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#
# Copyright 2007-2018 by the individuals mentioned in the source code history
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
setClass(Class = "SymmMatrix",
representation = representation(),
contains = "MxMatrix")
setMethod("imxSymmetricMatrix", "SymmMatrix",
function(.Object) { return(TRUE) }
)
setMethod("imxSquareMatrix", "SymmMatrix",
function(.Object) { return(TRUE) }
)
populateSymmTriangle <- function(input, n, default, byrow, strname) {
len <- length(input)
if (len == n * n || len == 1) {
output <- matrix(input, n, n, byrow)
} else if (len == n * (n + 1) / 2) {
if(byrow) {
output <- matrix(default, n, n)
output[upper.tri(output, TRUE)] <- input
output[lower.tri(output)] <- t(output)[lower.tri(output)]
} else {
output <- matrix(default, n, n)
output[lower.tri(output, TRUE)] <- input
output[upper.tri(output)] <- t(output)[upper.tri(output)]
}
} else {
stop(paste(
"illegal number of elements (", len,
") for '", strname, "' matrix in Symmetric MxMatrix construction", sep=""),
deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix")),
call. = FALSE)
}
return(output)
}
setMethod("imxCreateMatrix", "SymmMatrix",
function(.Object, labels, values, free, lbound, ubound, nrow, ncol, byrow, name, condenseSlots,
joinKey, joinModel) {
if (nrow != ncol) {
stop(paste("non-square MxMatrix attempted in 'nrow' and 'ncol' arguments to",
deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix"))),
call. = FALSE)
}
if (single.na(values)) {
values <- 0
}
if (is.vector(values)) {
values <- populateSymmTriangle(values, nrow, 0, byrow, 'values')
}
if(condenseSlots && all.false(free) && all.na(labels)){
labels <- as.character(NA)
free <- FALSE
}
else{
if (is.vector(labels)) {
labels <- populateSymmTriangle(labels, nrow, as.character(NA), byrow, 'labels')
}
if (is.vector(free)) {
free <- populateSymmTriangle(free, nrow, FALSE, byrow, 'free')
}}
if(condenseSlots && all.na(lbound)){lbound <- as.numeric(NA)}
else{if (is.vector(lbound)) {
lbound <- populateSymmTriangle(lbound, nrow, as.numeric(NA), byrow, 'lbound')
}}
if(condenseSlots && all.na(ubound)){ubound <- as.numeric(NA)}
else{if (is.vector(ubound)) {
ubound <- populateSymmTriangle(ubound, nrow, as.numeric(NA), byrow, 'ubound')
}}
return(callNextMethod(.Object, labels, values, free, lbound, ubound, nrow, ncol, byrow, name,
condenseSlots, joinKey, joinModel))
}
)
setMethod("imxVerifyMatrix", "SymmMatrix",
function(.Object) {
callNextMethod(.Object)
values <- .Object@values
free <- .Object@free
labels <- .Object@labels
lbound <- .Object@lbound
ubound <- .Object@ubound
mask <- is.na(values[upper.tri(values)])
if (any(is.na(t(values)[upper.tri(values)]) != mask)) {
stop(paste("NAs in 'values' matrix of Symmetric MxMatrix", omxQuotes(.Object@name),
"are not symmetric in "),
deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix")),
call. = FALSE)
}
if (any(values[upper.tri(values)][!mask] != t(values)[upper.tri(values)][!mask])) {
stop(paste("'values' matrix of Symmetric MxMatrix", omxQuotes(.Object@name),
"is not symmetric in "), deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix")),
call. = FALSE)
}
if (!all(free == t(free))) {
stop(paste("'free' matrix of Symmetric MxMatrix", omxQuotes(.Object@name),
"is not symmetric in "),
deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix")),
call. = FALSE)
}
if (!all(labels == t(labels), na.rm = TRUE) && all(is.na(labels) == is.na(t(labels)))) {
stop(paste("'labels' matrix of Symmetric MxMatrix", omxQuotes(.Object@name),
"is not symmetric in "),
deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix")),
call. = FALSE)
}
if (!all(lbound == t(lbound), na.rm = TRUE) && all(is.na(lbound) == is.na(t(lbound)))) {
stop(paste("'lbound' matrix of Symmetric MxMatrix", omxQuotes(.Object@name),
"is not symmetric in "),
deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix")),
call. = FALSE)
}
if (!all(ubound == t(ubound), na.rm = TRUE) && all(is.na(ubound) == is.na(t(ubound)))) {
stop(paste("'ubound' matrix of Symmetric MxMatrix", omxQuotes(.Object@name),
"is not symmetric in "),
deparse(width.cutoff = 400L, imxLocateFunction("mxMatrix")),
call. = FALSE)
}
}
)
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