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

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1 : bates 686 ### Define Methods that can be inherited for all subclasses
2 :    
3 : maechler 1447 ## This replaces many "d..Matrix" -> "dgeMatrix" ones
4 :     ## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed
5 :     ## ----- in ../src/Mutils.c
6 : bates 1460
7 : maechler 1447 setAs("ddenseMatrix", "dgeMatrix",
8 : mmaechler 2199 function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
9 : maechler 1575
10 : mmaechler 2199 setAs("ddenseMatrix", "matrix",
11 :     function(from) as(as(from, "dgeMatrix"), "matrix"))
12 : maechler 2112
13 : maechler 1447 ## d(ouble) to l(ogical):
14 : maechler 1747 setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
15 :     setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
16 :     setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
17 :     setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
18 :     setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))
19 : maechler 956
20 : mmaechler 2551 if(FALSE) ## FIXME, this fails for ("dtpMatrix" -> "CsparseMatrix") where .dense2C() works
21 : bates 1460 setAs("ddenseMatrix", "CsparseMatrix",
22 :     function(from) {
23 : maechler 1799 if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
24 :     as_Csparse(from)
25 :     else .Call(dense_to_Csparse, from)
26 : bates 1460 })
27 :    
28 :     ## special case
29 :     setAs("dgeMatrix", "dgCMatrix",
30 :     function(from) .Call(dense_to_Csparse, from))
31 :    
32 :     setAs("matrix", "CsparseMatrix",
33 : maechler 2115 function(from) .Call(dense_to_Csparse, from))
34 :     ## function(from) {
35 :     ## if(is.numeric(from))
36 :     ## .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
37 :     ## else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
38 :     ## as(Matrix(from, sparse=TRUE), "CsparseMatrix")
39 :     ## else stop('not-yet-implemented coercion to "CsparseMatrix"')
40 :     ## })
41 : bates 1460
42 : maechler 1618
43 : bates 1460 ## special case needed in the Matrix function
44 :     setAs("matrix", "dgCMatrix",
45 :     function(from) {
46 :     storage.mode(from) <- "double"
47 :     .Call(dense_to_Csparse, from)
48 :     })
49 :    
50 :     setAs("numeric", "CsparseMatrix",
51 :     function(from)
52 :     .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
53 :    
54 : maechler 1391 setMethod("as.numeric", signature(x = "ddenseMatrix"),
55 :     function(x, ...) as(x, "dgeMatrix")@x)
56 :    
57 : maechler 792 ## -- see also ./Matrix.R e.g., for a show() method
58 :    
59 : bates 686 ## These methods are the 'fallback' methods for all dense numeric
60 : maechler 792 ## matrices in that they simply coerce the ddenseMatrix to a
61 :     ## dgeMatrix. Methods for special forms override these.
62 : bates 686
63 :     setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
64 : maechler 2123 function(x, type, ...) norm(as(x, "dgeMatrix")))
65 : bates 686
66 :     setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
67 : maechler 2123 function(x, type, ...) norm(as(x, "dgeMatrix"), type))
68 : bates 686
69 : maechler 2158 setMethod("rcond", signature(x = "ddenseMatrix", norm = "missing"),
70 :     function(x, norm, ...) rcond(as(x, "dgeMatrix"), ...))
71 : bates 686
72 : maechler 2158 setMethod("rcond", signature(x = "ddenseMatrix", norm = "character"),
73 :     function(x, norm, ...) rcond(as(x, "dgeMatrix"), norm, ...))
74 : bates 686
75 : maechler 946 ## Not really useful; now require *identical* class for result:
76 :     ## setMethod("t", signature(x = "ddenseMatrix"),
77 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
78 : bates 686
79 : mmaechler 2811 ## "diag" --> specific methods for dge, dtr,dtp, dsy,dsp
80 : bates 686
81 : maechler 1945 setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
82 : maechler 2123 function(a, b, ...) solve(as(a, "dgeMatrix")))
83 : bates 686
84 : mmaechler 2472 for(.b in c("Matrix","ANY")) ## << against ambiguity notes
85 :     setMethod("solve", signature(a = "ddenseMatrix", b = .b),
86 :     function(a, b, ...) solve(as(a, "dgeMatrix"), b))
87 :     for(.b in c("matrix","numeric")) ## << against ambiguity notes
88 :     setMethod("solve", signature(a = "ddenseMatrix", b = .b),
89 :     function(a, b, ...) solve(as(a, "dgeMatrix"), Matrix(b)))
90 : mmaechler 2898 rm(.b)
91 : bates 686
92 :     setMethod("lu", signature(x = "ddenseMatrix"),
93 : mmaechler 2898 function(x, ...)
94 :     .set.factors(x, "LU", lu(as(x, "dgeMatrix"), ...)))
95 : bates 686
96 : maechler 2154 setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
97 : maechler 1654
98 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
99 : maechler 2123 function(x, logarithm, ...) determinant(as(x, "dgeMatrix")))
100 : bates 686
101 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
102 : maechler 2123 function(x, logarithm, ...)
103 :     determinant(as(x, "dgeMatrix"), logarithm))
104 : bates 686
105 : maechler 954 ## now done for "dMatrix":
106 :     ## setMethod("expm", signature(x = "ddenseMatrix"),
107 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
108 : bates 686
109 : maechler 1331
110 : maechler 2112 .trilDense <- function(x, k = 0, ...) {
111 :     k <- as.integer(k[1])
112 : maechler 2115 d <- dim(x)
113 :     stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
114 : maechler 2112 ## returns "lower triangular" if k <= 0 && sqr
115 : maechler 2115 .Call(dense_band, x, -d[1], k)
116 : maechler 2112 }
117 : bates 1453 ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
118 :     ## for triangular ["dtr" and "dtp"]
119 : maechler 2115 setMethod("tril", "denseMatrix", .trilDense)
120 :     setMethod("tril", "matrix", .trilDense)
121 : bates 1453
122 : maechler 2112 .triuDense <- function(x, k = 0, ...) {
123 :     k <- as.integer(k[1])
124 : maechler 2115 d <- dim(x)
125 :     stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
126 : maechler 2112 ## returns "upper triangular" if k >= 0
127 : maechler 2115 .Call(dense_band, x, k, d[2])
128 : maechler 2112 }
129 : maechler 2115 setMethod("triu", "denseMatrix", .triuDense)
130 :     setMethod("triu", "matrix", .triuDense)
131 : bates 1453
132 : maechler 2112 .bandDense <- function(x, k1, k2, ...) {
133 :     k1 <- as.integer(k1[1])
134 :     k2 <- as.integer(k2[1])
135 : mmaechler 2346 dd <- dim(x)
136 :     sqr <- dd[1] == dd[2]
137 :     stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
138 : maechler 2115 r <- .Call(dense_band, x, k1, k2)
139 :     if (sqr && k1 < 0 && k1 == -k2 && isSymmetric(x)) ## symmetric
140 :     forceSymmetric(r)
141 : maechler 2112 else
142 :     r
143 :     }
144 : maechler 2115 setMethod("band", "denseMatrix", .bandDense)
145 :     setMethod("band", "matrix", .bandDense)
146 : maechler 2112
147 :    
148 :     setMethod("symmpart", signature(x = "ddenseMatrix"),
149 :     function(x) .Call(ddense_symmpart, x))
150 :     setMethod("skewpart", signature(x = "ddenseMatrix"),
151 :     function(x) .Call(ddense_skewpart, x))
152 :    
153 : mmaechler 2814
154 :     setMethod("is.finite", signature(x = "dgeMatrix"),
155 :     function(x) {
156 :     if(all(ifin <- is.finite(x@x)))
157 :     allTrueMat(x)
158 :     else if(any(ifin)) {
159 :     r <- as(x, "lMatrix") #-> logical x-slot
160 :     r@x <- ifin
161 :     as(r, "nMatrix")
162 :     }
163 :     else is.na_nsp(x)
164 :     })
165 :    
166 :     ## TODO? -- rather methods for specific subclasses of ddenseMatrix
167 :     setMethod("is.finite", signature(x = "ddenseMatrix"),
168 :     function(x) {
169 :     if(all(ifin <- is.finite(x@x))) return(allTrueMat(x))
170 :     ## *NOT* dge, i.e., either triangular or symmetric
171 :     ## (possibly packed): has finite 0-triangle
172 :     cdx <- getClassDef(class(x))
173 :    
174 :     r <- new(if(extends(cdx,"symmetricMatrix"))"nsyMatrix" else "ngeMatrix")
175 :     r@Dim <- (d <- x@Dim)
176 :     r@Dimnames <- x@Dimnames
177 :     isPacked <- (le <- prod(d)) > length(ifin)
178 :     r@x <- rep.int(TRUE, le)
179 :     iTr <- indTri(d[1], upper= x@uplo == "U", diag= TRUE)
180 :     if(isPacked) { ## x@x is "usable"
181 :     r@x[iTr] <- ifin
182 :     } else {
183 :     r@x[iTr] <- ifin[iTr]
184 :     }
185 :     r
186 :     })
187 :    
188 :     setMethod("is.infinite", signature(x = "ddenseMatrix"),
189 :     function(x) {
190 :     if(any((isInf <- is.infinite(x@x)))) {
191 :     r <- as(x, "lMatrix")#-> logical x-slot; 0 |--> FALSE
192 :     r@x <- isInf
193 :     as(r, "nMatrix")# often sparse .. better way?
194 :     }
195 :     else is.na_nsp(x)
196 :     })

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