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[matrix] Annotation of /pkg/R/Matrix.R
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Annotation of /pkg/R/Matrix.R

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1 : maechler 607 #### Toplevel ``virtual'' class "Matrix"
2 :    
3 : maechler 1331
4 :     ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5 :    
6 :     setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7 :     setAs("Matrix", "denseMatrix", function(from) as_dense(from))
8 :    
9 : maechler 956 ## ## probably not needed eventually:
10 :     ## setAs(from = "ddenseMatrix", to = "matrix",
11 :     ## function(from) {
12 :     ## if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
13 :     ## array(from@x, dim = d, dimnames = dimnames(from))
14 :     ## })
15 : maechler 607
16 : maechler 676 ## should propagate to all subclasses:
17 : maechler 658 setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
18 : maechler 956 ## for 'Matrix' objects, as.array() should be equivalent:
19 :     setMethod("as.array", signature(x = "Matrix"), function(x) as(x, "matrix"))
20 : maechler 658
21 : maechler 1347 ## head and tail apply to all Matrix objects for which subscripting is allowed:
22 : maechler 1390 ## if(paste(R.version$major, R.version$minor, sep=".") < "2.4") {
23 : maechler 1389 setMethod("head", signature(x = "Matrix"), utils:::head.matrix)
24 :     setMethod("tail", signature(x = "Matrix"), utils:::tail.matrix)
25 : maechler 1390 ## } else { # R 2.4.0 and newer
26 :     ## setMethod("head", signature(x = "Matrix"), utils::head.matrix)
27 :     ## setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
28 :     ## }
29 :    
30 : maechler 956 ## slow "fall back" method {subclasses should have faster ones}:
31 :     setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
32 : maechler 1331 function(x) as.vector(as(x, "matrix")))
33 : maechler 956
34 : maechler 1389 ## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
35 :     setMethod("as.numeric", signature(x = "Matrix"),
36 :     function(x, ...) as.numeric(as.vector(x)))
37 :     setMethod("as.logical", signature(x = "Matrix"),
38 :     function(x, ...) as.logical(as.vector(x)))
39 : maechler 956
40 : maechler 1389
41 : maechler 1467 ## "base" has an isSymmetric() S3-generic since R 2.3.0
42 : maechler 1108 setMethod("isSymmetric", signature(object = "symmetricMatrix"),
43 : maechler 973 function(object,tol) TRUE)
44 : maechler 1108 setMethod("isSymmetric", signature(object = "triangularMatrix"),
45 : maechler 1174 ## TRUE iff diagonal:
46 :     function(object,tol) isDiagonal(object))
47 : maechler 1189
48 : maechler 1165 setMethod("isTriangular", signature(object = "triangularMatrix"),
49 : maechler 1238 function(object, ...) TRUE)
50 : maechler 1165
51 : maechler 1238 setMethod("isTriangular", signature(object = "matrix"), isTriMat)
52 :    
53 : maechler 1174 setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
54 : maechler 886
55 : maechler 1174
56 :    
57 : maechler 579 setMethod("dim", signature(x = "Matrix"),
58 : maechler 698 function(x) x@Dim, valueClass = "integer")
59 : maechler 579 setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
60 : maechler 607 ## not exported but used more than once for "dimnames<-" method :
61 :     ## -- or do only once for all "Matrix" classes ??
62 :     dimnamesGets <- function (x, value) {
63 :     d <- dim(x)
64 :     if (!is.list(value) || length(value) != 2 ||
65 : maechler 698 !(is.null(v1 <- value[[1]]) || length(v1) == d[1]) ||
66 :     !(is.null(v2 <- value[[2]]) || length(v2) == d[2]))
67 :     stop(sprintf("invalid dimnames given for '%s' object", class(x)))
68 : maechler 607 x@Dimnames <- list(if(!is.null(v1)) as.character(v1),
69 : maechler 698 if(!is.null(v2)) as.character(v2))
70 : maechler 607 x
71 :     }
72 :     setMethod("dimnames<-", signature(x = "Matrix", value = "list"),
73 : maechler 698 dimnamesGets)
74 : maechler 579
75 : maechler 658 setMethod("unname", signature("Matrix", force="missing"),
76 : maechler 698 function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
77 : maechler 607
78 : bates 10 Matrix <-
79 : maechler 954 function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
80 : maechler 1455 sparse = NULL, forceCheck = FALSE)
81 : bates 10 {
82 : maechler 954 sparseDefault <- function(m)
83 : maechler 1467 prod(dim(m)) > 2*sum(is.na(m <- as(m, "matrix")) | m != 0)
84 : maechler 954
85 :     i.M <- is(data, "Matrix")
86 :     if(is.null(sparse) && (i.M || is(data, "matrix")))
87 : maechler 1174 sparse <- sparseDefault(data)
88 : maechler 954
89 : maechler 1455 doDN <- TRUE
90 :     if (i.M && !forceCheck) {
91 : maechler 1174 sM <- is(data,"sparseMatrix")
92 :     if((sparse && sM) || (!sparse && !sM))
93 :     return(data)
94 :     ## else : convert dense <-> sparse -> at end
95 : maechler 954 }
96 :     else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
97 : maechler 698 if (missing(nrow))
98 :     nrow <- ceiling(length(data)/ncol)
99 :     else if (missing(ncol))
100 :     ncol <- ceiling(length(data)/nrow)
101 : maechler 1467 if(length(data) == 1 && !is.na(data) && data == 0 &&
102 :     !identical(sparse, FALSE)) {
103 :    
104 : maechler 1315 if(is.null(sparse)) sparse <- TRUE
105 :     ## will be sparse: do NOT construct full matrix!
106 :     data <- new(if(is.numeric(data)) "dgTMatrix" else
107 :     if(is.logical(data)) "lgTMatrix" else
108 :     stop("invalid 'data'"),
109 :     Dim = as.integer(c(nrow,ncol)),
110 : maechler 1332 Dimnames = if(is.null(dimnames)) list(NULL,NULL)
111 :     else dimnames)
112 : maechler 1315 } else { ## normal case
113 :     data <- .Internal(matrix(data, nrow, ncol, byrow))
114 :     if(is.null(sparse))
115 :     sparse <- sparseDefault(data)
116 :     dimnames(data) <- dimnames
117 :     }
118 : maechler 1455 doDN <- FALSE
119 :     }
120 :     ## 'data' is now a "matrix" or "Matrix"
121 :     if (doDN && !is.null(dimnames))
122 : maechler 1189 dimnames(data) <- dimnames
123 : maechler 954
124 : maechler 1174 ## check for symmetric / triangular / diagonal :
125 :     isSym <- isSymmetric(data)
126 :     if((isTri <- !isSym))
127 :     isTri <- isTriangular(data)
128 :     isDiag <- isSym # cannot be diagonal if it isn't symmetric
129 :     if(isDiag)
130 :     isDiag <- isDiagonal(data)
131 :    
132 : maechler 965 ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
133 : maechler 1174
134 :     ## Find proper matrix class 'cl'
135 :     cl <-
136 :     if(isDiag)
137 :     "diagonalMatrix" # -> will automatically check for type
138 :     else {
139 :     ## consider it's type
140 :     ctype <-
141 :     if(is(data,"Matrix")) class(data)
142 :     else {
143 :     if("complex" == (ctype <- typeof(data)))
144 :     "z" else ctype
145 :     }
146 :     ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
147 :     if(ctype == "z")
148 :     stop("complex matrices not yet implemented in Matrix package")
149 :     if(ctype == "i") {
150 :     warning("integer matrices not yet implemented in 'Matrix'; ",
151 :     "using 'double' ones'")
152 :     ctype <- "d"
153 :     }
154 :     paste(ctype,
155 :     if(sparse) {
156 :     if(isSym) "sCMatrix" else
157 :     if(isTri) "tCMatrix" else "gCMatrix"
158 :     } else { ## dense
159 :     if(isSym) "syMatrix" else
160 :     if(isTri) "trMatrix" else "geMatrix"
161 :     }, sep="")
162 :     }
163 :    
164 :     ## Now coerce and return
165 :     as(data, cl)
166 : bates 10 }
167 :    
168 : bates 683 ## Methods for operations where one argument is numeric
169 : maechler 512
170 : maechler 698 ## Using as.matrix() and rbind()
171 :     ## in order to get dimnames from names {at least potentially}:
172 :    
173 : bates 683 setMethod("%*%", signature(x = "Matrix", y = "numeric"),
174 : maechler 698 function(x, y) callGeneric(x, as.matrix(y)))
175 : bates 683
176 :     setMethod("%*%", signature(x = "numeric", y = "Matrix"),
177 : maechler 698 function(x, y) callGeneric(rbind(x), y))
178 : bates 683
179 :     setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
180 : maechler 698 function(x, y = NULL) callGeneric(x, as.matrix(y)))
181 : bates 683 setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
182 : maechler 1331 function(x, y = NULL) callGeneric(as.matrix(x), y))
183 : bates 683
184 : maechler 1331 ## The as.matrix() promotion seems illogical to MM,
185 :     ## but is according to help(tcrossprod, package = "base") :
186 :     setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
187 :     function(x, y = NULL) callGeneric(x, as.matrix(y)))
188 :     setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
189 :     function(x, y = NULL) callGeneric(as.matrix(x), y))
190 :    
191 : bates 683 setMethod("solve", signature(a = "Matrix", b = "numeric"),
192 : maechler 698 function(a, b, ...) callGeneric(a, as.matrix(b)))
193 : maechler 848
194 : maechler 925 ## bail-out methods in order to get better error messages
195 :     setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
196 :     function (x, y)
197 :     stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
198 :     class(x), class(y))))
199 : maechler 946
200 : maechler 925 setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
201 : maechler 946 function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
202 : maechler 956 setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
203 :     function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
204 : maechler 1331 setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
205 :     function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
206 :     setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
207 :     function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
208 : maechler 925
209 : maechler 1331 ## cheap fallbacks
210 :     setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
211 :     function(x, y = NULL) t(x) %*% y)
212 :     setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
213 :     function(x, y = NULL) x %*% t(y))
214 :    
215 : maechler 956 ## There are special sparse methods; this is a "fall back":
216 :     setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
217 :     FUN = "ANY", make.dimnames = "ANY"),
218 :     function(X, Y, FUN, make.dimnames, ...) {
219 :     X <- as(X, "matrix") ; Matrix(callGeneric()) })
220 :     setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
221 :     FUN = "ANY", make.dimnames = "ANY"),
222 :     function(X, Y, FUN, make.dimnames, ...) {
223 :     Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
224 :    
225 :    
226 : maechler 1315 setMethod("diag", signature(x = "Matrix"),
227 :     function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
228 : maechler 946 setMethod("t", signature(x = "Matrix"),
229 :     function(x) .bail.out.1(.Generic, class(x)))
230 : maechler 925
231 : maechler 956 ## Group Methods
232 :     setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
233 :     ## "fallback":
234 :     setMethod("-", signature(e1 = "Matrix", e2 = "missing"),
235 :     function(e1) {
236 :     warning("inefficient method used for \"- e1\"")
237 :     0-e1
238 :     })
239 :    
240 :     ## bail-outs:
241 : maechler 946 setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),
242 : maechler 954 function(e1, e2) {
243 :     d <- dimCheck(e1,e2)
244 :     .bail.out.2(.Generic, class(e1), class(e2))
245 :     })
246 : maechler 946 setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),
247 :     function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
248 :     setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),
249 :     function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
250 :    
251 :    
252 :    
253 : maechler 871 ### --------------------------------------------------------------------------
254 :     ###
255 :     ### Subsetting "[" and
256 :     ### SubAssign "[<-" : The "missing" cases can be dealt with here, "at the top":
257 : maechler 868
258 : maechler 886 ## Using "index" for indices should allow
259 : maechler 875 ## integer (numeric), logical, or character (names!) indices :
260 :    
261 : maechler 868 ## "x[]":
262 :     setMethod("[", signature(x = "Matrix",
263 :     i = "missing", j = "missing", drop = "ANY"),
264 :     function (x, i, j, drop) x)
265 : maechler 1225
266 : maechler 868 ## missing 'drop' --> 'drop = TRUE'
267 :     ## -----------
268 :     ## select rows
269 : maechler 886 setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
270 : maechler 868 drop = "missing"),
271 :     function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))
272 :     ## select columns
273 : maechler 886 setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
274 : maechler 868 drop = "missing"),
275 :     function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))
276 : maechler 886 setMethod("[", signature(x = "Matrix", i = "index", j = "index",
277 : maechler 868 drop = "missing"),
278 :     function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))
279 :    
280 : maechler 875 ## bail out if any of (i,j,drop) is "non-sense"
281 :     setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
282 :     function(x,i,j, drop)
283 :     stop("invalid or not-yet-implemented 'Matrix' subsetting"))
284 :    
285 : maechler 1225 ## "logical *vector* indexing, such as M [ M >= 10 ] :
286 :     setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
287 :     drop = "ANY"),
288 :     function (x, i, j, drop) {
289 :     as(x, geClass(x))@x[as.vector(i)]
290 : maechler 1329 ## -> error when lengths don't match
291 : maechler 1225 })
292 :    
293 : maechler 1329 ## FIXME: The following is good for M [ <logical> ]
294 :     ## *BUT* it also triggers for M [ <logical> , ] where it is *WRONG*
295 :     ## using nargs() does not help: it gives '3' for both cases
296 :     if(FALSE)
297 : maechler 1225 setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
298 :     drop = "ANY"),
299 : maechler 1329 function (x, i, j, drop) {
300 :     ## DEBUG
301 :     cat("[(Matrix,i,..): nargs=", nargs(),"\n")
302 :     as(x, geClass(x))@x[i] })
303 : maechler 1225
304 :    
305 : maechler 868 ## "FIXME:"
306 :     ## How can we get at A[ ij ] where ij is (i,j) 2-column matrix?
307 :     ## and A[ LL ] where LL is a logical *vector*
308 : maechler 886 ## -> [.data.frame uses nargs() - can we do this in the *generic* ?
309 : maechler 868
310 :    
311 : maechler 871 ### "[<-" : -----------------
312 : maechler 868
313 : maechler 871 ## x[] <- value :
314 :     setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
315 : maechler 1189 value = "ANY"),## double/logical/...
316 :     function (x, value) {
317 :     x@x <- value
318 :     validObject(x)# check if type and lengths above match
319 :     x
320 :     })
321 : maechler 871
322 : maechler 1189 ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
323 :     ## (ANY,ANY,ANY) is used when no `real method' is implemented :
324 : maechler 871 setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
325 :     value = "ANY"),
326 : maechler 1189 function (x, i, j, value) {
327 :     if(!is.atomic(value))
328 :     stop("RHS 'value' must match matrix class ", class(x))
329 :     else stop("not-yet-implemented 'Matrix[<-' method")
330 :     })
331 : maechler 871
332 :    
333 : maechler 1290 ## The trivial methods :
334 :     setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
335 :     function(x, y) x)
336 :     setMethod("cbind2", signature(x = "Matrix", y = "missing"),
337 :     function(x, y) x)
338 :     setMethod("cbind2", signature(x = "NULL", y="Matrix"),
339 :     function(x, y) x)
340 : maechler 871
341 : maechler 1290 setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
342 :     function(x, y) x)
343 :     setMethod("rbind2", signature(x = "Matrix", y = "missing"),
344 :     function(x, y) x)
345 :     setMethod("rbind2", signature(x = "NULL", y="Matrix"),
346 :     function(x, y) x)
347 : maechler 875
348 : maechler 1290 ## Makes sure one gets x decent error message for the unimplemented cases:
349 :     setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
350 :     function(x, y) {
351 :     rowCheck(x,y)
352 :     stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
353 :     class(x), class(y)))
354 :     })
355 : maechler 908
356 : maechler 1290 ## Use a working fall back {particularly useful for sparse}:
357 :     ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
358 :     setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
359 :     function(x, y) {
360 :     colCheck(x,y)
361 :     t(cbind2(t(x), t(y)))
362 :     })

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