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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 : bates 1460
35 : mmaechler 3018 ## for historical i.e. backcompatibility reasons ..
36 : bates 1460 setAs("matrix", "dgCMatrix",
37 :     function(from) {
38 :     storage.mode(from) <- "double"
39 :     .Call(dense_to_Csparse, from)
40 :     })
41 :    
42 :     setAs("numeric", "CsparseMatrix",
43 :     function(from)
44 :     .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
45 :    
46 : maechler 1391 setMethod("as.numeric", signature(x = "ddenseMatrix"),
47 :     function(x, ...) as(x, "dgeMatrix")@x)
48 :    
49 : maechler 792 ## -- see also ./Matrix.R e.g., for a show() method
50 :    
51 : bates 686 ## These methods are the 'fallback' methods for all dense numeric
52 : maechler 792 ## matrices in that they simply coerce the ddenseMatrix to a
53 :     ## dgeMatrix. Methods for special forms override these.
54 : bates 686
55 :     setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
56 : maechler 2123 function(x, type, ...) norm(as(x, "dgeMatrix")))
57 : bates 686
58 :     setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
59 : maechler 2123 function(x, type, ...) norm(as(x, "dgeMatrix"), type))
60 : bates 686
61 : maechler 2158 setMethod("rcond", signature(x = "ddenseMatrix", norm = "missing"),
62 :     function(x, norm, ...) rcond(as(x, "dgeMatrix"), ...))
63 : bates 686
64 : maechler 2158 setMethod("rcond", signature(x = "ddenseMatrix", norm = "character"),
65 :     function(x, norm, ...) rcond(as(x, "dgeMatrix"), norm, ...))
66 : bates 686
67 : maechler 946 ## Not really useful; now require *identical* class for result:
68 :     ## setMethod("t", signature(x = "ddenseMatrix"),
69 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
70 : bates 686
71 : mmaechler 2811 ## "diag" --> specific methods for dge, dtr,dtp, dsy,dsp
72 : bates 686
73 : maechler 1945 setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
74 : maechler 2123 function(a, b, ...) solve(as(a, "dgeMatrix")))
75 : bates 686
76 : mmaechler 2472 for(.b in c("Matrix","ANY")) ## << against ambiguity notes
77 :     setMethod("solve", signature(a = "ddenseMatrix", b = .b),
78 :     function(a, b, ...) solve(as(a, "dgeMatrix"), b))
79 :     for(.b in c("matrix","numeric")) ## << against ambiguity notes
80 :     setMethod("solve", signature(a = "ddenseMatrix", b = .b),
81 :     function(a, b, ...) solve(as(a, "dgeMatrix"), Matrix(b)))
82 : mmaechler 2898 rm(.b)
83 : bates 686
84 :     setMethod("lu", signature(x = "ddenseMatrix"),
85 : mmaechler 2898 function(x, ...)
86 :     .set.factors(x, "LU", lu(as(x, "dgeMatrix"), ...)))
87 : bates 686
88 : maechler 2154 setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
89 : maechler 1654
90 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
91 : maechler 2123 function(x, logarithm, ...) determinant(as(x, "dgeMatrix")))
92 : bates 686
93 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
94 : maechler 2123 function(x, logarithm, ...)
95 :     determinant(as(x, "dgeMatrix"), logarithm))
96 : bates 686
97 : maechler 954 ## now done for "dMatrix":
98 :     ## setMethod("expm", signature(x = "ddenseMatrix"),
99 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
100 : bates 686
101 : maechler 1331
102 : maechler 2112 .trilDense <- function(x, k = 0, ...) {
103 :     k <- as.integer(k[1])
104 : maechler 2115 d <- dim(x)
105 :     stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
106 : maechler 2112 ## returns "lower triangular" if k <= 0 && sqr
107 : maechler 2115 .Call(dense_band, x, -d[1], k)
108 : maechler 2112 }
109 : bates 1453 ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
110 :     ## for triangular ["dtr" and "dtp"]
111 : maechler 2115 setMethod("tril", "denseMatrix", .trilDense)
112 :     setMethod("tril", "matrix", .trilDense)
113 : bates 1453
114 : maechler 2112 .triuDense <- function(x, k = 0, ...) {
115 :     k <- as.integer(k[1])
116 : maechler 2115 d <- dim(x)
117 :     stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
118 : maechler 2112 ## returns "upper triangular" if k >= 0
119 : maechler 2115 .Call(dense_band, x, k, d[2])
120 : maechler 2112 }
121 : maechler 2115 setMethod("triu", "denseMatrix", .triuDense)
122 :     setMethod("triu", "matrix", .triuDense)
123 : bates 1453
124 : maechler 2112 .bandDense <- function(x, k1, k2, ...) {
125 :     k1 <- as.integer(k1[1])
126 :     k2 <- as.integer(k2[1])
127 : mmaechler 2346 dd <- dim(x)
128 :     sqr <- dd[1] == dd[2]
129 :     stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
130 : maechler 2115 r <- .Call(dense_band, x, k1, k2)
131 :     if (sqr && k1 < 0 && k1 == -k2 && isSymmetric(x)) ## symmetric
132 :     forceSymmetric(r)
133 : maechler 2112 else
134 :     r
135 :     }
136 : maechler 2115 setMethod("band", "denseMatrix", .bandDense)
137 :     setMethod("band", "matrix", .bandDense)
138 : maechler 2112
139 :    
140 :     setMethod("symmpart", signature(x = "ddenseMatrix"),
141 :     function(x) .Call(ddense_symmpart, x))
142 :     setMethod("skewpart", signature(x = "ddenseMatrix"),
143 :     function(x) .Call(ddense_skewpart, x))
144 :    
145 : mmaechler 2814
146 :     setMethod("is.finite", signature(x = "dgeMatrix"),
147 :     function(x) {
148 :     if(all(ifin <- is.finite(x@x)))
149 :     allTrueMat(x)
150 :     else if(any(ifin)) {
151 :     r <- as(x, "lMatrix") #-> logical x-slot
152 :     r@x <- ifin
153 :     as(r, "nMatrix")
154 :     }
155 :     else is.na_nsp(x)
156 :     })
157 :    
158 :     ## TODO? -- rather methods for specific subclasses of ddenseMatrix
159 :     setMethod("is.finite", signature(x = "ddenseMatrix"),
160 :     function(x) {
161 :     if(all(ifin <- is.finite(x@x))) return(allTrueMat(x))
162 :     ## *NOT* dge, i.e., either triangular or symmetric
163 :     ## (possibly packed): has finite 0-triangle
164 :     cdx <- getClassDef(class(x))
165 :    
166 :     r <- new(if(extends(cdx,"symmetricMatrix"))"nsyMatrix" else "ngeMatrix")
167 :     r@Dim <- (d <- x@Dim)
168 :     r@Dimnames <- x@Dimnames
169 :     isPacked <- (le <- prod(d)) > length(ifin)
170 :     r@x <- rep.int(TRUE, le)
171 :     iTr <- indTri(d[1], upper= x@uplo == "U", diag= TRUE)
172 :     if(isPacked) { ## x@x is "usable"
173 :     r@x[iTr] <- ifin
174 :     } else {
175 :     r@x[iTr] <- ifin[iTr]
176 :     }
177 :     r
178 :     })
179 :    
180 :     setMethod("is.infinite", signature(x = "ddenseMatrix"),
181 :     function(x) {
182 :     if(any((isInf <- is.infinite(x@x)))) {
183 :     r <- as(x, "lMatrix")#-> logical x-slot; 0 |--> FALSE
184 :     r@x <- isInf
185 :     as(r, "nMatrix")# often sparse .. better way?
186 :     }
187 :     else is.na_nsp(x)
188 :     })

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