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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2209, Mon Jul 14 19:39:39 2008 UTC
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1    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (.bdiag): also keep triangular
4    
5    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
8            symmetric- or nsparse-Matrix, also fixing the bug introduced with
9            the new version (.999375-10).
10    
11            * tests/Simple.R: regression test for the bugs.
12    
13    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/sparseVector.R (spV2M): fix for "isparseVector".
16            Further, fix <diag> -> <sparseVector> coercion
17            (repSpV): add rep(<sparseVector>, .) method
18    
19            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
20            use as.vector(.).
21    
22            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
23    
24            * R/AllClass.R: new (hidden) class union "scarceMatrix"
25            * R/AllClass.R: sparseVector: add prototype
26    
27            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
28            Kasper Kristensen
29    
30    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * tests/other-pkgs.R: add more interesting Matrix -> graph
33    
34    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
37            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
38    
39    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * DESCRIPTION: release 0.999375-10 to CRAN
42    
43            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
44            .bdiag().
45            * man/bdiag.Rd: update, including test.
46    
47    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * tests/Simple.R: add minimal bdiag() checks
50    
51            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
52              factor out the Tsparse - internal computation into new .bdiag()
53    
54    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/nsparseMatrix.R: specific fast all() and any() methods.
57    
58            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
59            when trying to produce too large result.
60    
61            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
62            very large matrices.
63    
64            * R/sparseMatrix.R (printSpMatrix2): new function, used by
65            show(<sparseMatrix>).
66    
67            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
68    
69    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * src/Mutils.c (m_encodeInd, m_encodeInd2):
72            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
73    
74            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
75            big matrices): -> 2nd argument 'di' instead of 'nr' !
76    
77    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/dtCMatrix.R: faster dgC* -> dtC* method
80            * tests/Simple.R: (hence removed "FIXME")
81    
82            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
83            which can be be turned off for possible speed gains.
84    
85    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
88    
89            * R/not.R: fix !<ldiMatrix>
90            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
91    
92            * R/diagMatrix.R (Ops): fix one-off thinko in
93            <diagonal> o <numeric> methods
94    
95            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
96    
97    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
100            * tests/Simple.R: testing the above
101    
102    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
105    
106    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
109            * NAMESPACE (unname): finally exported
110    
111    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Auxiliaries.R (cholMat): possibly keep packed
114    
115            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
116            for R < 2.7.0.
117    
118            * R/Tsparse.R ([): for triangularMatrix, check if result may be
119            triangular.
120            * tests/indexing.R: regression test
121    
122    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
125            * R/Ops.R: more methods, for lMatrix/nMatrix
126    
127    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/expm.R: new file for all expm() methods; notably new ones for
130            diagonal*, triangular*, symmetric* and also simple "matrix".
131    
132    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
135    
136            * inst/test-tools.R (assert.EQ.mat): better message when not equal
137    
138            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
139    
140            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
141            [dl]denseMatrix {identical slots; but more logical method dispatch}
142    
143    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
146    
147            * R/diagMatrix.R (determinant): method
148    
149    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
152    
153            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
154    
155            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
156            its diagonal
157    
158    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
161    
162            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
163    
164            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
165    
166            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
167    
168    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
171    
172            * R/Ops.R (.do.Logic.lsparse): fix NA case
173    
174            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
175    
176            * R/Auxiliaries.R (nnzero): fix special cases, using
177            * R/Auxiliaries.R (indDiag): new utility
178            * R/Auxiliaries.R (indTri): new argument 'diag'
179    
180            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
181    
182    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
185    
186            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
187            ".tCMatrix" triangular matrix.
188    
189            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
190            'clx' can be class *or* class representation.
191            (nnzSparse): new.
192            (non0ind): new 'xtendSymm' argument; used in
193            * R/Ops.R:
194    
195            * R/pMatrix.R: more efficient determinant() method
196    
197    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
200            * [disactivated] NAMESPACE: export(det)
201    
202            * R/diagMatrix.R (mkDiag): new substitute for diag()
203    
204            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
205            (as0, as1): new utility.
206    
207            * R/Csparse.R (diag, band): need diagU2N()
208    
209            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
210    
211            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
212    
213            * R/Ops.R (Compare): fix <nsp> o <nsp> case
214    
215            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
216    
217    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (signPerm): new utility for
220            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
221    
222            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
223            since we have our own error handler (and can use tryCatch() from R).
224    
225    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
228    
229            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
230            when not positive definite.
231    
232            * R/Auxiliaries.R (asTri): new auxiliary
233            (non0.i): make *much* faster for Tsparse with many non-zero
234            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
235    
236            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
237            test-tools.R , see below
238    
239            * R/dMatrix.R: fix "Summary" method: + diagU2N()
240    
241            * NAMESPACE, R/Matrix.R: add mean() method
242    
243    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
246            cold-hot colors; try *changed* default useAbs = FALSE
247            * man/image-methods.Rd:  nice examples
248    
249    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * inst/test-tools.R (checkMatrix): new function for modularizing part
252            of tstMatrixClass() in tests/Class+Meth.R
253    
254            * R/dsCMatrix.R: coercion from "matrix"
255            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
256    
257            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
258            add test for as(matrix(,0,0), <class>)
259    
260    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
263            work as determinant(matrix(,0,0)).
264    
265            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
266            * man/sparseLU-class.Rd: ditto
267    
268            * R/dgCMatrix.R (determinant): method building on lu()
269            * R/sparseMatrix.R, Matrix.R, ...: ditto
270    
271            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
272    
273    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
276            pattern matrices.
277    
278    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * src/dense.c (dense_to_Csparse): all declarations *before*
281            R_CheckStack(); needed e.g. for ancient gcc 2.96.
282    
283    
284  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
287          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
288    
289            * R/AllClass.R: drop "double" from "atomicVector" class union
290    
291            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
292            * R/dgeMatrix.R: ditto
293    
294          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
295    
296            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
297    
298  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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