if(!all(isim | isfun | isnum | iswin | istess))
stop(paste("Each entry in the list", covargname,
"should be an image, a function,",
"a window, a tessellation or a single number"))
if(sum(nzchar(names(covariates))) < length(covariates))
stop(paste("Some entries in the list",
covargname, "are un-named"))
## look up values of each covariate at the quadrature points
values <- unclass(covariates)
values[isim] <- lapply(covariates[isim], lookup.im, x=x, y=y,
naok=TRUE, strict=FALSE)
values[isfun] <- vf <- lapply(covariates[isfun], evalfxy, x=x, y=y,
extra=covfunargs)
values[isnum] <- lapply(covariates[isnum], rep, length(x))
values[iswin] <- lapply(covariates[iswin], insidexy, x=x, y=y)
values[istess] <- lapply(covariates[istess], tileindex, x=x, y=y)
result <- as.data.frame(values)
if(need.deriv && any(isfun)) {
## check for gradient/hessian attributes of function values
grad <- lapply(vf, attr, which="gradient")
hess <- lapply(vf, attr, which="hessian")
grad <- grad[!unlist(lapply(grad, is.null))]
hess <- hess[!unlist(lapply(hess, is.null))]
if(length(grad) > 0 || length(hess) > 0)
attr(result, "derivatives") <- list(gradient=grad, hessian=hess)
}
return(result)
}
stop(paste(covargname, "must be either a data frame or a list"))
}
## functions for 'apply'
evalfxy <- function(f, x, y, extra) {
if(length(extra) == 0)
return(f(x,y))
## extra arguments must be matched explicitly by name
ok <- names(extra) %in% names(formals(f))
z <- do.call(f, append(list(x,y), extra[ok]))
return(z)
}
insidexy <- function(w, x, y) { inside.owin(x, y, w) }
is.number <- function(x) { is.numeric(x) && (length(x) == 1) }
mpl.get.covariates
})
bt.frame <- function(Q, trend=~1, interaction=NULL,
...,
covariates=NULL,
correction="border", rbord=0,
use.gam=FALSE, allcovar=FALSE) {
prep <- mpl.engine(Q=Q, trend=trend, interaction=interaction,
..., covariates=covariates,
correction=correction, rbord=rbord,
use.gam=use.gam, allcovar=allcovar,
preponly=TRUE, forcefit=TRUE)
class(prep) <- c("bt.frame", class(prep))
return(prep)
}
print.bt.frame <- function(x, ...) {
cat("Model frame for Berman-Turner device\n")
df <- x$glmdata
cat(paste("$glmdata: Data frame with", nrow(df), "rows and",
ncol(df), "columns\n"))
cat(" Column names:\t")
cat(paste(paste(names(df),collapse="\t"), "\n"))
cat("Complete model formula ($fmla):\t")
print(x$fmla)
info <- x$info
if(info$want.trend) {
cat("Trend:\tyes\nTrend formula string ($trendfmla):\t")
cat(paste(x$trendfmla, "\n"))
} else cat("Trend:\tno\n")
cat("Interaction ($info$interaction):\t")
inte <- info$interaction
if(is.null(inte))
inte <- Poisson()
print(inte, family=FALSE, brief=TRUE)
if(!is.poisson.interact(inte)) {
cat("Internal names of interaction variables ($Vnames):\t")
cat(paste(x$Vnames, collapse="\t"))
cat("\n")
}
edge <- info$correction
cat(paste("Edge correction ($info$correction):\t", sQuote(edge), "\n"))
if(edge == "border")
cat(paste("\tBorder width ($info$rbord):\t", info$rbord, "\n"))
if(length(x$problems) > 0) {
cat("Problems:\n")
print(x$problems)
}
if(length(x$computed) > 0)
cat(paste("Frame contains saved computations for",
commasep(dQuote(names(x$computed)))))
return(invisible(NULL))
}
partialModelMatrix <- function(X, D, model, callstring="", ...) {
## X = 'data'
## D = 'dummy'
Q <- quad(X,D)
P <- union.quad(Q)
trend <- model$trend
inter <- model$interaction
covar <- model$covariates
prep <- mpl.prepare(Q, X, P, trend, inter, covar,
correction=model$correction,
rbord=model$rbord,
Pname="data points", callstring=callstring,
warn.unidentifiable=FALSE,
...)
fmla <- prep$fmla
glmdata <- prep$glmdata
mof <- model.frame(fmla, glmdata)
mom <- model.matrix(fmla, mof)
if(!identical(all.equal(colnames(mom), names(coef(model))), TRUE))
warning(paste("Internal error: mismatch between",
"column names of model matrix",
"and names of coefficient vector in fitted model"))
attr(mom, "mplsubset") <- glmdata$.mpl.SUBSET
return(mom)
}
oversize.quad <- function(Q, ..., nU, nX) {
## Determine whether the quadrature scheme is
## too large to handle in one piece (in mpl)
## for a generic interaction
## nU = number of quadrature points
## nX = number of data points
if(missing(nU))
nU <- n.quad(Q)
if(missing(nX))
nX <- npoints(Q$data)
nmat <- as.double(nU) * nX
nMAX <- spatstat.options("maxmatrix")
needsplit <- (nmat > nMAX)
return(needsplit)
}
## function that should be called to evaluate interaction terms
## between quadrature points and data points
evalInteraction <- function(X, P, E = equalpairs(P, X),
interaction, correction,
...,
precomputed=NULL,
savecomputed=FALSE) {
## evaluate the interaction potential
## (does not assign/touch the variable names)
verifyclass(interaction, "interact")
## handle Poisson case
if(is.poisson(interaction)) {
out <- matrix(, nrow=npoints(P), ncol=0)
attr(out, "IsOffset") <- logical(0)
return(out)
}
## determine whether to use fast evaluation in C
fastok <- (spatstat.options("fasteval") %in% c("on", "test"))
if(fastok) {
cando <- interaction$can.do.fast
par <- interaction$par
dofast <- !is.null(cando) && cando(X, correction, par)
} else dofast <- FALSE
## determine whether to split quadscheme into blocks
if(dofast) {
dosplit <- FALSE
} else {
## decide whether the quadrature scheme is too large to handle in one piece
needsplit <- oversize.quad(nU=npoints(P), nX=npoints(X))
## not implemented when savecomputed=TRUE
dosplit <- needsplit && !savecomputed
if(needsplit && savecomputed)
warning(paste("Oversize quadscheme cannot be split into blocks",
"because savecomputed=TRUE;",
"memory allocation error may occur"))
}
if(!dosplit) {
## normal case
V <- evalInterEngine(X=X, P=P, E=E,
interaction=interaction,
correction=correction,
...,
precomputed=precomputed,
savecomputed=savecomputed)
} else {
## Too many quadrature points: split into blocks
nX <- npoints(X)
nP <- npoints(P)
## Determine which evaluation points are data points
Pdata <- E[,2]
## hence which are dummy points
Pall <- seq_len(nP)
Pdummy <- if(length(Pdata) > 0) Pall[-Pdata] else Pall
nD <- length(Pdummy)
## size of full matrix
# nmat <- (nD + nX) * nX
nMAX <- spatstat.options("maxmatrix")
## Calculate number of dummy points in largest permissible X * (X+D) matrix
nperblock <- max(1, floor(nMAX/nX - nX))
## determine number of such blocks
nblocks <- ceiling(nD/nperblock)
## make blocks roughly equal (except for the last one)
nperblock <- min(nperblock, ceiling(nD/nblocks))
## announce
if(nblocks > 1) {
msg <- paste("Large quadrature scheme",
"split into blocks to avoid memory size limits;",
nD, "dummy points split into",
nblocks, "blocks,")
nfull <- nblocks - 1
nlastblock <- nD - nperblock * nfull
if(nlastblock == nperblock) {
msg <- paste(msg,
"each containing",
nperblock, "dummy points")
} else {
msg <- paste(msg,
"the first",
ngettext(nfull, "block", paste(nfull, "blocks")),
"containing",
nperblock,
ngettext(nperblock, "dummy point", "dummy points"),
"and the last block containing",
nlastblock,
ngettext(nlastblock, "dummy point", "dummy points"))
}
message(msg)
}
##
##
seqX <- seq_len(nX)
EX <- cbind(seqX, seqX)
##
for(iblock in 1:nblocks) {
first <- min(nD, (iblock - 1) * nperblock + 1)
last <- min(nD, iblock * nperblock)
## extract dummy points
Di <- P[Pdummy[first:last]]
Pi <- superimpose(X, Di, check=FALSE, W=X$window)
## evaluate potential
Vi <- evalInterEngine(X=X, P=Pi, E=EX,
interaction=interaction,
correction=correction,
...,
savecomputed=FALSE)
if(iblock == 1) {
V <- Vi
} else {
## tack on the glm variables for the extra DUMMY points only
V <- rbind(V, Vi[-seqX, , drop=FALSE])
}
}
## The first 'nX' rows of V contain values for X.
## The remaining rows of V contain values for dummy points.
if(length(Pdata) == 0) {
## simply discard rows corresponding to data
V <- V[-seqX, , drop=FALSE]
} else {
## replace data in correct position
ii <- integer(nP)
ii[Pdata] <- seqX
ii[Pdummy] <- (nX+1):nrow(V)
V <- V[ii, , drop=FALSE]
}
}
return(V)
}
## workhorse function that actually calls relevant code to evaluate interaction
evalInterEngine <- function(X, P, E,
interaction, correction,
...,
Reach = NULL,
precomputed=NULL,
savecomputed=FALSE) {
## fast evaluator (C code) may exist
fasteval <- interaction$fasteval
cando <- interaction$can.do.fast
par <- interaction$par
feopt <- spatstat.options("fasteval")
dofast <- !is.null(fasteval) &&
(is.null(cando) || cando(X, correction,par)) &&
(feopt %in% c("on", "test"))
V <- NULL
if(dofast) {
if(feopt == "test")
message("Calling fasteval")
V <- fasteval(X, P, E,
interaction$pot, interaction$par, correction, ...)
}
if(is.null(V)) {
## use generic evaluator for family
evaluate <- interaction$family$eval
if(is.null(Reach)) Reach <- reach(interaction)
if("precomputed" %in% names(formals(evaluate))) {
## Use precomputed data
## version 1.9-3 onward (pairwise and pairsat families)
V <- evaluate(X, P, E,
interaction$pot,
interaction$par,
correction, ...,
Reach=Reach,
precomputed=precomputed,
savecomputed=savecomputed)
} else {
## Cannot use precomputed data
## Object created by earlier version of ppm
## or not pairwise/pairsat interaction
V <- evaluate(X, P, E,
interaction$pot,
interaction$par,
correction, ..., Reach=Reach)
}
}
return(V)
}
deltasuffstat <- local({
deltasuffstat <- function(model, ...,
restrict=TRUE, dataonly=TRUE, force=FALSE) {
stopifnot(is.ppm(model))
if(dataonly) {
X <- data.ppm(model)
nX <- npoints(X)
} else {
X <- quad.ppm(model)
nX <- n.quad(X)
}
ncoef <- length(coef(model))
inte <- as.interact(model)
zeroes <- array(0, dim=c(nX, nX, ncoef))
if(is.poisson(inte))
return(zeroes)
## Get names of interaction terms in model (including offsets)
f <- fitin(model)
Inames <- f$Vnames
IsOffset <- f$IsOffset
## Offset terms do not contribute to sufficient statistic
if(all(IsOffset))
return(zeroes)
## Nontrivial interaction terms must be computed.
## Look for member function $delta2 in the interaction
v <- NULL
if(!is.null(delta2 <- inte$delta2) && is.function(delta2)) {
v <- delta2(X, inte, model$correction)
}
## Look for generic $delta2 function for the family
if(is.null(v) &&
!is.null(delta2 <- inte$family$delta2) &&
is.function(delta2))
v <- delta2(X, inte, model$correction)
## no luck?
if(is.null(v)) {
if(!force)
return(NULL)
## use brute force algorithm
v <- if(dataonly) deltasufX(model) else deltasufQ(model)
}
## make it a 3D array
if(length(dim(v)) == 2)
v <- array(v, dim=c(dim(v), 1))
if(restrict) {
## kill contributions from points outside the domain of pseudolikelihood
## (e.g. points in the border region)
use <- if(dataonly) getppmdatasubset(model) else getglmsubset(model)
if(any(kill <- !use)) {
kill <- array(outer(kill, kill, "&"), dim=dim(v))
v[kill] <- 0
}
}
## Output array: planes must correspond to model coefficients
result <- zeroes
## Planes of 'v' correspond to interaction terms (including offsets)
if(length(Inames) != dim(v)[3])
stop(paste("Internal error: deltasuffstat:",
"number of planes of v =", dim(v)[3],
"!= number of interaction terms =", length(Inames)),
call.=FALSE)
## Offset terms do not contribute to sufficient statistic
if(any(IsOffset)) {
v <- v[ , , !IsOffset, drop=FALSE]
Inames <- Inames[!IsOffset]
}
## Map planes of 'v' into coefficients
Imap <- match(Inames, names(coef(model)))
if(any(is.na(Imap)))
stop(paste("Internal error: deltasuffstat:",
"cannot match interaction coefficients"))
if(length(Imap) > 0) {
## insert 'v' into array
result[ , , Imap] <- v
}
return(result)
}
## compute deltasuffstat using partialModelMatrix
deltasufX <- function(model) {
stopifnot(is.ppm(model))
X <- data.ppm(model)
nX <- npoints(X)
p <- length(coef(model))
isdata <- is.data(quad.ppm(model))
m <- model.matrix(model)[isdata, ]
ok <- getppmdatasubset(model)
## canonical statistic before and after deleting X[j]
## mbefore[ , i, j] = h(X[i] | X)
## mafter[ , i, j] = h(X[i] | X[-j])
mafter <- mbefore <- array(t(m), dim=c(p, nX, nX))
## identify close pairs
R <- reach(model)
if(is.finite(R)) {
cl <- closepairs(X, R, what="indices")
I <- cl$i
J <- cl$j
cl2 <- closepairs(X, 2*R, what="indices")
I2 <- cl2$i
J2 <- cl2$j
} else {
## either infinite reach, or something wrong
IJ <- expand.grid(I=1:nX, J=1:nX)
IJ <- subset(IJ, I != J)
I2 <- I <- IJ$I
J2 <- J <- IJ$J
}
## filter: I and J must both belong to the nominated subset
okIJ <- ok[I] & ok[J]
I <- I[okIJ]
J <- J[okIJ]
##
if(length(I) > 0 && length(J) > 0) {
## .............. loop over pairs ........................
## The following ensures that 'empty' and 'X' have compatible marks
empty <- X[integer(0)]
## Run through pairs
for(i in unique(I)) {
## all points within 2R
J2i <- unique(J2[I2==i])
## all points within R
Ji <- unique(J[I==i])
nJi <- length(Ji)
if(nJi > 0) {
Xi <- X[i]
## neighbours of X[i]
XJi <- X[Ji]
## replace X[-i] by X[-i] \cap b(0, 2R)
X.i <- X[J2i]
nX.i <- length(J2i)
## index of XJi in X.i
J.i <- match(Ji, J2i)
if(any(is.na(J.i)))
stop("Internal error: Ji not a subset of J2i")
## equalpairs matrix
E.i <- cbind(J.i, seq_len(nJi))
## values of sufficient statistic
## h(X[j] | X[-i]) = h(X[j] | X[-c(i,j)]
## for all j
pmj <- partialModelMatrix(X.i, empty, model)[J.i, , drop=FALSE]
## sufficient statistic in reverse order
## h(X[i] | X[-j]) = h(X[i] | X[-c(i,j)]
## for all j
pmi <- matrix(, nJi, p)
for(k in 1:nJi) {
j <- Ji[k]
## X.ij <- X[-c(i,j)]
X.ij <- X.i[-J.i[k]]
pmi[k, ] <- partialModelMatrix(X.ij, Xi, model)[nX.i, ]
}
##
mafter[ , Ji, i] <- t(pmj)
mafter[ , i, Ji] <- t(pmi)
}
}
}
## delta[ ,i,j] = h(X[i] | X) - h(X[i] | X[-j])
delta <- mbefore - mafter
## delta[i, j, ] = h(X[i] | X) - h(X[i] | X[-j])
delta <- aperm(delta, c(2,3,1))
return(delta)
}
deltasufQ <- function(model) {
stopifnot(is.ppm(model))
Q <- quad.ppm(model)
X <- data.ppm(model)
U <- union.quad(Q)
nU <- npoints(U)
nX <- npoints(X)
isdata <- is.data(Q)
isdummy <- !isdata
p <- length(coef(model))
m <- model.matrix(model)[isdata, ]
ok <- getglmsubset(model)
## canonical statistic before and after adding/deleting U[j]
mafter <- mbefore <- array(t(m), dim=c(p, nU, nU))
delta <- array(0, dim=dim(mafter))
## mbefore[ , i, j] = h(U[i] | X)
## For data points X[j]
## mafter[ , i, j] = h(U[i] | X[-j])
## delta[ , i, j] = h(U[i] | X) - h(U[i] | X[-j])
## For dummy points X[j]
## mafter[ , i, j] = h(U[i] | X \cup U[j])
## delta[ , i, j] = h(U[i] | X \cup U[j]) - h(U[i] | X)
changesign <- ifelseAB(isdata, -1, 1)
## identify close pairs of quadrature points
R <- reach(model)
if(is.finite(R)) {
cl <- closepairs(U, R, what="indices")
I <- cl$i
J <- cl$j
cl2 <- closepairs(U, 2*R, what="indices")
I2 <- cl2$i
J2 <- cl2$j
} else {
## either infinite reach, or something wrong
IJ <- expand.grid(I=1:nU, J=1:nX)
IJ <- IJ[ with(IJ, I != J), ]
I2 <- I <- IJ$I
J2 <- J <- IJ$J
}
## filter: I and J must both belong to the nominated subset
okIJ <- ok[I] & ok[J]
I <- I[okIJ]
J <- J[okIJ]
##
if(length(I) > 0 && length(J) > 0) {
## .............. loop over pairs of quadrature points ...............
## Run through pairs
uI <- unique(I)
zI <- isdata[uI]
uIdata <- uI[zI]
uIdummy <- uI[!zI]
## Run through pairs i, j where 'i' is a data point
for(i in uIdata) {
## all DATA points within 2R of X[i]
## This represents X[-i]
J2i <- unique(J2[I2==i])
J2i <- J2i[isdata[J2i]]
## all QUADRATURE points within R of X[i]
Ji <- unique(J[I==i])
nJi <- length(Ji)
if(nJi > 0) {
isd <- isdata[Ji]
## data points which are neighbours of X[i]
XJi <- X[Ji[isd]]
## dummy points which are neighbours of X[i]
DJi <- U[Ji[!isd]]
## replace X[-i] by X[-i] \cap b(0, 2R)
X.i <- X[J2i]
nX.i <- length(J2i)
## index of XJi in X.i
J.i <- match(Ji[isd], J2i)
if(any(is.na(J.i)))
stop("Internal error: Ji[isd] not a subset of J2i")
## index of DJi in superimpose(X.i, DJi)
JDi <- nX.i + seq_len(sum(!isd))
## values of sufficient statistic
## h(X[j] | X[-i]) = h(X[j] | X[-c(i,j)]
## for all j
pmj <- partialModelMatrix(X.i, DJi, model)[c(J.i, JDi), , drop=FALSE]
##
mafter[ , Ji, i] <- t(pmj)
}
}
## Run through pairs i, j where 'i' is a dummy point
for(i in uIdummy) {
## all DATA points within 2R of U[i]
J2i <- unique(J2[I2==i])
J2i <- J2i[isdata[J2i]]
## all QUADRATURE points within R of U[i]
Ji <- unique(J[I==i])
nJi <- length(Ji)
if(nJi > 0) {
isd <- isdata[Ji]
JiData <- Ji[isd]
JiDummy <- Ji[!isd]
## data points which are neighbours of U[i]
XJi <- X[JiData]
## dummy points which are neighbours of U[i]
DJi <- U[JiDummy]
## replace X \cup U[i] by (X \cap b(0, 2R)) \cup U[i]
J2Ui <- c(J2i, i)
XUi <- U[J2Ui]
nXUi <- length(J2Ui)
## index of XJi in X.i
J.i <- match(JiData, J2Ui)
if(any(is.na(J.i)))
stop("Internal error: Ji[isd] not a subset of J2i")
## index of DJi in superimpose(X.i, DJi)
JDi <- nXUi + seq_len(length(JiDummy))
## values of sufficient statistic
## h(X[j] | X \cup U[i])
## for all j
pmj <- partialModelMatrix(XUi, DJi, model)[c(J.i, JDi), , drop=FALSE]
##
mafter[ , c(JiData, JiDummy), i] <- t(pmj)
}
}
}
## delta[ ,i,j] = h(X[i] | X) - h(X[i] | X[-j])
delta[ , , isdata] <- mbefore[, , isdata] - mafter[ , , isdata]
## delta[ ,i,j] = h(X[i] | X \cup U[j]) - h(X[i] | X)
delta[ , , isdummy] <- mafter[, , isdummy] - mbefore[ , , isdummy]
## rearrange: new delta[i,j,] = old delta[, i, j]
delta <- aperm(delta, c(2,3,1))
return(delta)
}
deltasuffstat
})