File: MxAlgebra.R

package info (click to toggle)
r-cran-openmx 2.21.1%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: bookworm
  • size: 14,412 kB
  • sloc: cpp: 36,577; ansic: 13,811; fortran: 2,001; sh: 1,440; python: 350; perl: 21; makefile: 5
file content (307 lines) | stat: -rwxr-xr-x 11,092 bytes parent folder | download | duplicates (3)
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
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
#
#   Copyright 2007-2019 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.

##' @name MxAlgebraFormula-class
##' 
##' @description
##' This is an internal class for the formulas used in \code{\link{mxAlgebra}} calls.
##' 
##' @aliases
##' MxAlgebraFormula
##' print,MxAlgebraFormula-method
##' show,MxAlgebraFormula-method
##' @rdname MxAlgebraFormula-class
##' @title MxAlgebraFormula
setClassUnion("MxAlgebraFormula", c("call", "name", "language", "logical", "numeric"))

setClass(Class = "MxAlgebra",
	representation = representation(
		formula = "MxAlgebraFormula",
		name = "character",
		fixed = "logical",
		.dimnames = "MxListOrNull",
	    result = "matrix",
	    joinModel = "MxCharOrNumber",
	    joinKey = "MxCharOrNumber",
	    verbose= "integer",
	    initial = "matrix"
	))
		
setMethod("initialize", "MxAlgebra",
	function(.Object, formula, name, fixed, joinKey, joinModel,
		 verbose, initial) {
		.Object@formula <- sys.call(which=-3)[[3]]
		.Object@name <- name
		.Object@fixed <- fixed
		.Object@.dimnames <- NULL
		.Object@joinKey <- joinKey
		.Object@joinModel <- joinModel
		.Object@verbose <- verbose
		.Object@initial <- initial
		return(.Object)
	}
)

setMethod("dimnames", "MxAlgebra",
	function(x) { x@.dimnames }
)

setReplaceMethod("dimnames", "MxAlgebra",
	function(x, value) {
		if (is.null(value)) {
		} else if (!is.list(value)) {
			stop("dimnames of MxAlgebra object must be either NULL or list of length 2")
		} else if (length(value) != 2) {
			stop("dimnames of MxAlgebra object must be either NULL or list of length 2")
		}
		x@.dimnames <- value
		return(x)
	}
)

setMethod("$", "MxAlgebra", imxExtractSlot)

setReplaceMethod("$", "MxAlgebra",
	function(x, name, value) {
        if(name == c("result")) {
            stop("You cannot set the result of an algebra.  Use mxRun() to populate the result, or mxEval() to compute it.")
        } 
		return(imxReplaceSlot(x, name, value, check=TRUE))
	}
)

setMethod("names", "MxAlgebra", slotNames)

mxAlgebra <- function(expression, name = NA, dimnames = NA, ..., fixed = FALSE,
		      joinKey=as.character(NA), joinModel=as.character(NA),
		      verbose=0L, initial=matrix(as.numeric(NA),1,1),
		      recompute=c('always','onDemand')) {
	prohibitDotdotdot(list(...))
	if (single.na(name)) {
		name <- imxUntitledName()
	}
	imxVerifyName(name, 0)
	if (!missing(fixed) && !missing(recompute)) stop("The 'fixed' argument is renamed to recompute")
	if (!missing(fixed) && fixed == TRUE) recompute <- 'onDemand'
	recompute <- match.arg(recompute)
	retval <- new("MxAlgebra", NA, name, recompute=='onDemand', joinKey, joinModel,
		as.integer(verbose), initial)
	formula <- match.call()$expression
	if(is.character(formula)){
		stop("mxAlgebra wants an unquoted expression or formula")
	}
	retval@formula <- formula
    algebraErrorChecking(retval@formula, "mxAlgebra")
	if(!(length(dimnames) == 1 && is.na(dimnames))) {
		dimnames(retval) <- dimnames
	}
	return(retval)	
}

#' Create MxAlgebra object from a string
#'
#' @param algString the character string to convert into an R expression
#' @param name An optional character string indicating the name of the object.
#' @param dimnames list. The dimnames attribute for the algebra: a list of length 2 giving the row and column names respectively. An empty list is treated as NULL, and a list of length one as row names. The list can be named, and the list names will be used as names for the dimensions.
#' @param ... Forwarded verbatim to \link{mxAlgebra}
#' @seealso \link{mxAlgebra}
#' @examples
#' A <- mxMatrix(values = runif(25), nrow = 5, ncol = 5, name = 'A')
#' B <- mxMatrix(values = runif(25), nrow = 5, ncol = 5, name = 'B')
#' model <- mxModel(A, B, name = 'model',
#'   mxAlgebraFromString("A * (B + A)", name = 'test'))
#' model <- mxRun(model)
#' model[['test']]$result
#' A$values * (B$values + A$values)
mxAlgebraFromString <- function(algString, name=NA, dimnames=NA, ...) {
	eval(substitute(mxAlgebra(tExp, name=name, dimnames=dimnames, ...),
			list(tExp = parse(text=algString)[[1]])))
}

algebraErrorChecking <- function(formula, context) {
	if(length(formula) < 2) {
		return()
	}
	operator <- as.character(formula[[1]])
	if (identical(operator, "(")) {
	} else if (operator %in% omxSymbolTable[,'R.name']) {
	} else {
		msg <- paste("Unknown matrix operator or function",
			omxQuotes(operator), "in",
			deparse(width.cutoff = 400L, imxLocateFunction(context)),
			"\n view the list of valid operators at help(mxAlgebra).\n",
			"nb: some R operators are implemented differently in algebras",
			", for instance diag() is implemented as diag2vec() and vec2diag()")
		stop(msg, call. = FALSE)
	}
	lapply(formula[-1], algebraErrorChecking, context)
}

formulaList <- function(x) {
	retval <- as.list(x)
	retval <- lapply(retval, function(x) {
		if(is.call(x)) {formulaList(x)} else {x}
	})
	return(retval)
}

algebraSymbolCheck <- function(formula, name) {
	formula <- unlist(formulaList(formula))
	test <- sapply(formula, function(x) {!is.numeric(x) && !is.character(x)})
	if(length(formula[test]) == 1) {
		msg <- paste("The reference", omxQuotes(formula[test]),
			"is unknown in the algebra named", omxQuotes(name))
		stop(msg, call. = FALSE)
	} else if (length(formula[test]) > 1) {
		msg <- paste("The references", omxQuotes(formula[test]),
			"are unknown in the algebra named", omxQuotes(name))
		stop(msg, call. = FALSE)		
	}
}

generateAlgebraHelper <- function(algebra, joinModel, joinKey, matrixNumbers, algebraNumbers) {
	retval <- algebra@formula
	retval <- eval(substitute(substitute(e, matrixNumbers), list(e = retval)))
	retval <- eval(substitute(substitute(e, algebraNumbers), list(e = retval)))
	retval <- substituteOperators(as.list(retval), algebra@name)
	algebraSymbolCheck(retval, algebra@name)
	initial <- matrix(as.numeric(NA),1,1)
	if (.hasSlot(algebra, 'initial')) {
		initial <- algebra@initial
		if (!algebra@fixed && !single.na(initial)) {
			stop(paste("In algebra", omxQuotes(algebra@name),
				"initial result will be immediately discarded"))
		}
		if (algebra@fixed && any(is.na(initial))) {
			stop(paste("Missing value found in initial result of algebra",
				omxQuotes(algebra@name)))
		}
	}
	return(list(algebra@.dimnames, algebra@verbose, algebra@fixed,
		initial, joinModel, joinKey, retval))
}

substituteOperators <- function(algebra, name) {
	if ((length(algebra) == 1) && (is.list(algebra))) {
		algebra <- list(0L, algebra[[1]])
	} else if ((length(algebra) > 1) && (!is.numeric(algebra[[1]]))) {
		if (as.character(algebra[[1]]) == '(') {
			return(substituteOperators(as.list(algebra[[2]]), name))
		}
		names <- omxSymbolTable["R.name"] == as.character(algebra[[1]])
        variableSymbols <- omxSymbolTable["Number.of.arguments"] == -1
		result <- omxSymbolTable[names & variableSymbols, "Num"]
		if (length(result) > 1) {
				msg <- paste("In algebra", omxQuotes(name), 
					"ambiguous function with name", algebra[[1]],
					"and", (length(algebra) - 1), "arguments.")
				stop(msg, call. = FALSE)
		} else if(length(result) == 1) {
			head <- as.integer(result[[1]])
			tail <- lapply(algebra[-1], substituteOperators, name)
			result <- append(tail, head, after=0)
			return(result)
		} else {
			length <- omxSymbolTable["Number.of.arguments"] == (length(algebra) - 1)
			result <- omxSymbolTable[names & length, "Num"]
			if (length(result) == 0) {
				msg <- paste("In algebra", omxQuotes(name),
					"could not find function with name", algebra[[1]],
					"and", (length(algebra) - 1), "arguments.")
				stop(msg, call. = FALSE)
			} else if (length(result) > 1) {
				msg <- paste("In algebra", omxQuotes(name),
					"ambiguous function with name", algebra[[1]],
					"and", (length(algebra) - 1), "arguments.")
				stop(msg, call. = FALSE)
			} else {
				head <- as.integer(result[[1]])
			    tail <- lapply(algebra[-1], substituteOperators, name)
				result <- append(tail, head, after=0)
				return(result)
			}
    	}
	}
	return(algebra)
}

checkEvaluation <- function(model, flatModel) {
	labelsData <- imxGenerateLabels(model)
	cache <- new.env(parent = emptyenv())
	checkConstraintEvaluation(model, flatModel, labelsData, cache)
	return(flatModel)
}

checkConstraintEvaluation <- function(model, flatModel, labelsData, cache) {
	if(length(flatModel@constraints) == 0) { return() }
	for(i in 1:length(flatModel@constraints)) {
		constraint <- flatModel@constraints[[i]]		
		lhsContext <- paste("the left-hand side of constraint", omxQuotes(constraint@name))
		rhsContext <- paste("the right-hand side of constraint", omxQuotes(constraint@name))		
		tuple <- evaluateAlgebraWithContext(flatModel[[constraint@alg1]], lhsContext, flatModel, labelsData, cache)
		lhs <- tuple[[1]]
		cache <- tuple[[2]]
		tuple <- evaluateAlgebraWithContext(flatModel[[constraint@alg2]], rhsContext, flatModel, labelsData, cache)
		rhs <- tuple[[1]]
		cache <- tuple[[2]]
		if (!all(dim(lhs) == dim(rhs))) {
			lhsName <- constraint@formula[[2]]
			rhsName <- constraint@formula[[3]]
			if (length(lhsName) == 1) {
				lhsName <- simplifyName(deparse(lhsName), model@name)
			} else {
				lhsName <- deparse(lhsName)
			}
			if (length(rhsName) == 1) {
				rhsName <- simplifyName(deparse(rhsName), model@name)
			} else {
				rhsName <- deparse(rhsName)
			}
			stop(paste("The algebras/matrices", 
				omxQuotes(c(lhsName, rhsName)),
				"in model", omxQuotes(model@name),
				"are in constraint", omxQuotes(simplifyName(constraint@name, model@name)),
				"and are not of identical dimensions. The left-hand side is",
				nrow(lhs), "x", ncol(lhs), "and the right-hand side is",
				nrow(rhs), "x", paste(ncol(rhs), ".", sep = '')), call. = FALSE)
		}
	}		
}

displayAlgebra <- function(mxAlgebra) {
	cat("mxAlgebra", omxQuotes(mxAlgebra@name), '\n')
	cat("$formula: ", deparse(mxAlgebra@formula, width.cutoff=500L), '\n')
	if (length(mxAlgebra@result) == 0) {
		cat("$result: (not yet computed) ")
	} else {
		cat("$result:\n")
	}
	print(mxAlgebra@result)
	if (is.null(dimnames(mxAlgebra))) {
			cat("dimnames: NULL\n")
	} else {
		cat("dimnames:\n")
		print(dimnames(mxAlgebra))
	}
	if (.hasSlot(mxAlgebra, 'joinModel') && !is.na(mxAlgebra@joinModel)) {
		cat("$joinModel : ", omxQuotes(mxAlgebra@joinModel), fill=TRUE)
	}
	if (.hasSlot(mxAlgebra, 'joinKey') && !is.na(mxAlgebra@joinKey)) {
		cat("$joinKey : ", omxQuotes(mxAlgebra@joinKey), fill=TRUE)
	}
}

setMethod("print", "MxAlgebra", function(x,...) { displayAlgebra(x) })
setMethod("show", "MxAlgebra", function(object) { displayAlgebra(object) })