1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
|
#
# fields is a package for analysis of spatial data written for
# the R software environment.
# Copyright (C) 2022 Colorado School of Mines
# 1500 Illinois St., Golden, CO 80401
# Contact: Douglas Nychka, douglasnychka@gmail.edu,
#
# 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$nZ)
}
c1 <- c(c1, "sigma Process stan. dev: ")
c2 <- c(c2, signif( sqrt(object$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$beta[,1]
pValue<- pnorm(abs(beta/SE), lower.tail = FALSE)*2
outObject$fixedEffectsTable<- cbind( signif(beta, digits),
signif(SE, digits),
signif(pValue, digits)
)
if( is.null( object$fixedEffectNames ) ){
outObject$fixedEffectNames<- paste0("d",1:(object$nt) )
}
else{
outObject$fixedEffectNames<- object$fixedEffectNames
}
dimnames( outObject$fixedEffectsTable) <- list( outObject$fixedEffectNames,
c("estimate", "SE", "pValue") )
}
}
else{
outObject$fixedEffectsTable<- 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)
}
|
