https://github.com/cran/spatstat
Tip revision: 97116a19ab5e4323b8c5566f016d2dc6d77b217b authored by Adrian Baddeley on 06 November 2009, 10:18:11 UTC
version 1.17-1
version 1.17-1
Tip revision: 97116a1
ppmclass.R
#
# ppmclass.R
#
# Class 'ppm' representing fitted point process models.
#
#
# $Revision: 2.34 $ $Date: 2009/10/13 05:27:48 $
#
# An object of class 'ppm' contains the following:
#
# $method model-fitting method (currently "mpl")
#
# $coef vector of fitted regular parameters
# as given by coef(glm(....))
#
# $trend the trend formula
# or NULL
#
# $interaction the interaction family
# (an object of class 'interact') or NULL
#
# $Q the quadrature scheme used
#
# $maxlogpl the maximised value of log pseudolikelihood
#
# $internal list of internal calculation results
#
# $correction name of edge correction method used
# $rbord erosion distance for border correction (or NULL)
#
# $the.call the originating call to ppm()
#
# $the.version version of mpl() which yielded the fit
#
#
#------------------------------------------------------------------------
is.ppm <- function(x) { inherits(x, "ppm") }
print.ppm <- function(x, ...) {
verifyclass(x, "ppm")
s <- summary.ppm(x)
notrend <- s$no.trend
stationary <- s$stationary
poisson <- s$poisson
markeddata <- s$marked
multitype <- s$multitype
markedpoisson <- poisson && markeddata
# ----------- Print model type -------------------
cat(s$name)
cat("\n")
if(markeddata) mrk <- s$entries$marks
if(multitype) {
cat("Possible marks: \n")
cat(paste(levels(mrk)))
cat("\n")
}
# ----- trend --------------------------
# cat(paste("\n", s$trend$name, ":\n", sep=""))
if(!notrend) {
cat("\nTrend formula: ")
print(s$trend$formula)
}
cat(paste("\n", s$trend$label, ":", sep=""))
tv <- s$trend$value
if(is.list(tv)) {
cat("\n")
for(i in seq(tv))
print(tv[[i]])
} else if(is.numeric(tv) && length(tv) == 1 && is.null(names(tv)))
# append to end of current line
cat("\t", paste(tv), "\n")
else {
cat("\n")
print(tv)
}
cat("\n")
# ---- Interaction ----------------------------
if(!poisson)
print(s$interaction, family=FALSE)
# ---- Warnings issued in mpl.prepare ---------------------
probs <- s$problems
if(!is.null(probs) && is.list(probs) && (length(probs) > 0))
lapply(probs,
function(x) {
if(is.list(x) && !is.null(p <- x$print))
cat(paste("Problem:\n", p, "\n\n"))
})
if(s$old)
warning(paste("Model fitted by old spatstat version", s$version))
# ---- Algorithm status ----------------------------
fitter <- s$fitter
converged <- s$converged
if(!is.null(fitter) && fitter %in% c("glm", "gam") && !converged)
cat(paste("*** Fitting algorithm for", sQuote(fitter),
"did not converge ***\n"))
return(invisible(NULL))
}
quad.ppm <- function(object, drop=FALSE) {
verifyclass(object, "ppm")
Q <- object$Q
if(!drop || is.null(Q))
return(Q)
ok <- object$internal$glmdata$.mpl.SUBSET
if(is.null(ok))
return(Q)
return(Q[ok])
}
data.ppm <- function(object) {
verifyclass(object, "ppm")
object$Q$data
}
dummy.ppm <- function(object, drop=FALSE) {
return(quad.ppm(object, drop=drop)$dummy)
}
# method for 'coef'
coef.ppm <- function(object, ...) {
verifyclass(object, "ppm")
object$coef
}
getglmfit <- function(object) {
verifyclass(object, "ppm")
glmfit <- object$internal$glmfit
if(is.null(glmfit))
return(NULL)
if(object$method != "mpl")
glmfit$coefficients <- object$coef
return(glmfit)
}
getglmdata <- function(object, drop=FALSE) {
verifyclass(object, "ppm")
gd <- object$internal$glmdata
if(!drop) return(gd)
return(gd[gd$.mpl.SUBSET,])
}
getglmsubset <- function(object) {
gd <- object$internal$glmdata
return(gd$.mpl.SUBSET)
}
# ??? method for 'effects' ???
valid.ppm <- function(object, na.value=TRUE) {
verifyclass(object, "ppm")
inte <- object$interaction
if(is.null(inte))
return(TRUE)
checker <- inte$valid
if(is.null(checker))
return(na.value)
Vnames <- object$internal$Vnames
coeffs <- coef(object)
Icoeffs <- coeffs[Vnames]
return(checker(Icoeffs, inte))
}
logLik.ppm <- function(object, ...) {
if(!is.poisson.ppm(object))
warning(paste("log likelihood is not available for non-Poisson model;",
"log-pseudolikelihood returned"))
ll <- object$maxlogpl
attr(ll, "df") <- length(coef(object))
class(ll) <- "logLik"
return(ll)
}
# more methods
formula.ppm <- function(x, ...) {
f <- x$trend
if(is.null(f)) f <- ~1
return(f)
}
terms.ppm <- function(x, ...) {
terms(formula(x), ...)
}
extractAIC.ppm <- function (fit, scale = 0, k = 2, ...)
{
edf <- length(coef(fit))
aic <- AIC(fit)
c(edf, aic + (k - 2) * edf)
}
#
# method for model.matrix
model.matrix.ppm <- function(object, ..., keepNA=TRUE) {
gf <- getglmfit(object)
if(is.null(gf)) {
newobject <- update(object, forcefit=TRUE)
gf <- getglmfit(newobject)
if(is.null(gf))
stop("internal error: unable to extract a glm fit")
}
mm <- model.matrix(gf, ...)
if(!keepNA)
return(mm)
cn <- colnames(mm)
gd <- getglmdata(object)
if(nrow(mm) != nrow(gd)) {
# can occur if covariates include NA's or interaction is -Inf
insubset <- getglmsubset(object)
isna <- is.na(insubset) | !insubset
if(sum(isna) + nrow(mm) == nrow(gd)) {
# insert rows of NA's
mmplus <- matrix( , nrow(gd), ncol(mm))
mmplus[isna, ] <- NA
mmplus[!isna, ] <- mm
mm <- mmplus
} else
stop("internal error: model matrix does not match glm data frame")
}
colnames(mm) <- cn
return(mm)
}
model.images <- function(object, W=as.owin(object), ...) {
X <- data.ppm(object)
# make a quadscheme with a dummy point at every pixel
Q <- pixelquad(X, W)
# construct Berman-Turner frame
needed <- c("trend", "interaction", "covariates", "correction", "rbord")
bt <- do.call("bt.frame", append(list(Q), object[needed]))
# compute model matrix
mf <- model.frame(bt$fmla, bt$glmdata, ...)
mm <- model.matrix(bt$fmla, mf, ...)
# retain only the entries for dummy points (pixels)
mm <- mm[!is.data(Q), , drop=FALSE]
# create template image
Z <- as.im(attr(Q, "M"))
# make images
imagenames <- colnames(mm)
result <- lapply(imagenames,
function(nama, Z, mm) {
values <- mm[, nama]
im(values, xcol=Z$xcol, yrow=Z$yrow,
lev=Z$lev, unitname=unitname(Z))
},
Z=Z, mm=mm)
result <- as.listof(result)
names(result) <- imagenames
return(result)
}