SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 2144, Tue Mar 18 23:08:12 2008 UTC
# Line 1  Line 1 
1    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
4    
5            * R/sparseMatrix.R (is.na): new simple method
6            * R/denseMatrix.R (is.na): ditto.
7    
8            * R/diagMatrix.R (.symDiagonal): newly exported utility.
9    
10            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
11    
12            * src/UFsparse_download.sh: -->
13            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
14    
15    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
18            functionality; barely tested in
19            * tests/factorizing.R
20    
21            * src/Csparse.c (diag_tC): new functionality to enable faster
22            determinant(<dsCMatrix>, .) in
23            * R/dsCMatrix.R
24    
25    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
26    
27            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
28              src/CHMfactor.c, src/CHMfactor.h,
29              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
30              Log-determinant of the parent matrix from a CHMfactor object as
31              chm_factor_ldetL2; documentation and support
32    
33    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
36    
37    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
40            warning.
41    
42    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
45    
46            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
47              <diagonal> o <sparse_triangular>
48              setAs(., "nMatrix") added.
49    
50            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
51    
52            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
53                    new argument 'checkDense = FALSE'.
54    
55    
56    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
59            back-permutation of the matrix exponential.
60    
61            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
62    
63            * DESCRIPTION (Date,Version): ready to release 0.999375-5
64    
65            * tests/simple.R: testing diagN2U
66    
67    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Auxiliaries.R (diagN2U): interface to
70    
71            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
72    
73            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
74    
75    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/chm_common.c (chm_diagN2U): new utility.
78    
79            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
80            make use of chm_diagN2U() and hence now preserve triangularity and
81            unit-triangularity.
82    
83            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
84    
85    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
88    
89            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
90            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
91    
92            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
93    
94            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
95    
96            * src/chm_common.c (AS_CHM_FINISH): add note about problem
97            for triangular (diag = "U").
98    
99    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
102            * R/bind.R:  .Call(dense_to_Csparse, *)
103    
104    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Matrix.R (Matrix): no longer use coercions to specific classes
107                    (since we are discouraging them in user code).
108    
109            * tests/*.R: also replaces coercions to specific classes by
110            coercions to super classes.
111    
112            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
113    
114    
115    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
118    
119            * src/dense.c (dense_band): generalized from ddense_band
120    
121            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
122              now for "denseMatrix" (instead of just "ddense*"); much
123              simplified setMethod()s for these.
124    
125            * src/dense.c (dense_to_symmetric): generalized from ddense_*
126    
127    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
130            version of as(*, "symmetricMatric").
131    
132            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
133            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
134    
135    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Matrix.R (subset.ij): utility, as first step to faster
138               M [ <ij-matrix> ] indexing.
139    
140            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
141    
142            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
143            for more efficient symmpart() and skewpart() methods.
144    
145            * src/Mutils.c (equal_string_vectors): utility
146    
147            * src/dense.c (ddense_to_symmetric): new function used in
148    
149            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
150    
151            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
152            order to match the generic (and evade .local(..)).
153    
154            * R/dsCMatrix.R: dgC -> dsC: use C code!
155    
156            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
157            as per TODO
158    
159            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
160    
161            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
162    
163    
164    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
167    
168            * R/Auxiliaries.R (non0.i): take out of non0ind
169    
170            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
171            make tril(), triu(), band() work for "matrix" and all "dense*"
172    
173            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
174            * tests/simple.R: test the fix above
175    
176            * R/sparseMatrix.R ([): simplification: no coerce to <general>
177                    before we use as(., <Tsparse>)[...] anyway
178    
179            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
180    
181            * R/triangularMatrix.R (isTriangular): methods for all subclasses
182            instead of "triangularMatrix" -- just to disambiguate
183    
184    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
187            * tests/indexing.R: example that fails above
188    
189    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
192            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
193                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
194    
195            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
196            * src/Tsparse.h, init.c: ditto
197            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
198                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
199            * R/sparseMatrix.R (isTriangular): hence simplified
200    
201    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Ops.R (.Arith.Csparse): new utility factored out of former
204              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
205    
206    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
209    
210            * inst/test-tools.R (isOrthogonal): new function; also file restructured
211    
212    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
215            coercion to "nMatrix" and "pMatrix"
216    
217            * R/AllClass.R: "Schur" class;  "number" class union
218            * man/number-class.Rd:
219            * man/Schur-class.Rd:
220    
221            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
222            (.simpleSchur): Schur() method for diagonal matrices
223            (.triSchur):    Schur() method for triangular matrices
224            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
225    
226    
227    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
230    
231    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
234                    in order to ensure 'system = *' is not lost;
235                    formals()$system instead of cut&paste.
236            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
237    
238    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Date): make ready for release --> 0.999375-4
241    
242            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
243    
244    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
247                    and hence does as.vector(.).
248            * man/pMatrix-class.Rd: docs
249            * R/sparseMatrix.R: fix for printing "integer sparse"
250    
251            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
252    
253            * R/Matrix.R and others: use "exact" function argument list for
254                    both "["   : (x, i,j, ..., drop)
255                    and  "[<-" : (x, i,j, ..., value)
256    
257            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
258            * R/Tsparse.R (replTmat):    ditto
259            * R/diagMatrix.R (replDiag): ditto
260            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
261            * tests/indexing.R: testing the above
262    
263    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/sparseMatrix.R (cov2cor): method for sparse matrices
266    
267            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
268    
269            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
270    
271            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
272    
273    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Matrix.R: "generic" cov2cor() method
276    
277            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
278                    speed up Q %*% D %*% t(Q)
279            * tests/dpoMatrix.R: test nearPD()
280    
281    2007-12-05  Doug Bates and Martin Maechler
282    
283            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
284            stats::xtabs() allowing to create sparse matrices.
285    
286    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
289    
290    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
293    
294    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/LU.R: solve() method for "denseLU"
297    
298    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * DESCRIPTION (Version): 0.999375-3 preparing for release
301    
302            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
303    
304            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
305    
306    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
309              thanks to Kasper Kristensen.
310            * tests/matprod.R: regression test for that.
311    
312    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
313    
314            * [r4778] R/AllGeneric.R: Check R version before defining generics for
315              primitives
316    
317    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/denseMatrix.R (rcond): method
320            * R/sparseQR.R (rcond): method, use x or t(x)
321    
322    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
325            matrices.
326            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
327    
328            * man/rcond.Rd: mention the more general definition, and add
329            example for non-square matrices.
330    
331            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
332    
333    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
336    
337    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
340            * tests/indexing.R: add new regression for the above cases.
341    
342    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * src/Mutils.h (__sun): clause for alloca.h on Solaris
345    
346    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * DESCRIPTION (Date, Version): 0.999375-2
349    
350    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/HBMM.R (readMM): make work for pattern matrices as well
353    
354    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
355    
356            * [r4730] src/Mutils.h: declare alloca
357            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
358              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
359              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
360              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
361              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
362              methods; switch writeMM to use CHOLMOD code; repair readMM
363    
364    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
367            Oehlschlaegel's ... result type still to be discussed!
368    
369    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * man/image-methods.Rd: new, combining all image() methods
372    
373    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
376            to work via dgC...
377    
378            * R/Matrix.R (Matrix): special treatment for "table" (S3)
379    
380    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/dgTMatrix.R (image): change defaults to
383                    aspect = "iso", colorkey = FALSE
384    
385    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
388            must copy its *expanded* x slot before LAPACK call.
389    
390            * tests/matprod.R: test the last days' changes.
391    
392    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
393    
394            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
395              as well as in sources
396            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
397              Lapack call
398    
399    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
402                    ("Matrix", "matrix") which is needed in some cases.
403            Ditto for solve().
404    
405            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
406            infinite recursion in dispatch for some cases.
407    
408    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
409    
410            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
411              so pointers match
412    
413    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * DESCRIPTION (Date): set ready for release -- 0.999375-1
416    
417    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
418    
419            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
420              src/chm_common.c, src/chm_common.h: Change API for
421              numeric_as_chm_dense and N_AS_CHM_DN
422    
423    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
426            * tests/matprod.R: regr.test for it
427    
428    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
431            * tests/group-methods.R: and regression-test it
432    
433    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
434    
435            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
436              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
437              triplet_to_sparse, documentation, use typedefs
438    
439    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * man/dpoMatrix-class.Rd: added 'corMatrix' example
442    
443            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
444            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
445            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
446    
447            * R/lsparseMatrix.R: bug fix in "all" method
448            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
449    
450            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
451            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
452                    + matrix |-> nMatrix coercion
453            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
454            * man/pMatrix-class.Rd: ditto
455    
456            * R/Matrix.R (Summary): method for non-dMatrix
457    
458            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
459            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
460                    test all Summary methods.
461    
462    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
465    
466    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
469    
470            * R/pMatrix.R (t?crossprod): methods for pMatrix
471    
472    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
473    
474            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
475    
476    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
477    
478            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
479              trying to fix a subtle bug - which has been somewhere else.
480    
481    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
482    
483            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
484              solve the bug
485    
486    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * src/dgCMatrix.c (compressed_to_TMatrix):
489    
490    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * src/Csparse.c (Rsparse_validate): new, to have some validity
493            checking for RsparseMatrix
494            * src/dgCMatrix.c (xRMatrix_validate): ditto
495            * src/dtCMatrix.c (tRMatrix_validate): ditto
496    
497    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
498    
499            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
500              lgRMatrix
501            * [r4568] DESCRIPTION: Prepare for bug-fix release
502            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
503              for declaration of cholmod_symmetry
504    
505    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
508            release.
509    
510    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
511    
512            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
513              functions - no longer used
514            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
515              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
516              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
517              Alloca
518    
519    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
520    
521            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
522              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
523              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
524              src/t_gCMatrix_colSums.c: more R_CheckStack()s
525    
526    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
527    
528            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
529              the required amount of memory then call M_numeric_as_chm_dense.
530            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
531              (like Calloc but calling alloca)
532    
533    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
536            and extended with more sophisticated 'col.names' option.
537            * NAMESPACE: export  printSparseMatrix()
538            * man/printSpMatrix.Rd: document, incl. examples
539    
540    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
541    
542            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
543              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
544              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
545    
546    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * DESCRIPTION (Version): 0.99875-4
549    
550            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
551            some dimnames perservation.
552    
553            * R/dsTMatrix.R (t-method): keep dimnames
554            * R/dtTMatrix.R:  ditto
555    
556            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
557            and ncol(.) < 10
558    
559            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
560            from Mutils.h
561    
562            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
563            e.g. in as(<ngCMatrix>, "matrix")
564    
565    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
566    
567            * [r4529] .: Create a branch for the API changes from the 0.99875
568              series to the 0.999375 series
569            * [r4530] DESCRIPTION, inst/include/Matrix.h,
570              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
571              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
572              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
573              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
574              as_cholmod_x functions
575    
576    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
577    
578            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
579              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
580              to Comparisons
581    
582    >>>>>>> .merge-right.r4561
583    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * DESCRIPTION (Version): 0.99875-3 ready to be released.
586    
587            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
588    
589            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
590            that should also work in a future version of R.
591    
592    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
595    
596            * R/sparseVector.R: more *sparseVector coercions, notably for
597            non - double ones.
598    
599    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
602              notably the new ones building on the new .Call(.)s:
603    
604            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
605            all 4 of [dlin]gCMatrix_colSums().
606    
607    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
608    
609            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
610            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
611              result
612    
613    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/kronecker.R: fix typo (could lead to inf.recursion)
616            * test/simple.R: testing that
617    
618            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
619            method as well (which can have arguments, show() can't).
620    
621    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
622    
623            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
624              added dgCMatrix_colSums for [col,row][Sums,Means]
625    
626    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
627    
628            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
629              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
630              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
631            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
632              class
633            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
634              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
635              row names to store the levels - duh!  Added an example.
636    
637    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * src/Csparse.c (Csparse_validate): check for *repeated* entries
640            thanks to example from Christian Buchta; with a test here:
641            * tests/simple.R:
642    
643    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
646            of colSums(*, sparseResult = TRUE)
647    
648    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
651            'na.rm = FALSE' as "everywhere" else in R.
652    
653    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
654    
655            * [r4421] src/CSparse_install.sh: Modify for new organization of
656              CSparse package
657            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
658              SuiteSparse
659            * [r4426] src/Makefile: add ./UFconfig to the include path for
660              compilation
661            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
662            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
663              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
664    
665    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
668            * R/sparseMatrix.R (prSpMatrix): now gives a message about
669            suppressed column names.
670    
671    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
672    
673            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
674              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
675              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
676              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
677              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
678              Remove warnings after change to const char* CHAR
679    
680    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
681    
682            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
683              type of M_cholmod_ssmult
684    
685    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
686    
687            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
688              src/init.c: Yet another cholmod export - cholmod_ssmult
689    
690    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * NAMESPACE: exported drop0(), since
693            * man/drop0.Rd: I have seen several cases, I really wanted to use
694            it, so our users may want too.
695    
696    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * man/colSums.Rd: separately document colSums() etc, since these
699            have the extra argument 'sparseResult'.
700    
701    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
704            * man/spMatrix.Rd: docu., including examples
705    
706            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
707            in order to make colMeans() etc fast *and* correct.
708            * R/sparseVector.R (replSPvec): "[<-" functionality for
709            sparseVectors; tested in
710            * tests/simple.R:
711    
712    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
715            (very) sparse Matrices; output similar to Matlab's print().
716    
717    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
718    
719            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
720            0-based, indices (Jose Quesada <quesada@gmail.com>).
721    
722    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
723    
724            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
725    
726    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * R/Auxiliaries.R (sparsapply): new utility, much faster than
729            tapply1() for large sparse matrices.
730    
731    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/Matrix.R (dim<-): reshape now via sparseVector.
734    
735            * R/sparseVector.R: methods and function for
736            * R/AllClass.R: new "sparseVector" class and daughters.
737            * NAMESPACE: export new classes
738    
739    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * DESCRIPTION (Version): 0.99875-1
742            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
743    
744    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
747            indexing
748            * tests/indexing.R: test set for that.
749    
750    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
753            entries.
754            * tests/indexing.R(out): add regression test for it
755    
756    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
759            name for "!" method definitions.
760    
761    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/Tsparse.R (intI): new utility, used for "[" :
764                    Cleanup up there, and fixes for duplicated indices - more TODO!
765    
766            * tests/indexing.R(out): more tests
767    
768    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
771            code that is now part of the R Lapack library.
772    
773            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
774            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
775    
776    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
779    
780    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
783            up with extraneous names '0'...'<n-1>'
784    
785    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/dgTMatrix.R (mat2dgT): care about NAs
788    
789    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/kronecker.R: triangularity preserving methods
792    
793    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/kronecker.R: new file collecting kronecker() methods in one
796                    place.  Goal: become much faster!
797    
798    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
801            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
802            can be much faster.
803    
804            * tests/matprod.R: add regression tests for these (upper & lower).
805    
806    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * R/Matrix.R (diff): method for our Matrices.
809    
810            * R/sparseMatrix.R (isDiagonal): check dim()!
811    
812    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/Matrix.R (dim<-): new method for "reshape()" built on a
815            proposal from Tamas Papp.
816    
817    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
820    
821            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
822            rather define and export  cBind() and rBind() only.
823            --> useRs *must* change code that used to have cbind()/rbind() !!
824    
825            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
826            * R/bind.Rout.save: ditto
827    
828    2007-02-16  Douglas Bates  <bates@r-project.org>
829    
830            * DESCRIPTION (Date, Version): 0.9975-11 with new date
831            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
832            const modifier on declaration of the array 'valid'
833    
834    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
835    
836            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
837    
838    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
841    
842            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
843            * tests/simple.R: test the above and some of these coercions:
844    
845            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
846                    be careful to avoid infinite recursion, using new coercions in
847            * R/ngCMatrix.R and nsC... and ntC...
848            * R/lsparseMatrix.R: ditto
849    
850            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
851    
852            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
853            * R/Rsparse.R: reactivate .Call()s
854    
855            * tests/Class+Meth.R: a bit more on actual classes
856    
857    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
858    
859            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
860    
861    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * DESCRIPTION (Version): 0.9975-10 to upload
864    
865            * tests/Class+Meth.R (tstMatrixClass): require coercions to
866            specific classes less unconditionally.
867    
868            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
869    
870            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
871    
872            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
873            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
874            R_to_CMatrix segfaults on one platform.
875            Eliminate most coercion method to *specific* classes, and replace
876            with virtual classes coercions.
877    
878    
879    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
880    
881            * src/init.c: export the CHM...._validate() placeholders, since
882            they *are* called.
883    
884            * tests/Class+Meth.R (classCanCoerce): and starting to test
885            all as(<from>, <to>)
886    
887    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
890            * tests/indexing.R: tested now
891            * tests/indexing.Rout.save: updated
892    
893            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
894            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
895            appropriate.
896    
897            * NAMESPACE: export a trivial
898            * R/Matrix.R: drop() Matrix-method
899    
900            * R/AllClass.R: moved all prototypes to virtual super classes.
901    
902            * R/Rsparse.R: many more coercions to have less exceptions in
903            * tests/Class+Meth.R:
904    
905            * R/Ops.R (Compare): tweak for case with NA
906            * tests/simpl.R: hence another 'FIXME' eliminated
907    
908    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
911            objects.
912    
913            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
914              and more of "!", "&", "|", all, any; coercions
915    
916            * R/Rsparse.R: many coercions (which enable quite a few other
917            methods), thanks to enhancements in
918            * src/dgCMatrix.c (R_to_CMatrix): new, and
919            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
920            symmetric & triangular and ..RMatrix objects.
921    
922            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
923            renamed file from src/dsTMatrix.c;
924            now dealing with symmetric and triangular Tsparse coercions, both
925            to dense and general.
926    
927    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
928    
929            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
930    
931            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
932            where sensible when the <numeric> is of length > 1.
933    
934    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * R/Matrix.R ([<-): for M[] <- value: fix length
937    
938    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
941            * R/ndenseMatrix.R: new coercions n* -> l*
942    
943    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
946    
947            * R/Ops.R ("Logic"): and other "Ops", many updates
948    
949    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * src/Mutils.h (SET_DimNames): new utility
952    
953            * R/Auxiliaries.R (nnzero): improved and now exported via
954    
955            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
956    
957    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
958    
959            * R/diagMatrix.R (!): fix typo.
960    
961    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * R/Auxiliaries.R (as_Csparse): and quite a few others:
964                    allow to pass class definition --> speedup
965            * R/sparseMatrix.R: apply the above
966    
967            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
968    
969            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
970            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
971            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
972    
973            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
974    
975            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
976            and use it for "sparse*" as well, since it's faster than the
977            as_Csparse(.) way.
978    
979    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
982    
983    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
986            as method for   M[ ij ] <- v
987            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
988    
989            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
990            FALSE answer
991    
992            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
993            * tests/indexing.R: test it, and some of the above
994    
995    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/Auxiliaries.R (is_duplicatedT): new utility
998    
999    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1000    
1001            * src/init.c (R_init_Matrix): export cholmod_scale
1002    
1003    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1006            base::as.matrix to (x, ...)
1007    
1008    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1009    
1010            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1011            file; start using "Logic", hence
1012    
1013            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1014            * NAMESPACE: import and export "Logic"
1015    
1016    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1019            only needed previously to R version 2.5.0.
1020    
1021    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1024    
1025            * R/Tsparse.R (replTmat): fix subassignment of triangular
1026            * R/Csparse.R (replCmat): ditto
1027            * tests/indexing.R: more tests, incl the above fix
1028    
1029    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1030    
1031            * R/Auxiliaries.R (drop0): extend for non CSparse
1032            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1033    
1034            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1035                    use uplo correctly (!); other places: use uplo_P() macro
1036    
1037            * R/Csparse.R (replCmat): call diagU2N() when needed
1038            * R/Tsparse.R (replTmat): ditto
1039    
1040            * src/dtCMatrix.c (tCMatrix_validate): new
1041            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1042            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1043    
1044            * R/diagMatrix.R (replDiag): to use in [<-
1045    
1046    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1049                    also more general diagU2N().
1050    
1051    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1054            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1055    
1056    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * tests/bind.R: a few more cases
1059            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1060    
1061            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1062            * R/ddenseMatrix.R (cbind2/rbind2)
1063            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1064            * tests/indexing.R
1065            * tests/indexing.Rout.save: updated
1066    
1067    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1070            * tests/indexing.R
1071    
1072    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1075            align with proper position of "0", i.e., right for integers.
1076            argument 'align' by default is "fancy".
1077    
1078    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1081            * R/Csparse.R: and fix "Compare" for more cases.
1082            * tests/Class+Meth.R: test some of these (m == m, m != m)
1083    
1084    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/lsparseMatrix.R: all() and any() methods
1087            * R/ldenseMatrix.R:      ditto
1088            * NAMESPACE, R/Matrix.R: ditto
1089    
1090            * man/all-methods.Rd: document them minimally
1091    
1092            * tests/simple.R: add a few examples for these
1093    
1094    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/Tsparse.R ([): fix long standing typo in symmetric case
1097            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1098    
1099    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1100    
1101            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1102            to LL before converting to a sparse matrix. (The LDL form can be
1103            converted to a sparse matrix but it is implicitly a unit
1104            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1105    
1106    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1107    
1108            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1109    
1110    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1111    
1112            * DESCRIPTION (Version): updated -> release 0.9975-7
1113            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1114    
1115    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1116    
1117            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1118    
1119    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1120    
1121            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1122            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1123            is exactly singular.
1124    
1125    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1126    
1127            * DESCRIPTION (Date): updated -> release 0.9975-6
1128    
1129    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1132            now returns symmetric.
1133    
1134            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1135    
1136            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1137            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1138    
1139            * R/Auxiliaries.R (.type.kind): added
1140    
1141    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1142    
1143            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1144            running src/CSparse_install.sh
1145    
1146            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1147    
1148    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1149    
1150            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1151            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1152    
1153            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1154    
1155            * tests/Class+Meth.R (tstMatrixClass): now assure
1156            the (important in method programming) property :
1157    
1158                    ###>>  Every "Matrix" is either
1159                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1160    
1161                    (where "*" stands for "Matrix")
1162    
1163            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1164    
1165            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1166            * tests/validObj.R: checks for "comparison"
1167    
1168            * R/sparseMatrix.R ([): improved indexing for sparse;
1169                    trying to keep <symmetric>[ n, n] symmmetric
1170    
1171            * tests/indexing.R: indexing for logical sparse now ok
1172    
1173    
1174    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1177    
1178            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1179    
1180    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1183    
1184            * tests/simple.R: validObject() checking the above.
1185    
1186            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1187            replacing both dgCMatrix_validate and lgCM*.
1188    
1189            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1190            fix dimnames setting in other places.
1191            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1192    
1193    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1194    
1195            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1196    
1197            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1198            symmetry test, via
1199            * R/Auxiliaries.R (.as.dgC.0.factors):
1200    
1201    2006-11-01  Douglas Bates  <bates@r-project.org>
1202    
1203            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1204            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1205            <CsparseMatrix>) added
1206    
1207    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1208    
1209            * tests/matprod.R: add a variation of Harri's example
1210    
1211            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1212            recursive infinitely.
1213    
1214            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1215    
1216            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1217    
1218    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1221            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1222            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1223            satisfy the above test.
1224    
1225    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1226    
1227            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1228    
1229            * R/dgCMatrix.R: solve(a, b="missing") based on
1230            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1231            RHS = NULL.
1232    
1233            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1234            add more (needed) [t]crossprod() methods.
1235    
1236            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1237    
1238            * R/Auxiliaries.R (as_CspClass): cleanup
1239            (drop0): internal utility for "Csparse_drop(*, 0)"
1240            (.bail.out.2): encourage active feedback
1241    
1242    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1245    
1246            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1247            non-valid or 'sorted' case).
1248    
1249            * R/dsparseMatrix.R: add "chol" method.
1250            * R/ddenseMatrix.R: ditto
1251    
1252            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1253            * NAMESPACE (Ops)
1254            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1255            coercion; deprecating direct lower level coercions.
1256    
1257            * R/*.R (seq): use seq_len() and seq_along() where possible.
1258    
1259    
1260    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1261    
1262            * DESCRIPTION (Version): 0.9975-5 ready for release
1263    
1264    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1265    
1266            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1267    
1268    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1269    
1270            * R/AllClass.R (corMatrix): add 'validity' check;
1271                    comment out unused "LDL" class definition
1272            * NAMESPACE: mention, but do not export "LDL" class
1273            * R/corMatrix.R: new (simple), needed for R-devel with
1274            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1275              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1276    
1277    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1278    
1279            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1280            use Rprintf and R's error handling.
1281    
1282    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1283    
1284            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1285            * tests/matprod.R: add tests for the bug fixed.
1286    
1287    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1288    
1289            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1290            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1291    
1292    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1293    
1294            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1295    
1296    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1297    
1298            * DESCRIPTION (Version): 0.9975-3
1299    
1300            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1301            (sparse) matrices.
1302            * man/bdiag.Rd: docu + examples
1303    
1304            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1305    
1306            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1307            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1308    
1309            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1310            that result is sparse or diagonal (and not dense).
1311    
1312            * man/Subassign-methods.Rd: fix examples
1313    
1314            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1315            should always return a sparse (and not sometimes a diagonal) matrix.
1316    
1317    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1318    
1319            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1320    
1321    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1322    
1323            * DESCRIPTION (Version): 0.9975-2
1324    
1325            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1326    
1327    2006-10-02  Douglas Bates  <bates@R-project.org>
1328    
1329            * tests/dg_Matrix.R: Simplify test taking into account new code.
1330    
1331    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1332    
1333            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1334    
1335            * R/lsTMatrix.R: new files w/ missing methods
1336            * R/nsTMatrix.R:  "  'for completeness'
1337    
1338            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1339    
1340            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1341    
1342    
1343    2006-09-28  Douglas Bates  <bates@R-project.org>
1344    
1345            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1346            included.
1347    
1348            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1349            Export C-callable functions used in Zt_create in lme4.
1350    
1351    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1352    
1353            * DESCRIPTION (Version): 0.9975-1
1354    
1355            * tests/simple.R: less checks fail; using NA, found that our
1356                    kronecker() is not base-compatible with NA's.
1357    
1358            * R/dMatrix.R: "Compare" method now implemented for all cases
1359    
1360            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1361    
1362            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1363    
1364            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1365            * src/dspMatrix.c (dspMatrix_validate): ditto
1366    
1367            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1368              including coercion to [nl]tTMatrix.
1369    
1370            * R/diagMatrix.R (show): print a header line as for other classes.
1371    
1372    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1373    
1374            * src/Makefile.win (SUBDIRS): fix typo
1375    
1376    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1377    
1378            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1379    
1380    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1381    
1382            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1383            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1384            accept a symmetric matrix).
1385            * tests/group-methods.R: Uncomment test of crossprod applied to
1386            lsCMatrix objects.
1387    
1388    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * R/AllClass.R (symmetricMatrix): add validity method (available
1391            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1392    
1393            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1394    
1395            * tests/indexing.Rout.save:
1396            * tests/indexing.R: additions, mainly for 'lsparse'
1397    
1398            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1399            case.
1400    
1401            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1402    
1403    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1404    
1405            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1406                    as 'N' (1-letter - Ok?)
1407    
1408            * tests/group-methods.R: add test for logical + NAs
1409    
1410            * R/dMatrix.R ("Compare"): fix to work with NA's
1411    
1412            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1413    
1414            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1415                    which is implemented.
1416    
1417    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1418    
1419            * src/chm_common.c: coerce logical <-> double instead of
1420            typecasting;  needed for "l" matrix handling in cholmod.
1421    
1422            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1423    
1424            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1425            (Tsp2grNEL): other fixes needed
1426    
1427    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1428    
1429            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1430                    Matrices, since "lMatrix", also "lsparseM" can have NA
1431            * R/ndenseMatrix.R, etc: new source files
1432            * man/nsparseMatrix-classes.Rd, etc: new help files
1433            * tests/: adaptions
1434            * src/chm_common.c (chm_dense_to_SEXP): and others:
1435                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1436            * src/Csparse.c, etc: ditto
1437    
1438    2006-09-11  Douglas Bates  <bates@R-project.org>
1439    
1440            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1441            alloc_d**Matrix functions to the lme4 package.
1442    
1443    2006-09-09  Douglas Bates  <bates@R-project.org>
1444    
1445            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1446            fixed
1447    
1448    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1449    
1450            * R/lMatrix.R: new
1451    
1452            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1453    
1454            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1455            * man/tcrossprod.Rd: ditto
1456    
1457    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1458    
1459            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1460            for exported functions
1461            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1462            Remove partitioning algorithms for sparse matrix reordering.  The
1463            copyright on the Metis code was problematic and the methods were
1464            rarely used.
1465            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1466            operations are now done entirely in CHOLMOD code.
1467    
1468    2006-09-06  Douglas Bates  <bates@R-project.org>
1469    
1470            * src/Mutils.h: Remove functions that are no longer used.
1471    
1472    2006-09-04  Douglas Bates  <bates@R-project.org>
1473    
1474            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1475            * src/DEPS.mkf: update
1476    
1477    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1478    
1479            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1480            * DESCRIPTION (Version): 0.9975-0
1481            (Depends): R (>= 2.4.0)
1482    
1483    2006-09-01  Douglas Bates  <bates@R-project.org>
1484    
1485            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1486    
1487    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1488    
1489            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1490            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1491    
1492            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1493    
1494    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1495    
1496            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1497            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1498            * R/dsparseMatrix.R: ditto
1499            * R/Csparse.R: ditto
1500    
1501    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1502    
1503            * R/dMatrix.R (Compare): improve availability of "<", etc
1504            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1505    
1506    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1507    
1508            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1509            of a 0-index which was used as 1-index (..hmm)
1510    
1511            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1512    
1513            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1514            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1515            (.is.diagonal): ditto
1516    
1517            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1518    
1519            * R/Matrix.R (Matrix): also work for NA data
1520    
1521    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1522    
1523            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1524            in all cases.
1525    
1526    2006-08-27  Douglas Bates  <bates@R-project.org>
1527    
1528            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1529            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1530    
1531    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1532    
1533            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1534            subclasses of "ddenseMatrix"
1535            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1536            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1537            instead of half dozen specialized ones.
1538    
1539    2006-08-25  Douglas Bates  <bates@R-project.org>
1540    
1541            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1542            <tillard@cirad.fr> - ordering standard errors to match effects.
1543    
1544    2006-08-24  Douglas Bates  <bates@R-project.org>
1545    
1546            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1547            on R_ldl.
1548            * R/lCholCMatrix.R,
1549            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1550            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1551            * many files in ./R and ./src: Use more general version of
1552            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1553            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1554            dtpMatrix, dspMatrix and dppMatrix conversions.
1555    
1556    
1557    2006-08-23  Douglas Bates  <bates@R-project.org>
1558    
1559            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1560            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1561            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1562            dgeMatrix_crossprod (may need to do this in other places).
1563            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1564            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1565    
1566    2006-08-22  Douglas Bates  <bates@R-project.org>
1567    
1568            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1569            types of classed Matrices, matrices or numeric or logical vectors.
1570            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1571            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1572            to Mutils.h (as an inline) and change name to Matrix_check_class;
1573            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1574            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1575            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1576            * src/Csparse.c: use diag_P and uplo_P macros.
1577    
1578    2006-08-21  Douglas Bates  <bates@R-project.org>
1579    
1580            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1581            valgrind.
1582            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1583            inverses.
1584            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1585            -Wall warnings.
1586            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1587            Use dup_mMatrix_as_dgeMatrix.
1588    
1589    2006-08-20  Douglas Bates  <bates@R-project.org>
1590    
1591            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1592            * tests/sparseQR.R: Added
1593            * man/sparseQR-class.Rd: Document methods for qr.* generics
1594            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1595    
1596    2006-08-19  Douglas Bates  <bates@R-project.org>
1597    
1598            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1599            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1600            and qr.fitted.
1601            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1602            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1603    
1604    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1605    
1606            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1607            the base version has no "..." argument.
1608    
1609            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1610    
1611            * R/Matrix.R: define and
1612            * NAMESPACE: export as.numeric() and as.logical() methods.
1613                    Let's hope these do not badly slow down something...
1614            Finally export the zapsmall() method.
1615    
1616    2006-08-17  Douglas Bates  <bates@R-project.org>
1617    
1618            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1619            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1620            * src/dtCMatrix.c :Remove code that is no longer used
1621            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1622    
1623    2006-08-14  Douglas Bates  <bates@R-project.org>
1624    
1625            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1626            Csparse_to_logical and Csparse_symmetric_to_general.
1627            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1628            coercion methods between CsparseMatrix and TsparseMatrix.
1629    
1630    2006-08-14  Douglas Bates  <bates@R-project.org>
1631    
1632            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1633            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1634            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1635            possible.
1636    
1637  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
1638    
1639          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

Legend:
Removed from v.1368  
changed lines
  Added in v.2144

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge