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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 2110, Sat Jan 26 20:59:26 2008 UTC
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1    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
4            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
5                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
6    
7            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
8            * src/Tsparse.h, init.c: ditto
9            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
10                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
11            * R/sparseMatrix.R (isTriangular): hence simplified
12    
13    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/Ops.R (.Arith.Csparse): new utility factored out of former
16              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
17    
18    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
21    
22            * inst/test-tools.R (isOrthogonal): new function; also file restructured
23    
24    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
27            coercion to "nMatrix" and "pMatrix"
28    
29            * R/AllClass.R: "Schur" class;  "number" class union
30            * man/number-class.Rd:
31            * man/Schur-class.Rd:
32    
33            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
34            (.simpleSchur): Schur() method for diagonal matrices
35            (.triSchur):    Schur() method for triangular matrices
36            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
37    
38    
39    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
42    
43    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
46                    in order to ensure 'system = *' is not lost;
47                    formals()$system instead of cut&paste.
48            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
49    
50    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * DESCRIPTION (Date): make ready for release --> 0.999375-4
53    
54            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
55    
56    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
59                    and hence does as.vector(.).
60            * man/pMatrix-class.Rd: docs
61            * R/sparseMatrix.R: fix for printing "integer sparse"
62    
63            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
64    
65            * R/Matrix.R and others: use "exact" function argument list for
66                    both "["   : (x, i,j, ..., drop)
67                    and  "[<-" : (x, i,j, ..., value)
68    
69            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
70            * R/Tsparse.R (replTmat):    ditto
71            * R/diagMatrix.R (replDiag): ditto
72            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
73            * tests/indexing.R: testing the above
74    
75    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R (cov2cor): method for sparse matrices
78    
79            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
80    
81            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
82    
83            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
84    
85    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Matrix.R: "generic" cov2cor() method
88    
89            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
90                    speed up Q %*% D %*% t(Q)
91            * tests/dpoMatrix.R: test nearPD()
92    
93    2007-12-05  Doug Bates and Martin Maechler
94    
95            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
96            stats::xtabs() allowing to create sparse matrices.
97    
98    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
101    
102    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
105    
106    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/LU.R: solve() method for "denseLU"
109    
110    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * DESCRIPTION (Version): 0.999375-3 preparing for release
113    
114            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
115    
116            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
117    
118    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
121              thanks to Kasper Kristensen.
122            * tests/matprod.R: regression test for that.
123    
124    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4778] R/AllGeneric.R: Check R version before defining generics for
127              primitives
128    
129    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/denseMatrix.R (rcond): method
132            * R/sparseQR.R (rcond): method, use x or t(x)
133    
134    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
137            matrices.
138            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
139    
140            * man/rcond.Rd: mention the more general definition, and add
141            example for non-square matrices.
142    
143            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
144    
145    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
148    
149    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
152            * tests/indexing.R: add new regression for the above cases.
153    
154    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/Mutils.h (__sun): clause for alloca.h on Solaris
157    
158    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * DESCRIPTION (Date, Version): 0.999375-2
161    
162    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/HBMM.R (readMM): make work for pattern matrices as well
165    
166    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
167    
168            * [r4730] src/Mutils.h: declare alloca
169            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
170              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
171              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
172              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
173              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
174              methods; switch writeMM to use CHOLMOD code; repair readMM
175    
176    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
179            Oehlschlaegel's ... result type still to be discussed!
180    
181    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * man/image-methods.Rd: new, combining all image() methods
184    
185    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
188            to work via dgC...
189    
190            * R/Matrix.R (Matrix): special treatment for "table" (S3)
191    
192    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/dgTMatrix.R (image): change defaults to
195                    aspect = "iso", colorkey = FALSE
196    
197    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
200            must copy its *expanded* x slot before LAPACK call.
201    
202            * tests/matprod.R: test the last days' changes.
203    
204    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
205    
206            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
207              as well as in sources
208            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
209              Lapack call
210    
211    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
214                    ("Matrix", "matrix") which is needed in some cases.
215            Ditto for solve().
216    
217            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
218            infinite recursion in dispatch for some cases.
219    
220    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
221    
222            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
223              so pointers match
224    
225    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * DESCRIPTION (Date): set ready for release -- 0.999375-1
228    
229    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
230    
231            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
232              src/chm_common.c, src/chm_common.h: Change API for
233              numeric_as_chm_dense and N_AS_CHM_DN
234    
235    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
238            * tests/matprod.R: regr.test for it
239    
240    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
243            * tests/group-methods.R: and regression-test it
244    
245    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
246    
247            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
248              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
249              triplet_to_sparse, documentation, use typedefs
250    
251    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * man/dpoMatrix-class.Rd: added 'corMatrix' example
254    
255            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
256            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
257            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
258    
259            * R/lsparseMatrix.R: bug fix in "all" method
260            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
261    
262            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
263            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
264                    + matrix |-> nMatrix coercion
265            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
266            * man/pMatrix-class.Rd: ditto
267    
268            * R/Matrix.R (Summary): method for non-dMatrix
269    
270            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
271            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
272                    test all Summary methods.
273    
274    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
277    
278    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
281    
282            * R/pMatrix.R (t?crossprod): methods for pMatrix
283    
284    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
287    
288    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
289    
290            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
291              trying to fix a subtle bug - which has been somewhere else.
292    
293    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
294    
295            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
296              solve the bug
297    
298    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * src/dgCMatrix.c (compressed_to_TMatrix):
301    
302    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * src/Csparse.c (Rsparse_validate): new, to have some validity
305            checking for RsparseMatrix
306            * src/dgCMatrix.c (xRMatrix_validate): ditto
307            * src/dtCMatrix.c (tRMatrix_validate): ditto
308    
309    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
310    
311            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
312              lgRMatrix
313            * [r4568] DESCRIPTION: Prepare for bug-fix release
314            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
315              for declaration of cholmod_symmetry
316    
317    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
320            release.
321    
322    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
323    
324            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
325              functions - no longer used
326            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
327              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
328              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
329              Alloca
330    
331    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
332    
333            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
334              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
335              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
336              src/t_gCMatrix_colSums.c: more R_CheckStack()s
337    
338    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
339    
340            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
341              the required amount of memory then call M_numeric_as_chm_dense.
342            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
343              (like Calloc but calling alloca)
344    
345    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
348            and extended with more sophisticated 'col.names' option.
349            * NAMESPACE: export  printSparseMatrix()
350            * man/printSpMatrix.Rd: document, incl. examples
351    
352    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
353    
354            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
355              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
356              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
357    
358    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * DESCRIPTION (Version): 0.99875-4
361    
362            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
363            some dimnames perservation.
364    
365            * R/dsTMatrix.R (t-method): keep dimnames
366            * R/dtTMatrix.R:  ditto
367    
368            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
369            and ncol(.) < 10
370    
371            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
372            from Mutils.h
373    
374            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
375            e.g. in as(<ngCMatrix>, "matrix")
376    
377    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
378    
379            * [r4529] .: Create a branch for the API changes from the 0.99875
380              series to the 0.999375 series
381            * [r4530] DESCRIPTION, inst/include/Matrix.h,
382              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
383              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
384              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
385              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
386              as_cholmod_x functions
387    
388    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
389    
390            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
391              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
392              to Comparisons
393    
394    >>>>>>> .merge-right.r4561
395    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * DESCRIPTION (Version): 0.99875-3 ready to be released.
398    
399            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
400    
401            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
402            that should also work in a future version of R.
403    
404    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
407    
408            * R/sparseVector.R: more *sparseVector coercions, notably for
409            non - double ones.
410    
411    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
414              notably the new ones building on the new .Call(.)s:
415    
416            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
417            all 4 of [dlin]gCMatrix_colSums().
418    
419    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
420    
421            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
422            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
423              result
424    
425    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/kronecker.R: fix typo (could lead to inf.recursion)
428            * test/simple.R: testing that
429    
430            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
431            method as well (which can have arguments, show() can't).
432    
433    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
434    
435            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
436              added dgCMatrix_colSums for [col,row][Sums,Means]
437    
438    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
439    
440            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
441              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
442              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
443            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
444              class
445            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
446              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
447              row names to store the levels - duh!  Added an example.
448    
449    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * src/Csparse.c (Csparse_validate): check for *repeated* entries
452            thanks to example from Christian Buchta; with a test here:
453            * tests/simple.R:
454    
455    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
458            of colSums(*, sparseResult = TRUE)
459    
460    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
463            'na.rm = FALSE' as "everywhere" else in R.
464    
465    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
466    
467            * [r4421] src/CSparse_install.sh: Modify for new organization of
468              CSparse package
469            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
470              SuiteSparse
471            * [r4426] src/Makefile: add ./UFconfig to the include path for
472              compilation
473            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
474            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
475              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
476    
477    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
478    
479            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
480            * R/sparseMatrix.R (prSpMatrix): now gives a message about
481            suppressed column names.
482    
483    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
484    
485            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
486              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
487              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
488              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
489              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
490              Remove warnings after change to const char* CHAR
491    
492    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
493    
494            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
495              type of M_cholmod_ssmult
496    
497    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
498    
499            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
500              src/init.c: Yet another cholmod export - cholmod_ssmult
501    
502    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * NAMESPACE: exported drop0(), since
505            * man/drop0.Rd: I have seen several cases, I really wanted to use
506            it, so our users may want too.
507    
508    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * man/colSums.Rd: separately document colSums() etc, since these
511            have the extra argument 'sparseResult'.
512    
513    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
516            * man/spMatrix.Rd: docu., including examples
517    
518            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
519            in order to make colMeans() etc fast *and* correct.
520            * R/sparseVector.R (replSPvec): "[<-" functionality for
521            sparseVectors; tested in
522            * tests/simple.R:
523    
524    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
527            (very) sparse Matrices; output similar to Matlab's print().
528    
529    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
530    
531            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
532            0-based, indices (Jose Quesada <quesada@gmail.com>).
533    
534    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
535    
536            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
537    
538    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/Auxiliaries.R (sparsapply): new utility, much faster than
541            tapply1() for large sparse matrices.
542    
543    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Matrix.R (dim<-): reshape now via sparseVector.
546    
547            * R/sparseVector.R: methods and function for
548            * R/AllClass.R: new "sparseVector" class and daughters.
549            * NAMESPACE: export new classes
550    
551    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * DESCRIPTION (Version): 0.99875-1
554            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
555    
556    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
559            indexing
560            * tests/indexing.R: test set for that.
561    
562    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
565            entries.
566            * tests/indexing.R(out): add regression test for it
567    
568    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
571            name for "!" method definitions.
572    
573    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * R/Tsparse.R (intI): new utility, used for "[" :
576                    Cleanup up there, and fixes for duplicated indices - more TODO!
577    
578            * tests/indexing.R(out): more tests
579    
580    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
581    
582            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
583            code that is now part of the R Lapack library.
584    
585            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
586            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
587    
588    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
591    
592    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
595            up with extraneous names '0'...'<n-1>'
596    
597    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/dgTMatrix.R (mat2dgT): care about NAs
600    
601    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/kronecker.R: triangularity preserving methods
604    
605    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/kronecker.R: new file collecting kronecker() methods in one
608                    place.  Goal: become much faster!
609    
610    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
613            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
614            can be much faster.
615    
616            * tests/matprod.R: add regression tests for these (upper & lower).
617    
618    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/Matrix.R (diff): method for our Matrices.
621    
622            * R/sparseMatrix.R (isDiagonal): check dim()!
623    
624    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Matrix.R (dim<-): new method for "reshape()" built on a
627            proposal from Tamas Papp.
628    
629    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
632    
633            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
634            rather define and export  cBind() and rBind() only.
635            --> useRs *must* change code that used to have cbind()/rbind() !!
636    
637            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
638            * R/bind.Rout.save: ditto
639    
640    2007-02-16  Douglas Bates  <bates@r-project.org>
641    
642            * DESCRIPTION (Date, Version): 0.9975-11 with new date
643            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
644            const modifier on declaration of the array 'valid'
645    
646    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
649    
650    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
653    
654            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
655            * tests/simple.R: test the above and some of these coercions:
656    
657            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
658                    be careful to avoid infinite recursion, using new coercions in
659            * R/ngCMatrix.R and nsC... and ntC...
660            * R/lsparseMatrix.R: ditto
661    
662            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
663    
664            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
665            * R/Rsparse.R: reactivate .Call()s
666    
667            * tests/Class+Meth.R: a bit more on actual classes
668    
669    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
670    
671            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
672    
673    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
674    
675            * DESCRIPTION (Version): 0.9975-10 to upload
676    
677            * tests/Class+Meth.R (tstMatrixClass): require coercions to
678            specific classes less unconditionally.
679    
680            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
681    
682            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
683    
684            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
685            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
686            R_to_CMatrix segfaults on one platform.
687            Eliminate most coercion method to *specific* classes, and replace
688            with virtual classes coercions.
689    
690    
691    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
692    
693            * src/init.c: export the CHM...._validate() placeholders, since
694            they *are* called.
695    
696            * tests/Class+Meth.R (classCanCoerce): and starting to test
697            all as(<from>, <to>)
698    
699    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
702            * tests/indexing.R: tested now
703            * tests/indexing.Rout.save: updated
704    
705            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
706            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
707            appropriate.
708    
709            * NAMESPACE: export a trivial
710            * R/Matrix.R: drop() Matrix-method
711    
712            * R/AllClass.R: moved all prototypes to virtual super classes.
713    
714            * R/Rsparse.R: many more coercions to have less exceptions in
715            * tests/Class+Meth.R:
716    
717            * R/Ops.R (Compare): tweak for case with NA
718            * tests/simpl.R: hence another 'FIXME' eliminated
719    
720    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
723            objects.
724    
725            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
726              and more of "!", "&", "|", all, any; coercions
727    
728            * R/Rsparse.R: many coercions (which enable quite a few other
729            methods), thanks to enhancements in
730            * src/dgCMatrix.c (R_to_CMatrix): new, and
731            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
732            symmetric & triangular and ..RMatrix objects.
733    
734            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
735            renamed file from src/dsTMatrix.c;
736            now dealing with symmetric and triangular Tsparse coercions, both
737            to dense and general.
738    
739    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
742    
743            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
744            where sensible when the <numeric> is of length > 1.
745    
746    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/Matrix.R ([<-): for M[] <- value: fix length
749    
750    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
753            * R/ndenseMatrix.R: new coercions n* -> l*
754    
755    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
758    
759            * R/Ops.R ("Logic"): and other "Ops", many updates
760    
761    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * src/Mutils.h (SET_DimNames): new utility
764    
765            * R/Auxiliaries.R (nnzero): improved and now exported via
766    
767            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
768    
769    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/diagMatrix.R (!): fix typo.
772    
773    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/Auxiliaries.R (as_Csparse): and quite a few others:
776                    allow to pass class definition --> speedup
777            * R/sparseMatrix.R: apply the above
778    
779            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
780    
781            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
782            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
783            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
784    
785            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
786    
787            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
788            and use it for "sparse*" as well, since it's faster than the
789            as_Csparse(.) way.
790    
791    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
794    
795    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
798            as method for   M[ ij ] <- v
799            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
800    
801            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
802            FALSE answer
803    
804            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
805            * tests/indexing.R: test it, and some of the above
806    
807    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/Auxiliaries.R (is_duplicatedT): new utility
810    
811    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
812    
813            * src/init.c (R_init_Matrix): export cholmod_scale
814    
815    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
818            base::as.matrix to (x, ...)
819    
820    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
823            file; start using "Logic", hence
824    
825            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
826            * NAMESPACE: import and export "Logic"
827    
828    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
831            only needed previously to R version 2.5.0.
832    
833    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
836    
837            * R/Tsparse.R (replTmat): fix subassignment of triangular
838            * R/Csparse.R (replCmat): ditto
839            * tests/indexing.R: more tests, incl the above fix
840    
841    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
842    
843            * R/Auxiliaries.R (drop0): extend for non CSparse
844            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
845    
846            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
847                    use uplo correctly (!); other places: use uplo_P() macro
848    
849            * R/Csparse.R (replCmat): call diagU2N() when needed
850            * R/Tsparse.R (replTmat): ditto
851    
852            * src/dtCMatrix.c (tCMatrix_validate): new
853            * src/dtTMatrix.c (tTMatrix_validate): new, used in
854            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
855    
856            * R/diagMatrix.R (replDiag): to use in [<-
857    
858    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
861                    also more general diagU2N().
862    
863    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
866            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
867    
868    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * tests/bind.R: a few more cases
871            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
872    
873            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
874            * R/ddenseMatrix.R (cbind2/rbind2)
875            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
876            * tests/indexing.R
877            * tests/indexing.Rout.save: updated
878    
879    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
882            * tests/indexing.R
883    
884    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
887            align with proper position of "0", i.e., right for integers.
888            argument 'align' by default is "fancy".
889    
890    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
893            * R/Csparse.R: and fix "Compare" for more cases.
894            * tests/Class+Meth.R: test some of these (m == m, m != m)
895    
896    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
897    
898            * R/lsparseMatrix.R: all() and any() methods
899            * R/ldenseMatrix.R:      ditto
900            * NAMESPACE, R/Matrix.R: ditto
901    
902            * man/all-methods.Rd: document them minimally
903    
904            * tests/simple.R: add a few examples for these
905    
906    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908            * R/Tsparse.R ([): fix long standing typo in symmetric case
909            * man/dsCMatrix-class.Rd: add example exhibiting the above case
910    
911    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
912    
913            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
914            to LL before converting to a sparse matrix. (The LDL form can be
915            converted to a sparse matrix but it is implicitly a unit
916            triangular matrix and a diagonal matrix overwritten on the diagonal.)
917    
918    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
919    
920            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
921    
922    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
923    
924            * DESCRIPTION (Version): updated -> release 0.9975-7
925            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
926    
927    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
928    
929            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
930    
931    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
932    
933            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
934            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
935            is exactly singular.
936    
937    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * DESCRIPTION (Date): updated -> release 0.9975-6
940    
941    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
944            now returns symmetric.
945    
946            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
947    
948            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
949            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
950    
951            * R/Auxiliaries.R (.type.kind): added
952    
953    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
956            running src/CSparse_install.sh
957    
958            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
959    
960    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
963            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
964    
965            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
966    
967            * tests/Class+Meth.R (tstMatrixClass): now assure
968            the (important in method programming) property :
969    
970                    ###>>  Every "Matrix" is either
971                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
972    
973                    (where "*" stands for "Matrix")
974    
975            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
976    
977            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
978            * tests/validObj.R: checks for "comparison"
979    
980            * R/sparseMatrix.R ([): improved indexing for sparse;
981                    trying to keep <symmetric>[ n, n] symmmetric
982    
983            * tests/indexing.R: indexing for logical sparse now ok
984    
985    
986    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * src/Tsparse.c: use xTsparse_validate() , and hence remove
989    
990            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
991    
992    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
995    
996            * tests/simple.R: validObject() checking the above.
997    
998            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
999            replacing both dgCMatrix_validate and lgCM*.
1000    
1001            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1002            fix dimnames setting in other places.
1003            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1004    
1005    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1008    
1009            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1010            symmetry test, via
1011            * R/Auxiliaries.R (.as.dgC.0.factors):
1012    
1013    2006-11-01  Douglas Bates  <bates@r-project.org>
1014    
1015            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1016            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1017            <CsparseMatrix>) added
1018    
1019    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * tests/matprod.R: add a variation of Harri's example
1022    
1023            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1024            recursive infinitely.
1025    
1026            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1027    
1028            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1029    
1030    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1033            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1034            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1035            satisfy the above test.
1036    
1037    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1038    
1039            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1040    
1041            * R/dgCMatrix.R: solve(a, b="missing") based on
1042            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1043            RHS = NULL.
1044    
1045            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1046            add more (needed) [t]crossprod() methods.
1047    
1048            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1049    
1050            * R/Auxiliaries.R (as_CspClass): cleanup
1051            (drop0): internal utility for "Csparse_drop(*, 0)"
1052            (.bail.out.2): encourage active feedback
1053    
1054    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1055    
1056            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1057    
1058            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1059            non-valid or 'sorted' case).
1060    
1061            * R/dsparseMatrix.R: add "chol" method.
1062            * R/ddenseMatrix.R: ditto
1063    
1064            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1065            * NAMESPACE (Ops)
1066            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1067            coercion; deprecating direct lower level coercions.
1068    
1069            * R/*.R (seq): use seq_len() and seq_along() where possible.
1070    
1071    
1072    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * DESCRIPTION (Version): 0.9975-5 ready for release
1075    
1076    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1077    
1078            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1079    
1080    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1081    
1082            * R/AllClass.R (corMatrix): add 'validity' check;
1083                    comment out unused "LDL" class definition
1084            * NAMESPACE: mention, but do not export "LDL" class
1085            * R/corMatrix.R: new (simple), needed for R-devel with
1086            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1087              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1088    
1089    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1090    
1091            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1092            use Rprintf and R's error handling.
1093    
1094    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1097            * tests/matprod.R: add tests for the bug fixed.
1098    
1099    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1100    
1101            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1102            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1103    
1104    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1105    
1106            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1107    
1108    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1109    
1110            * DESCRIPTION (Version): 0.9975-3
1111    
1112            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1113            (sparse) matrices.
1114            * man/bdiag.Rd: docu + examples
1115    
1116            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1117    
1118            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1119            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1120    
1121            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1122            that result is sparse or diagonal (and not dense).
1123    
1124            * man/Subassign-methods.Rd: fix examples
1125    
1126            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1127            should always return a sparse (and not sometimes a diagonal) matrix.
1128    
1129    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1132    
1133    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1134    
1135            * DESCRIPTION (Version): 0.9975-2
1136    
1137            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1138    
1139    2006-10-02  Douglas Bates  <bates@R-project.org>
1140    
1141            * tests/dg_Matrix.R: Simplify test taking into account new code.
1142    
1143    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1144    
1145            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1146    
1147            * R/lsTMatrix.R: new files w/ missing methods
1148            * R/nsTMatrix.R:  "  'for completeness'
1149    
1150            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1151    
1152            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1153    
1154    
1155    2006-09-28  Douglas Bates  <bates@R-project.org>
1156    
1157            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1158            included.
1159    
1160            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1161            Export C-callable functions used in Zt_create in lme4.
1162    
1163    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1164    
1165            * DESCRIPTION (Version): 0.9975-1
1166    
1167            * tests/simple.R: less checks fail; using NA, found that our
1168                    kronecker() is not base-compatible with NA's.
1169    
1170            * R/dMatrix.R: "Compare" method now implemented for all cases
1171    
1172            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1173    
1174            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1175    
1176            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1177            * src/dspMatrix.c (dspMatrix_validate): ditto
1178    
1179            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1180              including coercion to [nl]tTMatrix.
1181    
1182            * R/diagMatrix.R (show): print a header line as for other classes.
1183    
1184    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * src/Makefile.win (SUBDIRS): fix typo
1187    
1188    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1191    
1192    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1193    
1194            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1195            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1196            accept a symmetric matrix).
1197            * tests/group-methods.R: Uncomment test of crossprod applied to
1198            lsCMatrix objects.
1199    
1200    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * R/AllClass.R (symmetricMatrix): add validity method (available
1203            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1204    
1205            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1206    
1207            * tests/indexing.Rout.save:
1208            * tests/indexing.R: additions, mainly for 'lsparse'
1209    
1210            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1211            case.
1212    
1213            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1214    
1215    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1216    
1217            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1218                    as 'N' (1-letter - Ok?)
1219    
1220            * tests/group-methods.R: add test for logical + NAs
1221    
1222            * R/dMatrix.R ("Compare"): fix to work with NA's
1223    
1224            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1225    
1226            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1227                    which is implemented.
1228    
1229    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1230    
1231            * src/chm_common.c: coerce logical <-> double instead of
1232            typecasting;  needed for "l" matrix handling in cholmod.
1233    
1234            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1235    
1236            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1237            (Tsp2grNEL): other fixes needed
1238    
1239    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1240    
1241            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1242                    Matrices, since "lMatrix", also "lsparseM" can have NA
1243            * R/ndenseMatrix.R, etc: new source files
1244            * man/nsparseMatrix-classes.Rd, etc: new help files
1245            * tests/: adaptions
1246            * src/chm_common.c (chm_dense_to_SEXP): and others:
1247                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1248            * src/Csparse.c, etc: ditto
1249    
1250    2006-09-11  Douglas Bates  <bates@R-project.org>
1251    
1252            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1253            alloc_d**Matrix functions to the lme4 package.
1254    
1255    2006-09-09  Douglas Bates  <bates@R-project.org>
1256    
1257            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1258            fixed
1259    
1260    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1261    
1262            * R/lMatrix.R: new
1263    
1264            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1265    
1266            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1267            * man/tcrossprod.Rd: ditto
1268    
1269    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1270    
1271            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1272            for exported functions
1273            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1274            Remove partitioning algorithms for sparse matrix reordering.  The
1275            copyright on the Metis code was problematic and the methods were
1276            rarely used.
1277            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1278            operations are now done entirely in CHOLMOD code.
1279    
1280    2006-09-06  Douglas Bates  <bates@R-project.org>
1281    
1282            * src/Mutils.h: Remove functions that are no longer used.
1283    
1284    2006-09-04  Douglas Bates  <bates@R-project.org>
1285    
1286            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1287            * src/DEPS.mkf: update
1288    
1289    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1290    
1291            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1292            * DESCRIPTION (Version): 0.9975-0
1293            (Depends): R (>= 2.4.0)
1294    
1295    2006-09-01  Douglas Bates  <bates@R-project.org>
1296    
1297            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1298    
1299    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1300    
1301            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1302            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1303    
1304            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1305    
1306    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1307    
1308            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1309            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1310            * R/dsparseMatrix.R: ditto
1311            * R/Csparse.R: ditto
1312    
1313    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1314    
1315            * R/dMatrix.R (Compare): improve availability of "<", etc
1316            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1317    
1318    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1321            of a 0-index which was used as 1-index (..hmm)
1322    
1323            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1324    
1325            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1326            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1327            (.is.diagonal): ditto
1328    
1329            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1330    
1331            * R/Matrix.R (Matrix): also work for NA data
1332    
1333  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1334    
1335          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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