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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2239, Mon Jul 28 19:26:40 2008 UTC
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1    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
4            "denseMatrix".  This renders "scarceMatrix" dispensable and
5            invalidates part of MM's presentations on "space of Matrix
6            classes", but seems cleaner overall.
7    
8            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
9            "sparseMatrix" in method signatures;
10            further, instead of coercing to "sparseMatrix", coerce to
11            "TsparseMatrix" now.
12    
13    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
16            .Call(.)
17            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
18    
19    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
22            recursion in new test in
23            * tests/matprod.R: testing the above and another solve() case, below
24    
25            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
26            e.g. triangular 'x'.
27    
28            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
29            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
30            correctly with unit-triangular x
31    
32            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
33            instead of not checking diagU.
34    
35            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
36            experiments where diagonalMatrix would extend sparse*.
37    
38    
39    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
42            "x@p[ncol(x)]" instead of length(x@i).
43            * R/Auxiliaries.R (nnzero): ditto
44    
45            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
46            since that fails for over-allocated i.
47    
48            * tests/validObj.R: more testing of over-allocated (i,x) slots
49    
50    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
53            'sort_in_place' and set it to TRUE in call from
54            * src/Csparse.c (Csparse_validate): sort in place, making sure that
55            validObject() continues sort the columns if needed.
56    
57            * tests/validObj.R: now tests that more thoroughly, and
58            * man/CsparseMatrix-class.Rd: documents it.
59    
60    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
63            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
64            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
65            diagU2N().
66    
67            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
68            .spDiagonal() and new .trDiagonal().
69    
70            * R/dtCMatrix.R (solve): make use of .trDiagonal()
71    
72    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
75            stumbled upon by Michael H.
76    
77            * tests/validObj.R: testing the bug-fix
78    
79            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
80            versions.
81    
82            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
83            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
84    
85            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
86              AS_CHM_SP() which includes diagU2N.
87    
88            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
89            adapt to 3 arguments.
90    
91    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
92    
93            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
94              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
95              new solve method
96            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
97              Csparse_diagU2N functionality into Matrix_as_cs
98    
99    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
102    
103    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
106              argument with default TRUE
107            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
108              Csparse_diagU2N
109            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
110              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
111              parent array; new solve method for signature(a = "dtCMatrix", b =
112              "sparseMatrix")
113    
114    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/diagMatrix.R (.bdiag): also keep result triangular
117    
118    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
119    
120            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
121              messages
122    
123    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
126            symmetric- or nsparse-Matrix, also fixing the bug introduced with
127            the new version (.999375-10).
128    
129            * tests/Simple.R: regression test for the bugs.
130    
131    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/sparseVector.R (spV2M): fix for "isparseVector".
134            Further, fix <diag> -> <sparseVector> coercion
135            (repSpV): add rep(<sparseVector>, .) method
136    
137            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
138            use as.vector(.).
139    
140            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
141    
142            * R/AllClass.R: new (hidden) class union "scarceMatrix"
143            * R/AllClass.R: sparseVector: add prototype
144    
145            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
146            Kasper Kristensen
147    
148    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * tests/other-pkgs.R: add more interesting Matrix -> graph
151    
152    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
155            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
156    
157    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * DESCRIPTION: release 0.999375-10 to CRAN
160    
161            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
162            .bdiag().
163            * man/bdiag.Rd: update, including test.
164    
165    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * tests/Simple.R: add minimal bdiag() checks
168    
169            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
170              factor out the Tsparse - internal computation into new .bdiag()
171    
172    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/nsparseMatrix.R: specific fast all() and any() methods.
175    
176            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
177            when trying to produce too large result.
178    
179            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
180            very large matrices.
181    
182            * R/sparseMatrix.R (printSpMatrix2): new function, used by
183            show(<sparseMatrix>).
184    
185            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
186    
187    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * src/Mutils.c (m_encodeInd, m_encodeInd2):
190            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
191    
192            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
193            big matrices): -> 2nd argument 'di' instead of 'nr' !
194    
195    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/dtCMatrix.R: faster dgC* -> dtC* method
198            * tests/Simple.R: (hence removed "FIXME")
199    
200            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
201            which can be be turned off for possible speed gains.
202    
203    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
206    
207            * R/not.R: fix !<ldiMatrix>
208            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
209    
210            * R/diagMatrix.R (Ops): fix one-off thinko in
211            <diagonal> o <numeric> methods
212    
213            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
214    
215    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
218            * tests/Simple.R: testing the above
219    
220    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
223    
224    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
227            * NAMESPACE (unname): finally exported
228    
229    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/Auxiliaries.R (cholMat): possibly keep packed
232    
233            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
234            for R < 2.7.0.
235    
236            * R/Tsparse.R ([): for triangularMatrix, check if result may be
237            triangular.
238            * tests/indexing.R: regression test
239    
240    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
243            * R/Ops.R: more methods, for lMatrix/nMatrix
244    
245    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/expm.R: new file for all expm() methods; notably new ones for
248            diagonal*, triangular*, symmetric* and also simple "matrix".
249    
250    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
253    
254            * inst/test-tools.R (assert.EQ.mat): better message when not equal
255    
256            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
257    
258            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
259            [dl]denseMatrix {identical slots; but more logical method dispatch}
260    
261    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
264    
265            * R/diagMatrix.R (determinant): method
266    
267    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
270    
271            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
272    
273            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
274            its diagonal
275    
276    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
279    
280            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
281    
282            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
283    
284            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
285    
286    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
289    
290            * R/Ops.R (.do.Logic.lsparse): fix NA case
291    
292            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
293    
294            * R/Auxiliaries.R (nnzero): fix special cases, using
295            * R/Auxiliaries.R (indDiag): new utility
296            * R/Auxiliaries.R (indTri): new argument 'diag'
297    
298            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
299    
300    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
303    
304            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
305            ".tCMatrix" triangular matrix.
306    
307            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
308            'clx' can be class *or* class representation.
309            (nnzSparse): new.
310            (non0ind): new 'xtendSymm' argument; used in
311            * R/Ops.R:
312    
313            * R/pMatrix.R: more efficient determinant() method
314    
315    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
318            * [disactivated] NAMESPACE: export(det)
319    
320            * R/diagMatrix.R (mkDiag): new substitute for diag()
321    
322            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
323            (as0, as1): new utility.
324    
325            * R/Csparse.R (diag, band): need diagU2N()
326    
327            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
328    
329            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
330    
331            * R/Ops.R (Compare): fix <nsp> o <nsp> case
332    
333            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
334    
335    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Auxiliaries.R (signPerm): new utility for
338            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
339    
340            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
341            since we have our own error handler (and can use tryCatch() from R).
342    
343    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
346    
347            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
348            when not positive definite.
349    
350            * R/Auxiliaries.R (asTri): new auxiliary
351            (non0.i): make *much* faster for Tsparse with many non-zero
352            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
353    
354            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
355            test-tools.R , see below
356    
357            * R/dMatrix.R: fix "Summary" method: + diagU2N()
358    
359            * NAMESPACE, R/Matrix.R: add mean() method
360    
361    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
364            cold-hot colors; try *changed* default useAbs = FALSE
365            * man/image-methods.Rd:  nice examples
366    
367    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * inst/test-tools.R (checkMatrix): new function for modularizing part
370            of tstMatrixClass() in tests/Class+Meth.R
371    
372            * R/dsCMatrix.R: coercion from "matrix"
373            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
374    
375            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
376            add test for as(matrix(,0,0), <class>)
377    
378    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
381            work as determinant(matrix(,0,0)).
382    
383            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
384            * man/sparseLU-class.Rd: ditto
385    
386            * R/dgCMatrix.R (determinant): method building on lu()
387            * R/sparseMatrix.R, Matrix.R, ...: ditto
388    
389            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
390    
391    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
394            pattern matrices.
395    
396    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * src/dense.c (dense_to_Csparse): all declarations *before*
399            R_CheckStack(); needed e.g. for ancient gcc 2.96.
400    
401    
402  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
405          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
406    
407            * R/AllClass.R: drop "double" from "atomicVector" class union
408    
409            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
410            * R/dgeMatrix.R: ditto
411    
412          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
413    
414            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
415    
416  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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