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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2225, Sat Jul 19 09:44:48 2008 UTC
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1    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
4            stumbled upon by Michael H.
5    
6            * tests/validObj.R: testing the bug-fix
7    
8            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
9            versions.
10    
11            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
12            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
13    
14            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
15              AS_CHM_SP() which includes diagU2N.
16    
17            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
18            adapt to 3 arguments.
19    
20    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
21    
22            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
23              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
24              new solve method
25            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
26              Csparse_diagU2N functionality into Matrix_as_cs
27    
28    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
31              vignette
32            * [r2214] R/AllGeneric.R: cosmetic
33            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
34    
35    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
36    
37            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
38              argument with default TRUE
39            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
40              Csparse_diagU2N
41            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
42              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
43              parent array; new solve method for signature(a = "dtCMatrix", b =
44              "sparseMatrix")
45    
46    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/diagMatrix.R (.bdiag): also keep triangular
49            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
50              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
51              bdiag() improvements of last week
52    
53    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
54    
55            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
56              messages
57    
58    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
61            symmetric- or nsparse-Matrix, also fixing the bug introduced with
62            the new version (.999375-10).
63    
64            * tests/Simple.R: regression test for the bugs.
65    
66    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/sparseVector.R (spV2M): fix for "isparseVector".
69            Further, fix <diag> -> <sparseVector> coercion
70            (repSpV): add rep(<sparseVector>, .) method
71    
72            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
73            use as.vector(.).
74    
75            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
76    
77            * R/AllClass.R: new (hidden) class union "scarceMatrix"
78            * R/AllClass.R: sparseVector: add prototype
79    
80            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
81            Kasper Kristensen
82    
83    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * tests/other-pkgs.R: add more interesting Matrix -> graph
86    
87    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
90            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
91    
92    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION: release 0.999375-10 to CRAN
95    
96            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
97            .bdiag().
98            * man/bdiag.Rd: update, including test.
99    
100    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/Simple.R: add minimal bdiag() checks
103    
104            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
105              factor out the Tsparse - internal computation into new .bdiag()
106    
107    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/nsparseMatrix.R: specific fast all() and any() methods.
110    
111            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
112            when trying to produce too large result.
113    
114            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
115            very large matrices.
116    
117            * R/sparseMatrix.R (printSpMatrix2): new function, used by
118            show(<sparseMatrix>).
119    
120            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
121    
122    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/Mutils.c (m_encodeInd, m_encodeInd2):
125            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
126    
127            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
128            big matrices): -> 2nd argument 'di' instead of 'nr' !
129    
130    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/dtCMatrix.R: faster dgC* -> dtC* method
133            * tests/Simple.R: (hence removed "FIXME")
134    
135            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
136            which can be be turned off for possible speed gains.
137    
138    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
141    
142            * R/not.R: fix !<ldiMatrix>
143            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
144    
145            * R/diagMatrix.R (Ops): fix one-off thinko in
146            <diagonal> o <numeric> methods
147    
148            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
149    
150    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
153            * tests/Simple.R: testing the above
154    
155    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
158    
159    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
162            * NAMESPACE (unname): finally exported
163    
164    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Auxiliaries.R (cholMat): possibly keep packed
167    
168            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
169            for R < 2.7.0.
170    
171            * R/Tsparse.R ([): for triangularMatrix, check if result may be
172            triangular.
173            * tests/indexing.R: regression test
174    
175    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
178            * R/Ops.R: more methods, for lMatrix/nMatrix
179    
180    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/expm.R: new file for all expm() methods; notably new ones for
183            diagonal*, triangular*, symmetric* and also simple "matrix".
184    
185    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
188    
189            * inst/test-tools.R (assert.EQ.mat): better message when not equal
190    
191            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
192    
193            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
194            [dl]denseMatrix {identical slots; but more logical method dispatch}
195    
196    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
199    
200            * R/diagMatrix.R (determinant): method
201    
202    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
205    
206            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
207    
208            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
209            its diagonal
210    
211    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
214    
215            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
216    
217            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
218    
219            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
220    
221    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
224    
225            * R/Ops.R (.do.Logic.lsparse): fix NA case
226    
227            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
228    
229            * R/Auxiliaries.R (nnzero): fix special cases, using
230            * R/Auxiliaries.R (indDiag): new utility
231            * R/Auxiliaries.R (indTri): new argument 'diag'
232    
233            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
234    
235    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
238    
239            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
240            ".tCMatrix" triangular matrix.
241    
242            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
243            'clx' can be class *or* class representation.
244            (nnzSparse): new.
245            (non0ind): new 'xtendSymm' argument; used in
246            * R/Ops.R:
247    
248            * R/pMatrix.R: more efficient determinant() method
249    
250    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
253            * [disactivated] NAMESPACE: export(det)
254    
255            * R/diagMatrix.R (mkDiag): new substitute for diag()
256    
257            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
258            (as0, as1): new utility.
259    
260            * R/Csparse.R (diag, band): need diagU2N()
261    
262            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
263    
264            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
265    
266            * R/Ops.R (Compare): fix <nsp> o <nsp> case
267    
268            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
269    
270    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/Auxiliaries.R (signPerm): new utility for
273            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
274    
275            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
276            since we have our own error handler (and can use tryCatch() from R).
277    
278    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
281    
282            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
283            when not positive definite.
284    
285            * R/Auxiliaries.R (asTri): new auxiliary
286            (non0.i): make *much* faster for Tsparse with many non-zero
287            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
288    
289            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
290            test-tools.R , see below
291    
292            * R/dMatrix.R: fix "Summary" method: + diagU2N()
293    
294            * NAMESPACE, R/Matrix.R: add mean() method
295    
296    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
299            cold-hot colors; try *changed* default useAbs = FALSE
300            * man/image-methods.Rd:  nice examples
301    
302    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * inst/test-tools.R (checkMatrix): new function for modularizing part
305            of tstMatrixClass() in tests/Class+Meth.R
306    
307            * R/dsCMatrix.R: coercion from "matrix"
308            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
309    
310            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
311            add test for as(matrix(,0,0), <class>)
312    
313    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
316            work as determinant(matrix(,0,0)).
317    
318            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
319            * man/sparseLU-class.Rd: ditto
320    
321            * R/dgCMatrix.R (determinant): method building on lu()
322            * R/sparseMatrix.R, Matrix.R, ...: ditto
323    
324            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
325    
326    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
329            pattern matrices.
330    
331    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * src/dense.c (dense_to_Csparse): all declarations *before*
334            R_CheckStack(); needed e.g. for ancient gcc 2.96.
335    
336    
337  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
340          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
341    
342            * R/AllClass.R: drop "double" from "atomicVector" class union
343    
344            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
345            * R/dgeMatrix.R: ditto
346    
347          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
348    
349            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
350    
351  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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