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#
# fields is a package for analysis of spatial data written for
# the R software environment.
# Copyright (C) 2024 Colorado School of Mines
# 1500 Illinois St., Golden, CO 80401
# Contact: Douglas Nychka, douglasnychka@gmail.com,
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with the R software environment if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
# or see http://www.r-project.org/Licenses/GPL-2
##END HEADER
summary.spatialProcess <- function(object, ...) {
# output list
outObject<- list()
digits<- 4
if (is.matrix(object$residuals)) {
n <- nrow(object$residuals)
nData <- ncol(object$residuals)
}
else {
n <- length(object$residuals)
nData <- 1
}
c1 <- "Number of Observations:"
c2 <- n
if (nData > 1) {
c1 <- c(c1, "Number of data sets fit:")
c2 <- c(c2, nData)
}
c1 <- c(c1, "Degree of polynomial in fixed part: ")
if(object$m !=0 ){
c2 <- c(c2, object$m - 1)
}
else{
c2 <- c(c2, NA)
}
c1 <- c(c1, "Total number of parameters in fixed part: ")
c2 <- c(c2, object$nt)
if (object$nZ > 0) {
c1 <- c(c1, "Number of additional covariates (Z)")
c2 <- c(c2, object$nZ)
}
if (!is.na(object$gamma[1]) ) {
c1 <- c(c1, "Number of common covariates (ZCommon)")
c2 <- c(c2, length(object$gamma))
}
c1 <- c(c1, "sigma Process stan. dev: ")
c2 <- c(c2, signif( sqrt(object$MLESummary["sigma2"]), digits))
c1 <- c(c1, "tau Nugget stan. dev:")
c2 <- c(c2, signif(object$MLESummary["tau"], digits))
c1 <- c(c1, "lambda tau^2/sigma^2: ")
c2 <- c(c2, signif(object$MLESummary["lambda"], digits))
c1 <- c(c1, "aRange parameter (in units of distance): ")
c2 <- c(c2, signif(object$MLESummary["aRange"], digits))
if (!is.na(object$eff.df)) {
c1 <- c(c1, "Approx. degrees of freedom for curve")
c2 <- c(c2, signif(object$eff.df, digits))
if (length(object$trA.info) < object$np) {
c1 <- c(c1, " Standard Error of df estimate: ")
c2 <- c(c2, signif(sd(object$trA.info)/sqrt(length(object$trA.info)),
digits))
}
}
c1 <- c(c1, "log Likelihood: ")
c2 <- c(c2, object$summary["lnProfileLike.FULL"])
c1 <- c(c1, "log Likelihood REML: ")
c2 <- c(c2, object$summary["lnProfileREML.FULL"])
summaryStuff <- cbind(c1, c2)
dimnames(summaryStuff) <- list(rep("",
dim(summaryStuff)[1]),
rep("", dim(summaryStuff)[2]))
###########
outObject$summaryTable <- summaryStuff
outObject$collapseFixedEffect <- object$collapseFixedEffect
outObject$CITable <- object$CITable
###########
if (!is.null(object$MLEInfo)) {
outObject$MLEpars <- names(object$MLEInfo$pars.MLE)
outObject$MLESummary <- object$summary
}
else{
outObject$MLEpars <- NA
outObject$MLESummary <- object$summary
}
########### information for SE for fixed effects
if (!is.null(object$beta)){
if (outObject$collapseFixedEffect | (nData == 1)) {
outObject$fixedEffectsCov <- object$fixedEffectsCov
SE <- sqrt(diag(outObject$fixedEffectsCov))
beta <- object$beta[, 1]
SEbeta <- SE[1:length(beta)]
pValue <- pnorm(abs(beta / SEbeta), lower.tail = FALSE) * 2
outObject$fixedEffectsTable <- cbind(signif(beta, digits),
signif(SEbeta, digits),
signif(pValue, digits))
# get row names
if (is.null(object$fixedEffectNames)) {
outObject$fixedEffectNames <- paste0("d", 1:(object$nt))
}
else{
outObject$fixedEffectNames <- object$fixedEffectNames
}
dimnames(outObject$fixedEffectsTable) <-
list(outObject$fixedEffectNames,
c("estimate", "SE", "pValue"))
}
else{
# if more that one realization just summarize the coefficients
outObject$fixedEffectsTable <- stats(t(object$beta))
}
}
if (is.null(object$beta)) {
outObject$fixedEffectsTable <- NA
}
if (!is.null(object$gamma)) {
gamma <- object$gamma
if( object$collapseFixedEffect){
SE <- sqrt(diag(object$fixedEffectsCov))
SEgamma <- SE[(1:length(gamma)) + length(beta)]
}
else{
SEgamma <- sqrt(diag(object$fixedEffectsCovCommon))
}
pValue <- pnorm(abs(gamma / SEgamma), lower.tail = FALSE) * 2
outObject$fixedEffectsTableCommon <-
cbind(signif(gamma, digits),
signif(SEgamma, digits),
signif(pValue, digits))
tmp <- paste0("gamma", 1:length(gamma))
dimnames(outObject$fixedEffectsTableCommon) <- list(tmp,
c("estimate", "SE", "pValue"))
}
if (is.null(object$gamma)) {
outObject$fixedEffectsTableCommon <- NA
}
#####################
outObject$nData <- nData
outObject$call <- object$call
outObject$cov.function <- object$cov.function
outObject$args <- object$args
outObject$nonzero.entries <- object$nonzero.entries
outObject$MLEInfo <- object$MLEInfo
class(outObject) <- "spatialProcessSummary"
return(outObject)
}
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