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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2244, Sat Aug 23 18:09:51 2008 UTC
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1    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
4              documentation for CHMfactor class
5            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
6              pMatrix
7    
8    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
11    
12    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
15            variable assignments {from "next version" codetools}.
16            * R/Csparse.R, R/Tsparse.R: ditto
17    
18    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/sparseVector.R (sp2vec, coerce to sparseVector):
21            make sure no integer overflows happen, and use double precision
22            (n, index) where appropriate.
23    
24            * tests/Simple.R: test "large" sparse vectors.
25    
26    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
29            just integer (allowing much longer length).
30    
31    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
34            "denseMatrix".  This renders "scarceMatrix" dispensable and
35            invalidates part of MM's presentations on "space of Matrix
36            classes", but seems cleaner overall.
37    
38            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
39            "sparseMatrix" in method signatures;
40            further, instead of coercing to "sparseMatrix", coerce to
41            "TsparseMatrix" now.
42    
43    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
46            .Call(.)
47            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
48    
49    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
52            recursion in new test in
53            * tests/matprod.R: testing the above and another solve() case, below
54    
55            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
56            e.g. triangular 'x'.
57    
58            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
59            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
60            correctly with unit-triangular x
61    
62            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
63            instead of not checking diagU.
64    
65            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
66            experiments where diagonalMatrix would extend sparse*.
67    
68    
69    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
72            "x@p[ncol(x)]" instead of length(x@i).
73            * R/Auxiliaries.R (nnzero): ditto
74    
75            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
76            since that fails for over-allocated i.
77    
78            * tests/validObj.R: more testing of over-allocated (i,x) slots
79    
80    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
83            'sort_in_place' and set it to TRUE in call from
84            * src/Csparse.c (Csparse_validate): sort in place, making sure that
85            validObject() continues sort the columns if needed.
86    
87            * tests/validObj.R: now tests that more thoroughly, and
88            * man/CsparseMatrix-class.Rd: documents it.
89    
90    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
91    
92            * [r2233] src/chm_common.c: sort columns more carefully in
93              as_cholmod_sparse
94            * [r2231] src/chm_common.c: check for sorted columns in
95              as_cholmod_sparse instead of assuming it
96            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
97              expanding diagonal
98    
99    
100    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
103            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
104            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
105            diagU2N().
106    
107            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
108            .spDiagonal() and new .trDiagonal().
109    
110            * R/dtCMatrix.R (solve): make use of .trDiagonal()
111    
112    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
115            stumbled upon by Michael H.
116    
117            * tests/validObj.R: testing the bug-fix
118    
119            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
120            versions.
121    
122            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
123            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
124    
125            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
126              AS_CHM_SP() which includes diagU2N.
127    
128            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
129            adapt to 3 arguments.
130    
131    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
132    
133            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
134              dtCMatrix_sparse_solve
135            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
136              storage
137            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
138              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
139              new solve method
140            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
141              Csparse_diagU2N functionality into Matrix_as_cs
142    
143    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
146    
147    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
148    
149            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
150              argument with default TRUE
151            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
152              Csparse_diagU2N
153            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
154              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
155              parent array; new solve method for signature(a = "dtCMatrix", b =
156              "sparseMatrix")
157    
158    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/diagMatrix.R (.bdiag): also keep result triangular
161    
162    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
163    
164            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
165              messages
166    
167    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
170            symmetric- or nsparse-Matrix, also fixing the bug introduced with
171            the new version (.999375-10).
172    
173            * tests/Simple.R: regression test for the bugs.
174    
175    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/sparseVector.R (spV2M): fix for "isparseVector".
178            Further, fix <diag> -> <sparseVector> coercion
179            (repSpV): add rep(<sparseVector>, .) method
180    
181            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
182            use as.vector(.).
183    
184            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
185    
186            * R/AllClass.R: new (hidden) class union "scarceMatrix"
187            * R/AllClass.R: sparseVector: add prototype
188    
189            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
190            Kasper Kristensen
191    
192    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * tests/other-pkgs.R: add more interesting Matrix -> graph
195    
196    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
199            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
200    
201    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * DESCRIPTION: release 0.999375-10 to CRAN
204    
205            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
206            .bdiag().
207            * man/bdiag.Rd: update, including test.
208    
209    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * tests/Simple.R: add minimal bdiag() checks
212    
213            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
214              factor out the Tsparse - internal computation into new .bdiag()
215    
216    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/nsparseMatrix.R: specific fast all() and any() methods.
219    
220            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
221            when trying to produce too large result.
222    
223            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
224            very large matrices.
225    
226            * R/sparseMatrix.R (printSpMatrix2): new function, used by
227            show(<sparseMatrix>).
228    
229            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
230    
231    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * src/Mutils.c (m_encodeInd, m_encodeInd2):
234            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
235    
236            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
237            big matrices): -> 2nd argument 'di' instead of 'nr' !
238    
239    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dtCMatrix.R: faster dgC* -> dtC* method
242            * tests/Simple.R: (hence removed "FIXME")
243    
244            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
245            which can be be turned off for possible speed gains.
246    
247    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
250    
251            * R/not.R: fix !<ldiMatrix>
252            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
253    
254            * R/diagMatrix.R (Ops): fix one-off thinko in
255            <diagonal> o <numeric> methods
256    
257            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
258    
259    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
262            * tests/Simple.R: testing the above
263    
264    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
267    
268    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
271            * NAMESPACE (unname): finally exported
272    
273    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Auxiliaries.R (cholMat): possibly keep packed
276    
277            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
278            for R < 2.7.0.
279    
280            * R/Tsparse.R ([): for triangularMatrix, check if result may be
281            triangular.
282            * tests/indexing.R: regression test
283    
284    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
287            * R/Ops.R: more methods, for lMatrix/nMatrix
288    
289    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/expm.R: new file for all expm() methods; notably new ones for
292            diagonal*, triangular*, symmetric* and also simple "matrix".
293    
294    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
297    
298            * inst/test-tools.R (assert.EQ.mat): better message when not equal
299    
300            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
301    
302            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
303            [dl]denseMatrix {identical slots; but more logical method dispatch}
304    
305    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
308    
309            * R/diagMatrix.R (determinant): method
310    
311    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
314    
315            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
316    
317            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
318            its diagonal
319    
320    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
323    
324            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
325    
326            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
327    
328            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
329    
330    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
333    
334            * R/Ops.R (.do.Logic.lsparse): fix NA case
335    
336            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
337    
338            * R/Auxiliaries.R (nnzero): fix special cases, using
339            * R/Auxiliaries.R (indDiag): new utility
340            * R/Auxiliaries.R (indTri): new argument 'diag'
341    
342            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
343    
344    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
347    
348            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
349            ".tCMatrix" triangular matrix.
350    
351            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
352            'clx' can be class *or* class representation.
353            (nnzSparse): new.
354            (non0ind): new 'xtendSymm' argument; used in
355            * R/Ops.R:
356    
357            * R/pMatrix.R: more efficient determinant() method
358    
359    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
362            * [disactivated] NAMESPACE: export(det)
363    
364            * R/diagMatrix.R (mkDiag): new substitute for diag()
365    
366            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
367            (as0, as1): new utility.
368    
369            * R/Csparse.R (diag, band): need diagU2N()
370    
371            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
372    
373            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
374    
375            * R/Ops.R (Compare): fix <nsp> o <nsp> case
376    
377            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
378    
379    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Auxiliaries.R (signPerm): new utility for
382            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
383    
384            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
385            since we have our own error handler (and can use tryCatch() from R).
386    
387    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
390    
391            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
392            when not positive definite.
393    
394            * R/Auxiliaries.R (asTri): new auxiliary
395            (non0.i): make *much* faster for Tsparse with many non-zero
396            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
397    
398            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
399            test-tools.R , see below
400    
401            * R/dMatrix.R: fix "Summary" method: + diagU2N()
402    
403            * NAMESPACE, R/Matrix.R: add mean() method
404    
405    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
408            cold-hot colors; try *changed* default useAbs = FALSE
409            * man/image-methods.Rd:  nice examples
410    
411    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * inst/test-tools.R (checkMatrix): new function for modularizing part
414            of tstMatrixClass() in tests/Class+Meth.R
415    
416            * R/dsCMatrix.R: coercion from "matrix"
417            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
418    
419            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
420            add test for as(matrix(,0,0), <class>)
421    
422    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
425            work as determinant(matrix(,0,0)).
426    
427            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
428            * man/sparseLU-class.Rd: ditto
429    
430            * R/dgCMatrix.R (determinant): method building on lu()
431            * R/sparseMatrix.R, Matrix.R, ...: ditto
432    
433            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
434    
435    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
438            pattern matrices.
439    
440    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/dense.c (dense_to_Csparse): all declarations *before*
443            R_CheckStack(); needed e.g. for ancient gcc 2.96.
444    
445    
446  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
449          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
450    
451            * R/AllClass.R: drop "double" from "atomicVector" class union
452    
453            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
454            * R/dgeMatrix.R: ditto
455    
456          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
457    
458            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
459    
460  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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