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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 956 ## ## probably not needed eventually:
4 :     ## setAs(from = "ddenseMatrix", to = "matrix",
5 :     ## function(from) {
6 :     ## if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
7 :     ## array(from@x, dim = d, dimnames = dimnames(from))
8 :     ## })
9 : maechler 607
10 : maechler 676 ## should propagate to all subclasses:
11 : maechler 658 setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
12 : maechler 956 ## for 'Matrix' objects, as.array() should be equivalent:
13 :     setMethod("as.array", signature(x = "Matrix"), function(x) as(x, "matrix"))
14 : maechler 658
15 : maechler 956 ## slow "fall back" method {subclasses should have faster ones}:
16 :     setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
17 :     function(x) as.vector(as(x, "matrix")))
18 :    
19 :    
20 : maechler 1174 ## Note that isSymmetric is *not* exported
21 :     ## but that "base" has an isSymmetric() S3-generic since R 2.3.0
22 : maechler 1108 setMethod("isSymmetric", signature(object = "symmetricMatrix"),
23 : maechler 973 function(object,tol) TRUE)
24 : maechler 1108 setMethod("isSymmetric", signature(object = "triangularMatrix"),
25 : maechler 1174 ## TRUE iff diagonal:
26 :     function(object,tol) isDiagonal(object))
27 : maechler 1189
28 : maechler 1174 if(paste(R.version$major, R.version$minor, sep=".") < "2.3")
29 :     ## need a "matrix" method as in R 2.3 and later
30 :     setMethod("isSymmetric", signature(object = "matrix"),
31 : maechler 1189 function(object, tol = 100*.Machine$double.eps, ...)
32 :     {
33 :     ## pretest: is it square?
34 :     d <- dim(object)
35 :     if(d[1] != d[2]) return(FALSE)
36 :     ## for `broken' all.equal in R <= 2.2.x:
37 :     dn <- dimnames(object)
38 :     if(!identical(dn[1], dn[2])) return(FALSE)
39 :     test <-
40 :     if(is.complex(object))
41 :     all.equal.numeric(object, Conj(t(object)), tol = tol, ...)
42 :     else # numeric, character, ..
43 :     all.equal(object, t(object), tol = tol, ...)
44 :     isTRUE(test)
45 :     })
46 : maechler 973
47 : maechler 1174
48 : maechler 1165 setMethod("isTriangular", signature(object = "triangularMatrix"),
49 :     function(object,tol) TRUE)
50 : maechler 1174 setMethod("isTriangular", signature(object = "matrix"),
51 :     .is.triangular)
52 : maechler 1165
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 1174 sparse = NULL)
81 : bates 10 {
82 : maechler 954 sparseDefault <- function(m)
83 : maechler 1174 prod(dim(m)) > 2*sum(as(m, "matrix") != 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 :     if (i.M) {
90 : maechler 1174 sM <- is(data,"sparseMatrix")
91 :     if((sparse && sM) || (!sparse && !sM))
92 :     return(data)
93 :     ## else : convert dense <-> sparse -> at end
94 : maechler 954 }
95 :     else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
96 : maechler 698 if (missing(nrow))
97 :     nrow <- ceiling(length(data)/ncol)
98 :     else if (missing(ncol))
99 :     ncol <- ceiling(length(data)/nrow)
100 : maechler 954 data <- .Internal(matrix(data, nrow, ncol, byrow))
101 : maechler 1174 if(is.null(sparse))
102 :     sparse <- sparseDefault(data)
103 : maechler 954 dimnames(data) <- dimnames
104 : maechler 1189 } else if (!is.null(dimnames))
105 :     dimnames(data) <- dimnames
106 : maechler 954
107 :     ## 'data' is now a "matrix" or "Matrix"
108 : maechler 1174
109 :     ## check for symmetric / triangular / diagonal :
110 :     isSym <- isSymmetric(data)
111 :     if((isTri <- !isSym))
112 :     isTri <- isTriangular(data)
113 :     isDiag <- isSym # cannot be diagonal if it isn't symmetric
114 :     if(isDiag)
115 :     isDiag <- isDiagonal(data)
116 :    
117 : maechler 965 ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
118 : maechler 1174
119 :     ## Find proper matrix class 'cl'
120 :     cl <-
121 :     if(isDiag)
122 :     "diagonalMatrix" # -> will automatically check for type
123 :     else {
124 :     ## consider it's type
125 :     ctype <-
126 :     if(is(data,"Matrix")) class(data)
127 :     else {
128 :     if("complex" == (ctype <- typeof(data)))
129 :     "z" else ctype
130 :     }
131 :     ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
132 :     if(ctype == "z")
133 :     stop("complex matrices not yet implemented in Matrix package")
134 :     if(ctype == "i") {
135 :     warning("integer matrices not yet implemented in 'Matrix'; ",
136 :     "using 'double' ones'")
137 :     ctype <- "d"
138 :     }
139 :     paste(ctype,
140 :     if(sparse) {
141 :     if(isSym) "sCMatrix" else
142 :     if(isTri) "tCMatrix" else "gCMatrix"
143 :     } else { ## dense
144 :     if(isSym) "syMatrix" else
145 :     if(isTri) "trMatrix" else "geMatrix"
146 :     }, sep="")
147 :     }
148 :    
149 :     ## Now coerce and return
150 :     as(data, cl)
151 : bates 10 }
152 :    
153 : bates 683 ## Methods for operations where one argument is numeric
154 : maechler 512
155 : maechler 698 ## Using as.matrix() and rbind()
156 :     ## in order to get dimnames from names {at least potentially}:
157 :    
158 : bates 683 setMethod("%*%", signature(x = "Matrix", y = "numeric"),
159 : maechler 698 function(x, y) callGeneric(x, as.matrix(y)))
160 : bates 683
161 :     setMethod("%*%", signature(x = "numeric", y = "Matrix"),
162 : maechler 698 function(x, y) callGeneric(rbind(x), y))
163 : bates 683
164 :     setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
165 : maechler 698 function(x, y = NULL) callGeneric(x, as.matrix(y)))
166 : bates 683
167 :     setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
168 : maechler 698 function(x, y = NULL) callGeneric(rbind(x), y))
169 : bates 683
170 :     setMethod("solve", signature(a = "Matrix", b = "numeric"),
171 : maechler 698 function(a, b, ...) callGeneric(a, as.matrix(b)))
172 : maechler 848
173 : maechler 925 ## bail-out methods in order to get better error messages
174 :     setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
175 :     function (x, y)
176 :     stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
177 :     class(x), class(y))))
178 : maechler 946
179 : maechler 925 setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
180 : maechler 946 function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
181 : maechler 956 setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
182 :     function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
183 : maechler 925
184 : maechler 956 ## There are special sparse methods; this is a "fall back":
185 :     setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
186 :     FUN = "ANY", make.dimnames = "ANY"),
187 :     function(X, Y, FUN, make.dimnames, ...) {
188 :     X <- as(X, "matrix") ; Matrix(callGeneric()) })
189 :     setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
190 :     FUN = "ANY", make.dimnames = "ANY"),
191 :     function(X, Y, FUN, make.dimnames, ...) {
192 :     Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
193 :    
194 :    
195 : maechler 946 setMethod("t", signature(x = "Matrix"),
196 :     function(x) .bail.out.1(.Generic, class(x)))
197 : maechler 925
198 : maechler 956 ## Group Methods
199 :     setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
200 :     ## "fallback":
201 :     setMethod("-", signature(e1 = "Matrix", e2 = "missing"),
202 :     function(e1) {
203 :     warning("inefficient method used for \"- e1\"")
204 :     0-e1
205 :     })
206 :    
207 :     ## bail-outs:
208 : maechler 946 setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),
209 : maechler 954 function(e1, e2) {
210 :     d <- dimCheck(e1,e2)
211 :     .bail.out.2(.Generic, class(e1), class(e2))
212 :     })
213 : maechler 946 setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),
214 :     function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
215 :     setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),
216 :     function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
217 :    
218 :    
219 :    
220 : maechler 871 ### --------------------------------------------------------------------------
221 :     ###
222 :     ### Subsetting "[" and
223 :     ### SubAssign "[<-" : The "missing" cases can be dealt with here, "at the top":
224 : maechler 868
225 : maechler 886 ## Using "index" for indices should allow
226 : maechler 875 ## integer (numeric), logical, or character (names!) indices :
227 :    
228 : maechler 868 ## "x[]":
229 :     setMethod("[", signature(x = "Matrix",
230 :     i = "missing", j = "missing", drop = "ANY"),
231 :     function (x, i, j, drop) x)
232 : maechler 1225
233 : maechler 868 ## missing 'drop' --> 'drop = TRUE'
234 :     ## -----------
235 :     ## select rows
236 : maechler 886 setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
237 : maechler 868 drop = "missing"),
238 :     function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))
239 :     ## select columns
240 : maechler 886 setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
241 : maechler 868 drop = "missing"),
242 :     function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))
243 : maechler 886 setMethod("[", signature(x = "Matrix", i = "index", j = "index",
244 : maechler 868 drop = "missing"),
245 :     function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))
246 :    
247 : maechler 875 ## bail out if any of (i,j,drop) is "non-sense"
248 :     setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
249 :     function(x,i,j, drop)
250 :     stop("invalid or not-yet-implemented 'Matrix' subsetting"))
251 :    
252 : maechler 1225 ## "logical *vector* indexing, such as M [ M >= 10 ] :
253 :     setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
254 :     drop = "ANY"),
255 :     function (x, i, j, drop) {
256 :     as(x, geClass(x))@x[as.vector(i)]
257 :     # -> error when lengths don't match
258 :     })
259 :    
260 :     setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
261 :     drop = "ANY"),
262 :     function (x, i, j, drop) as(x, geClass(x))@x[i])
263 :    
264 :    
265 : maechler 868 ## "FIXME:"
266 :     ## How can we get at A[ ij ] where ij is (i,j) 2-column matrix?
267 :     ## and A[ LL ] where LL is a logical *vector*
268 : maechler 886 ## -> [.data.frame uses nargs() - can we do this in the *generic* ?
269 : maechler 868
270 :    
271 : maechler 871 ### "[<-" : -----------------
272 : maechler 868
273 : maechler 871 ## x[] <- value :
274 :     setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
275 : maechler 1189 value = "ANY"),## double/logical/...
276 :     function (x, value) {
277 :     x@x <- value
278 :     validObject(x)# check if type and lengths above match
279 :     x
280 :     })
281 : maechler 871
282 : maechler 1189 ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
283 :     ## (ANY,ANY,ANY) is used when no `real method' is implemented :
284 : maechler 871 setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
285 :     value = "ANY"),
286 : maechler 1189 function (x, i, j, value) {
287 :     if(!is.atomic(value))
288 :     stop("RHS 'value' must match matrix class ", class(x))
289 :     else stop("not-yet-implemented 'Matrix[<-' method")
290 :     })
291 : maechler 871
292 :    
293 :    
294 : maechler 908 ## NOTE: the following only works for R 2.2.x (and later) ---
295 :     ## ---- *and* 'Matrix' must have been *installed* by R >= 2.2.x
296 : maechler 875
297 : maechler 908 if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {
298 :    
299 :     ## The trivial methods :
300 :     setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
301 :     function(x, y) x)
302 :     setMethod("cbind2", signature(x = "Matrix", y = "missing"),
303 :     function(x, y) x)
304 :     setMethod("cbind2", signature(x = "NULL", y="Matrix"),
305 :     function(x, y) x)
306 :    
307 : maechler 925 setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
308 :     function(x, y) x)
309 :     setMethod("rbind2", signature(x = "Matrix", y = "missing"),
310 :     function(x, y) x)
311 :     setMethod("rbind2", signature(x = "NULL", y="Matrix"),
312 :     function(x, y) x)
313 :    
314 : maechler 908 ## Makes sure one gets x decent error message for the unimplemented cases:
315 :     setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
316 :     function(x, y) {
317 :     rowCheck(x,y)
318 :     stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
319 :     class(x), class(y)))
320 :     })
321 :    
322 : maechler 956 ## Use a working fall back {particularly useful for sparse}:
323 :     ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
324 : maechler 908 setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
325 :     function(x, y) {
326 :     colCheck(x,y)
327 : maechler 956 t(cbind2(t(x), t(y)))
328 : maechler 908 })
329 : maechler 956
330 : maechler 908 }## R-2.2.x and newer

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