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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2237, Fri Jul 25 06:55:42 2008 UTC
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1    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
4            recursion in new test in
5            * tests/matprod.R: testing the above and another solve() case, below
6    
7            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
8            e.g. triangular 'x'.
9    
10            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
11            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
12            correctly with unit-triangular x
13    
14            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
15            instead of not checking diagU.
16    
17            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
18            experiments where diagonalMatrix would extend sparse*.
19    
20    
21    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
24            "x@p[ncol(x)]" instead of length(x@i).
25            * R/Auxiliaries.R (nnzero): ditto
26    
27            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
28            since that fails for over-allocated i.
29    
30            * tests/validObj.R: more testing of over-allocated (i,x) slots
31    
32    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
35            'sort_in_place' and set it to TRUE in call from
36            * src/Csparse.c (Csparse_validate): sort in place, making sure that
37            validObject() continues sort the columns if needed.
38    
39            * tests/validObj.R: now tests that more thoroughly, and
40            * man/CsparseMatrix-class.Rd: documents it.
41    
42    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
45            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
46            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
47            diagU2N().
48    
49            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
50            .spDiagonal() and new .trDiagonal().
51    
52            * R/dtCMatrix.R (solve): make use of .trDiagonal()
53    
54    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
57            stumbled upon by Michael H.
58    
59            * tests/validObj.R: testing the bug-fix
60    
61            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
62            versions.
63    
64            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
65            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
66    
67            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
68              AS_CHM_SP() which includes diagU2N.
69    
70            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
71            adapt to 3 arguments.
72    
73    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
76              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
77              new solve method
78            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
79              Csparse_diagU2N functionality into Matrix_as_cs
80    
81    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
84    
85    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
86    
87            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
88              argument with default TRUE
89            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
90              Csparse_diagU2N
91            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
92              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
93              parent array; new solve method for signature(a = "dtCMatrix", b =
94              "sparseMatrix")
95    
96    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/diagMatrix.R (.bdiag): also keep result triangular
99    
100    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
101    
102            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
103              messages
104    
105    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
108            symmetric- or nsparse-Matrix, also fixing the bug introduced with
109            the new version (.999375-10).
110    
111            * tests/Simple.R: regression test for the bugs.
112    
113    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/sparseVector.R (spV2M): fix for "isparseVector".
116            Further, fix <diag> -> <sparseVector> coercion
117            (repSpV): add rep(<sparseVector>, .) method
118    
119            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
120            use as.vector(.).
121    
122            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
123    
124            * R/AllClass.R: new (hidden) class union "scarceMatrix"
125            * R/AllClass.R: sparseVector: add prototype
126    
127            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
128            Kasper Kristensen
129    
130    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * tests/other-pkgs.R: add more interesting Matrix -> graph
133    
134    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
137            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
138    
139    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * DESCRIPTION: release 0.999375-10 to CRAN
142    
143            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
144            .bdiag().
145            * man/bdiag.Rd: update, including test.
146    
147    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * tests/Simple.R: add minimal bdiag() checks
150    
151            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
152              factor out the Tsparse - internal computation into new .bdiag()
153    
154    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/nsparseMatrix.R: specific fast all() and any() methods.
157    
158            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
159            when trying to produce too large result.
160    
161            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
162            very large matrices.
163    
164            * R/sparseMatrix.R (printSpMatrix2): new function, used by
165            show(<sparseMatrix>).
166    
167            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
168    
169    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * src/Mutils.c (m_encodeInd, m_encodeInd2):
172            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
173    
174            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
175            big matrices): -> 2nd argument 'di' instead of 'nr' !
176    
177    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/dtCMatrix.R: faster dgC* -> dtC* method
180            * tests/Simple.R: (hence removed "FIXME")
181    
182            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
183            which can be be turned off for possible speed gains.
184    
185    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
188    
189            * R/not.R: fix !<ldiMatrix>
190            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
191    
192            * R/diagMatrix.R (Ops): fix one-off thinko in
193            <diagonal> o <numeric> methods
194    
195            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
196    
197    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
200            * tests/Simple.R: testing the above
201    
202    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
205    
206    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
209            * NAMESPACE (unname): finally exported
210    
211    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Auxiliaries.R (cholMat): possibly keep packed
214    
215            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
216            for R < 2.7.0.
217    
218            * R/Tsparse.R ([): for triangularMatrix, check if result may be
219            triangular.
220            * tests/indexing.R: regression test
221    
222    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
225            * R/Ops.R: more methods, for lMatrix/nMatrix
226    
227    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/expm.R: new file for all expm() methods; notably new ones for
230            diagonal*, triangular*, symmetric* and also simple "matrix".
231    
232    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
235    
236            * inst/test-tools.R (assert.EQ.mat): better message when not equal
237    
238            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
239    
240            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
241            [dl]denseMatrix {identical slots; but more logical method dispatch}
242    
243    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
246    
247            * R/diagMatrix.R (determinant): method
248    
249    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
252    
253            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
254    
255            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
256            its diagonal
257    
258    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
261    
262            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
263    
264            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
265    
266            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
267    
268    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
271    
272            * R/Ops.R (.do.Logic.lsparse): fix NA case
273    
274            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
275    
276            * R/Auxiliaries.R (nnzero): fix special cases, using
277            * R/Auxiliaries.R (indDiag): new utility
278            * R/Auxiliaries.R (indTri): new argument 'diag'
279    
280            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
281    
282    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
285    
286            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
287            ".tCMatrix" triangular matrix.
288    
289            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
290            'clx' can be class *or* class representation.
291            (nnzSparse): new.
292            (non0ind): new 'xtendSymm' argument; used in
293            * R/Ops.R:
294    
295            * R/pMatrix.R: more efficient determinant() method
296    
297    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
300            * [disactivated] NAMESPACE: export(det)
301    
302            * R/diagMatrix.R (mkDiag): new substitute for diag()
303    
304            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
305            (as0, as1): new utility.
306    
307            * R/Csparse.R (diag, band): need diagU2N()
308    
309            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
310    
311            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
312    
313            * R/Ops.R (Compare): fix <nsp> o <nsp> case
314    
315            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
316    
317    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Auxiliaries.R (signPerm): new utility for
320            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
321    
322            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
323            since we have our own error handler (and can use tryCatch() from R).
324    
325    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
328    
329            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
330            when not positive definite.
331    
332            * R/Auxiliaries.R (asTri): new auxiliary
333            (non0.i): make *much* faster for Tsparse with many non-zero
334            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
335    
336            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
337            test-tools.R , see below
338    
339            * R/dMatrix.R: fix "Summary" method: + diagU2N()
340    
341            * NAMESPACE, R/Matrix.R: add mean() method
342    
343    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
346            cold-hot colors; try *changed* default useAbs = FALSE
347            * man/image-methods.Rd:  nice examples
348    
349    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * inst/test-tools.R (checkMatrix): new function for modularizing part
352            of tstMatrixClass() in tests/Class+Meth.R
353    
354            * R/dsCMatrix.R: coercion from "matrix"
355            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
356    
357            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
358            add test for as(matrix(,0,0), <class>)
359    
360    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
363            work as determinant(matrix(,0,0)).
364    
365            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
366            * man/sparseLU-class.Rd: ditto
367    
368            * R/dgCMatrix.R (determinant): method building on lu()
369            * R/sparseMatrix.R, Matrix.R, ...: ditto
370    
371            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
372    
373    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
376            pattern matrices.
377    
378    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * src/dense.c (dense_to_Csparse): all declarations *before*
381            R_CheckStack(); needed e.g. for ancient gcc 2.96.
382    
383    
384  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
387          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
388    
389            * R/AllClass.R: drop "double" from "atomicVector" class union
390    
391            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
392            * R/dgeMatrix.R: ditto
393    
394          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
395    
396            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
397    
398  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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