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revision 1360, Tue Aug 8 17:29:03 2006 UTC revision 2159, Sat Mar 29 08:09:05 2008 UTC
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1    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375-9 --- need to release
4            for R-devel (and R 2.7.0 alpha soon).
5    
6            * R/sparseMatrix.R (summary): count NAs
7    
8    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
11            order to become compatible to new R 2.7.0 base::rcond().
12    
13    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
16    
17            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
18    
19            * inst/test-tools.R (isValid): new utility, used much in
20            * tests/simple.R:
21    
22            * man/BunchKaufman-methods.Rd: added too
23    
24    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dsyMatrix.R: add BunchKaufman() methods.
27            * R/dspMatrix.R:
28    
29            * src/init.c: add dsyMatrix_trf
30    
31    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
32    
33            * DESCRIPTION (Version): release 0.999375-7
34            * src/CHMfactor.c (CHMfactor_update): fix
35    
36    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
39            internal_chm_factor().
40    
41            * R/AllGeneric.R: do *not* define a "chol" generic
42                    (but rather use the implicit one *without* making pivot
43                    part of the signature)
44            * R/*.R: drop the 'pivot' from chol's signature and make
45                    'pivot=FALSE' a default argument of method definitions.
46    
47            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
48            version of Matrix
49    
50    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
53    
54            * R/sparseMatrix.R (is.na): new simple method
55            * R/denseMatrix.R (is.na): ditto.
56    
57            * R/diagMatrix.R (.symDiagonal): newly exported utility.
58    
59            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
60    
61            * src/UFsparse_download.sh: -->
62            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
63    
64    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
67            functionality; barely tested in
68            * tests/factorizing.R
69    
70            * src/Csparse.c (diag_tC): new functionality to enable faster
71            determinant(<dsCMatrix>, .) in
72            * R/dsCMatrix.R
73    
74    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
75    
76            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
77              src/CHMfactor.c, src/CHMfactor.h,
78              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
79              Log-determinant of the parent matrix from a CHMfactor object as
80              chm_factor_ldetL2; documentation and support
81    
82    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
85    
86    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
89            warning.
90    
91    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
94    
95            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
96              <diagonal> o <sparse_triangular>
97              setAs(., "nMatrix") added.
98    
99            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
100    
101            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
102                    new argument 'checkDense = FALSE'.
103    
104    
105    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
108            back-permutation of the matrix exponential.
109    
110            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
111    
112            * DESCRIPTION (Date,Version): ready to release 0.999375-5
113    
114            * tests/simple.R: testing diagN2U
115    
116    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Auxiliaries.R (diagN2U): interface to
119    
120            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
121    
122            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
123    
124    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * src/chm_common.c (chm_diagN2U): new utility.
127    
128            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
129            make use of chm_diagN2U() and hence now preserve triangularity and
130            unit-triangularity.
131    
132            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
133    
134    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
137    
138            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
139            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
140    
141            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
142    
143            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
144    
145            * src/chm_common.c (AS_CHM_FINISH): add note about problem
146            for triangular (diag = "U").
147    
148    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
151            * R/bind.R:  .Call(dense_to_Csparse, *)
152    
153    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Matrix.R (Matrix): no longer use coercions to specific classes
156                    (since we are discouraging them in user code).
157    
158            * tests/*.R: also replaces coercions to specific classes by
159            coercions to super classes.
160    
161            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
162    
163    
164    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
167    
168            * src/dense.c (dense_band): generalized from ddense_band
169    
170            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
171              now for "denseMatrix" (instead of just "ddense*"); much
172              simplified setMethod()s for these.
173    
174            * src/dense.c (dense_to_symmetric): generalized from ddense_*
175    
176    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
179            version of as(*, "symmetricMatric").
180    
181            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
182            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
183    
184    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Matrix.R (subset.ij): utility, as first step to faster
187               M [ <ij-matrix> ] indexing.
188    
189            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
190    
191            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
192            for more efficient symmpart() and skewpart() methods.
193    
194            * src/Mutils.c (equal_string_vectors): utility
195    
196            * src/dense.c (ddense_to_symmetric): new function used in
197    
198            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
199    
200            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
201            order to match the generic (and evade .local(..)).
202    
203            * R/dsCMatrix.R: dgC -> dsC: use C code!
204    
205            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
206            as per TODO
207    
208            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
209    
210            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
211    
212    
213    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
216    
217            * R/Auxiliaries.R (non0.i): take out of non0ind
218    
219            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
220            make tril(), triu(), band() work for "matrix" and all "dense*"
221    
222            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
223            * tests/simple.R: test the fix above
224    
225            * R/sparseMatrix.R ([): simplification: no coerce to <general>
226                    before we use as(., <Tsparse>)[...] anyway
227    
228            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
229    
230            * R/triangularMatrix.R (isTriangular): methods for all subclasses
231            instead of "triangularMatrix" -- just to disambiguate
232    
233    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
236            * tests/indexing.R: example that fails above
237    
238    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
241            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
242                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
243    
244            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
245            * src/Tsparse.h, init.c: ditto
246            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
247                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
248            * R/sparseMatrix.R (isTriangular): hence simplified
249    
250    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/Ops.R (.Arith.Csparse): new utility factored out of former
253              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
254    
255    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
258    
259            * inst/test-tools.R (isOrthogonal): new function; also file restructured
260    
261    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
264            coercion to "nMatrix" and "pMatrix"
265    
266            * R/AllClass.R: "Schur" class;  "number" class union
267            * man/number-class.Rd:
268            * man/Schur-class.Rd:
269    
270            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
271            (.simpleSchur): Schur() method for diagonal matrices
272            (.triSchur):    Schur() method for triangular matrices
273            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
274    
275    
276    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
279    
280    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
283                    in order to ensure 'system = *' is not lost;
284                    formals()$system instead of cut&paste.
285            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
286    
287    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * DESCRIPTION (Date): make ready for release --> 0.999375-4
290    
291            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
292    
293    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
296                    and hence does as.vector(.).
297            * man/pMatrix-class.Rd: docs
298            * R/sparseMatrix.R: fix for printing "integer sparse"
299    
300            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
301    
302            * R/Matrix.R and others: use "exact" function argument list for
303                    both "["   : (x, i,j, ..., drop)
304                    and  "[<-" : (x, i,j, ..., value)
305    
306            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
307            * R/Tsparse.R (replTmat):    ditto
308            * R/diagMatrix.R (replDiag): ditto
309            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
310            * tests/indexing.R: testing the above
311    
312    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/sparseMatrix.R (cov2cor): method for sparse matrices
315    
316            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
317    
318            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
319    
320            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
321    
322    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Matrix.R: "generic" cov2cor() method
325    
326            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
327                    speed up Q %*% D %*% t(Q)
328            * tests/dpoMatrix.R: test nearPD()
329    
330    2007-12-05  Doug Bates and Martin Maechler
331    
332            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
333            stats::xtabs() allowing to create sparse matrices.
334    
335    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
338    
339    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
342    
343    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/LU.R: solve() method for "denseLU"
346    
347    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * DESCRIPTION (Version): 0.999375-3 preparing for release
350    
351            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
352    
353            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
354    
355    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
358              thanks to Kasper Kristensen.
359            * tests/matprod.R: regression test for that.
360    
361    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
362    
363            * [r4778] R/AllGeneric.R: Check R version before defining generics for
364              primitives
365    
366    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/denseMatrix.R (rcond): method
369            * R/sparseQR.R (rcond): method, use x or t(x)
370    
371    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
374            matrices.
375            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
376    
377            * man/rcond.Rd: mention the more general definition, and add
378            example for non-square matrices.
379    
380            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
381    
382    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
385    
386    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
389            * tests/indexing.R: add new regression for the above cases.
390    
391    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * src/Mutils.h (__sun): clause for alloca.h on Solaris
394    
395    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * DESCRIPTION (Date, Version): 0.999375-2
398    
399    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/HBMM.R (readMM): make work for pattern matrices as well
402    
403    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
404    
405            * [r4730] src/Mutils.h: declare alloca
406            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
407              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
408              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
409              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
410              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
411              methods; switch writeMM to use CHOLMOD code; repair readMM
412    
413    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
416            Oehlschlaegel's ... result type still to be discussed!
417    
418    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * man/image-methods.Rd: new, combining all image() methods
421    
422    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
425            to work via dgC...
426    
427            * R/Matrix.R (Matrix): special treatment for "table" (S3)
428    
429    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/dgTMatrix.R (image): change defaults to
432                    aspect = "iso", colorkey = FALSE
433    
434    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
437            must copy its *expanded* x slot before LAPACK call.
438    
439            * tests/matprod.R: test the last days' changes.
440    
441    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
442    
443            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
444              as well as in sources
445            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
446              Lapack call
447    
448    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
451                    ("Matrix", "matrix") which is needed in some cases.
452            Ditto for solve().
453    
454            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
455            infinite recursion in dispatch for some cases.
456    
457    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
458    
459            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
460              so pointers match
461    
462    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * DESCRIPTION (Date): set ready for release -- 0.999375-1
465    
466    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
467    
468            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
469              src/chm_common.c, src/chm_common.h: Change API for
470              numeric_as_chm_dense and N_AS_CHM_DN
471    
472    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
475            * tests/matprod.R: regr.test for it
476    
477    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
478    
479            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
480            * tests/group-methods.R: and regression-test it
481    
482    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
483    
484            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
485              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
486              triplet_to_sparse, documentation, use typedefs
487    
488    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * man/dpoMatrix-class.Rd: added 'corMatrix' example
491    
492            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
493            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
494            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
495    
496            * R/lsparseMatrix.R: bug fix in "all" method
497            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
498    
499            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
500            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
501                    + matrix |-> nMatrix coercion
502            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
503            * man/pMatrix-class.Rd: ditto
504    
505            * R/Matrix.R (Summary): method for non-dMatrix
506    
507            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
508            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
509                    test all Summary methods.
510    
511    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
514    
515    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
518    
519            * R/pMatrix.R (t?crossprod): methods for pMatrix
520    
521    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
522    
523            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
524    
525    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
526    
527            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
528              trying to fix a subtle bug - which has been somewhere else.
529    
530    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
531    
532            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
533              solve the bug
534    
535    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * src/dgCMatrix.c (compressed_to_TMatrix):
538    
539    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * src/Csparse.c (Rsparse_validate): new, to have some validity
542            checking for RsparseMatrix
543            * src/dgCMatrix.c (xRMatrix_validate): ditto
544            * src/dtCMatrix.c (tRMatrix_validate): ditto
545    
546    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
547    
548            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
549              lgRMatrix
550            * [r4568] DESCRIPTION: Prepare for bug-fix release
551            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
552              for declaration of cholmod_symmetry
553    
554    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
557            release.
558    
559    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
560    
561            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
562              functions - no longer used
563            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
564              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
565              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
566              Alloca
567    
568    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
569    
570            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
571              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
572              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
573              src/t_gCMatrix_colSums.c: more R_CheckStack()s
574    
575    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
576    
577            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
578              the required amount of memory then call M_numeric_as_chm_dense.
579            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
580              (like Calloc but calling alloca)
581    
582    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
585            and extended with more sophisticated 'col.names' option.
586            * NAMESPACE: export  printSparseMatrix()
587            * man/printSpMatrix.Rd: document, incl. examples
588    
589    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
590    
591            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
592              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
593              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
594    
595    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * DESCRIPTION (Version): 0.99875-4
598    
599            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
600            some dimnames perservation.
601    
602            * R/dsTMatrix.R (t-method): keep dimnames
603            * R/dtTMatrix.R:  ditto
604    
605            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
606            and ncol(.) < 10
607    
608            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
609            from Mutils.h
610    
611            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
612            e.g. in as(<ngCMatrix>, "matrix")
613    
614    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
615    
616            * [r4529] .: Create a branch for the API changes from the 0.99875
617              series to the 0.999375 series
618            * [r4530] DESCRIPTION, inst/include/Matrix.h,
619              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
620              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
621              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
622              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
623              as_cholmod_x functions
624    
625    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
626    
627            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
628              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
629              to Comparisons
630    
631    >>>>>>> .merge-right.r4561
632    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * DESCRIPTION (Version): 0.99875-3 ready to be released.
635    
636            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
637    
638            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
639            that should also work in a future version of R.
640    
641    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
644    
645            * R/sparseVector.R: more *sparseVector coercions, notably for
646            non - double ones.
647    
648    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
651              notably the new ones building on the new .Call(.)s:
652    
653            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
654            all 4 of [dlin]gCMatrix_colSums().
655    
656    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
657    
658            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
659            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
660              result
661    
662    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/kronecker.R: fix typo (could lead to inf.recursion)
665            * test/simple.R: testing that
666    
667            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
668            method as well (which can have arguments, show() can't).
669    
670    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
671    
672            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
673              added dgCMatrix_colSums for [col,row][Sums,Means]
674    
675    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
676    
677            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
678              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
679              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
680            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
681              class
682            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
683              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
684              row names to store the levels - duh!  Added an example.
685    
686    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * src/Csparse.c (Csparse_validate): check for *repeated* entries
689            thanks to example from Christian Buchta; with a test here:
690            * tests/simple.R:
691    
692    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
695            of colSums(*, sparseResult = TRUE)
696    
697    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
700            'na.rm = FALSE' as "everywhere" else in R.
701    
702    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
703    
704            * [r4421] src/CSparse_install.sh: Modify for new organization of
705              CSparse package
706            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
707              SuiteSparse
708            * [r4426] src/Makefile: add ./UFconfig to the include path for
709              compilation
710            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
711            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
712              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
713    
714    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
717            * R/sparseMatrix.R (prSpMatrix): now gives a message about
718            suppressed column names.
719    
720    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
721    
722            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
723              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
724              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
725              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
726              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
727              Remove warnings after change to const char* CHAR
728    
729    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
730    
731            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
732              type of M_cholmod_ssmult
733    
734    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
735    
736            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
737              src/init.c: Yet another cholmod export - cholmod_ssmult
738    
739    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * NAMESPACE: exported drop0(), since
742            * man/drop0.Rd: I have seen several cases, I really wanted to use
743            it, so our users may want too.
744    
745    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * man/colSums.Rd: separately document colSums() etc, since these
748            have the extra argument 'sparseResult'.
749    
750    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
753            * man/spMatrix.Rd: docu., including examples
754    
755            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
756            in order to make colMeans() etc fast *and* correct.
757            * R/sparseVector.R (replSPvec): "[<-" functionality for
758            sparseVectors; tested in
759            * tests/simple.R:
760    
761    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
764            (very) sparse Matrices; output similar to Matlab's print().
765    
766    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
767    
768            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
769            0-based, indices (Jose Quesada <quesada@gmail.com>).
770    
771    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
772    
773            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
774    
775    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/Auxiliaries.R (sparsapply): new utility, much faster than
778            tapply1() for large sparse matrices.
779    
780    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * R/Matrix.R (dim<-): reshape now via sparseVector.
783    
784            * R/sparseVector.R: methods and function for
785            * R/AllClass.R: new "sparseVector" class and daughters.
786            * NAMESPACE: export new classes
787    
788    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * DESCRIPTION (Version): 0.99875-1
791            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
792    
793    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
796            indexing
797            * tests/indexing.R: test set for that.
798    
799    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
802            entries.
803            * tests/indexing.R(out): add regression test for it
804    
805    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
808            name for "!" method definitions.
809    
810    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/Tsparse.R (intI): new utility, used for "[" :
813                    Cleanup up there, and fixes for duplicated indices - more TODO!
814    
815            * tests/indexing.R(out): more tests
816    
817    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
818    
819            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
820            code that is now part of the R Lapack library.
821    
822            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
823            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
824    
825    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
826    
827            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
828    
829    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
832            up with extraneous names '0'...'<n-1>'
833    
834    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/dgTMatrix.R (mat2dgT): care about NAs
837    
838    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/kronecker.R: triangularity preserving methods
841    
842    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/kronecker.R: new file collecting kronecker() methods in one
845                    place.  Goal: become much faster!
846    
847    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
850            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
851            can be much faster.
852    
853            * tests/matprod.R: add regression tests for these (upper & lower).
854    
855    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/Matrix.R (diff): method for our Matrices.
858    
859            * R/sparseMatrix.R (isDiagonal): check dim()!
860    
861    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/Matrix.R (dim<-): new method for "reshape()" built on a
864            proposal from Tamas Papp.
865    
866    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
869    
870            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
871            rather define and export  cBind() and rBind() only.
872            --> useRs *must* change code that used to have cbind()/rbind() !!
873    
874            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
875            * R/bind.Rout.save: ditto
876    
877    2007-02-16  Douglas Bates  <bates@r-project.org>
878    
879            * DESCRIPTION (Date, Version): 0.9975-11 with new date
880            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
881            const modifier on declaration of the array 'valid'
882    
883    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
884    
885            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
886    
887    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
890    
891            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
892            * tests/simple.R: test the above and some of these coercions:
893    
894            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
895                    be careful to avoid infinite recursion, using new coercions in
896            * R/ngCMatrix.R and nsC... and ntC...
897            * R/lsparseMatrix.R: ditto
898    
899            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
900    
901            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
902            * R/Rsparse.R: reactivate .Call()s
903    
904            * tests/Class+Meth.R: a bit more on actual classes
905    
906    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
907    
908            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
909    
910    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * DESCRIPTION (Version): 0.9975-10 to upload
913    
914            * tests/Class+Meth.R (tstMatrixClass): require coercions to
915            specific classes less unconditionally.
916    
917            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
918    
919            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
920    
921            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
922            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
923            R_to_CMatrix segfaults on one platform.
924            Eliminate most coercion method to *specific* classes, and replace
925            with virtual classes coercions.
926    
927    
928    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
929    
930            * src/init.c: export the CHM...._validate() placeholders, since
931            they *are* called.
932    
933            * tests/Class+Meth.R (classCanCoerce): and starting to test
934            all as(<from>, <to>)
935    
936    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
939            * tests/indexing.R: tested now
940            * tests/indexing.Rout.save: updated
941    
942            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
943            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
944            appropriate.
945    
946            * NAMESPACE: export a trivial
947            * R/Matrix.R: drop() Matrix-method
948    
949            * R/AllClass.R: moved all prototypes to virtual super classes.
950    
951            * R/Rsparse.R: many more coercions to have less exceptions in
952            * tests/Class+Meth.R:
953    
954            * R/Ops.R (Compare): tweak for case with NA
955            * tests/simpl.R: hence another 'FIXME' eliminated
956    
957    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
958    
959            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
960            objects.
961    
962            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
963              and more of "!", "&", "|", all, any; coercions
964    
965            * R/Rsparse.R: many coercions (which enable quite a few other
966            methods), thanks to enhancements in
967            * src/dgCMatrix.c (R_to_CMatrix): new, and
968            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
969            symmetric & triangular and ..RMatrix objects.
970    
971            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
972            renamed file from src/dsTMatrix.c;
973            now dealing with symmetric and triangular Tsparse coercions, both
974            to dense and general.
975    
976    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
979    
980            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
981            where sensible when the <numeric> is of length > 1.
982    
983    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * R/Matrix.R ([<-): for M[] <- value: fix length
986    
987    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
988    
989            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
990            * R/ndenseMatrix.R: new coercions n* -> l*
991    
992    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
995    
996            * R/Ops.R ("Logic"): and other "Ops", many updates
997    
998    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * src/Mutils.h (SET_DimNames): new utility
1001    
1002            * R/Auxiliaries.R (nnzero): improved and now exported via
1003    
1004            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1005    
1006    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * R/diagMatrix.R (!): fix typo.
1009    
1010    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1013                    allow to pass class definition --> speedup
1014            * R/sparseMatrix.R: apply the above
1015    
1016            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1017    
1018            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1019            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1020            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1021    
1022            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1023    
1024            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1025            and use it for "sparse*" as well, since it's faster than the
1026            as_Csparse(.) way.
1027    
1028    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1031    
1032    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1035            as method for   M[ ij ] <- v
1036            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1037    
1038            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1039            FALSE answer
1040    
1041            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1042            * tests/indexing.R: test it, and some of the above
1043    
1044    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1045    
1046            * R/Auxiliaries.R (is_duplicatedT): new utility
1047    
1048    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1049    
1050            * src/init.c (R_init_Matrix): export cholmod_scale
1051    
1052    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1053    
1054            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1055            base::as.matrix to (x, ...)
1056    
1057    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1058    
1059            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1060            file; start using "Logic", hence
1061    
1062            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1063            * NAMESPACE: import and export "Logic"
1064    
1065    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1068            only needed previously to R version 2.5.0.
1069    
1070    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1071    
1072            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1073    
1074            * R/Tsparse.R (replTmat): fix subassignment of triangular
1075            * R/Csparse.R (replCmat): ditto
1076            * tests/indexing.R: more tests, incl the above fix
1077    
1078    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * R/Auxiliaries.R (drop0): extend for non CSparse
1081            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1082    
1083            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1084                    use uplo correctly (!); other places: use uplo_P() macro
1085    
1086            * R/Csparse.R (replCmat): call diagU2N() when needed
1087            * R/Tsparse.R (replTmat): ditto
1088    
1089            * src/dtCMatrix.c (tCMatrix_validate): new
1090            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1091            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1092    
1093            * R/diagMatrix.R (replDiag): to use in [<-
1094    
1095    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1098                    also more general diagU2N().
1099    
1100    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1103            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1104    
1105    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1106    
1107            * tests/bind.R: a few more cases
1108            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1109    
1110            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1111            * R/ddenseMatrix.R (cbind2/rbind2)
1112            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1113            * tests/indexing.R
1114            * tests/indexing.Rout.save: updated
1115    
1116    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1119            * tests/indexing.R
1120    
1121    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1124            align with proper position of "0", i.e., right for integers.
1125            argument 'align' by default is "fancy".
1126    
1127    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1130            * R/Csparse.R: and fix "Compare" for more cases.
1131            * tests/Class+Meth.R: test some of these (m == m, m != m)
1132    
1133    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1134    
1135            * R/lsparseMatrix.R: all() and any() methods
1136            * R/ldenseMatrix.R:      ditto
1137            * NAMESPACE, R/Matrix.R: ditto
1138    
1139            * man/all-methods.Rd: document them minimally
1140    
1141            * tests/simple.R: add a few examples for these
1142    
1143    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1144    
1145            * R/Tsparse.R ([): fix long standing typo in symmetric case
1146            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1147    
1148    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1149    
1150            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1151            to LL before converting to a sparse matrix. (The LDL form can be
1152            converted to a sparse matrix but it is implicitly a unit
1153            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1154    
1155    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1156    
1157            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1158    
1159    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1160    
1161            * DESCRIPTION (Version): updated -> release 0.9975-7
1162            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1163    
1164    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1165    
1166            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1167    
1168    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1169    
1170            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1171            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1172            is exactly singular.
1173    
1174    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * DESCRIPTION (Date): updated -> release 0.9975-6
1177    
1178    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1181            now returns symmetric.
1182    
1183            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1184    
1185            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1186            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1187    
1188            * R/Auxiliaries.R (.type.kind): added
1189    
1190    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1193            running src/CSparse_install.sh
1194    
1195            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1196    
1197    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1200            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1201    
1202            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1203    
1204            * tests/Class+Meth.R (tstMatrixClass): now assure
1205            the (important in method programming) property :
1206    
1207                    ###>>  Every "Matrix" is either
1208                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1209    
1210                    (where "*" stands for "Matrix")
1211    
1212            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1213    
1214            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1215            * tests/validObj.R: checks for "comparison"
1216    
1217            * R/sparseMatrix.R ([): improved indexing for sparse;
1218                    trying to keep <symmetric>[ n, n] symmmetric
1219    
1220            * tests/indexing.R: indexing for logical sparse now ok
1221    
1222    
1223    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1226    
1227            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1228    
1229    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1230    
1231            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1232    
1233            * tests/simple.R: validObject() checking the above.
1234    
1235            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1236            replacing both dgCMatrix_validate and lgCM*.
1237    
1238            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1239            fix dimnames setting in other places.
1240            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1241    
1242    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1245    
1246            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1247            symmetry test, via
1248            * R/Auxiliaries.R (.as.dgC.0.factors):
1249    
1250    2006-11-01  Douglas Bates  <bates@r-project.org>
1251    
1252            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1253            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1254            <CsparseMatrix>) added
1255    
1256    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1257    
1258            * tests/matprod.R: add a variation of Harri's example
1259    
1260            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1261            recursive infinitely.
1262    
1263            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1264    
1265            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1266    
1267    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1268    
1269            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1270            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1271            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1272            satisfy the above test.
1273    
1274    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1275    
1276            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1277    
1278            * R/dgCMatrix.R: solve(a, b="missing") based on
1279            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1280            RHS = NULL.
1281    
1282            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1283            add more (needed) [t]crossprod() methods.
1284    
1285            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1286    
1287            * R/Auxiliaries.R (as_CspClass): cleanup
1288            (drop0): internal utility for "Csparse_drop(*, 0)"
1289            (.bail.out.2): encourage active feedback
1290    
1291    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1294    
1295            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1296            non-valid or 'sorted' case).
1297    
1298            * R/dsparseMatrix.R: add "chol" method.
1299            * R/ddenseMatrix.R: ditto
1300    
1301            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1302            * NAMESPACE (Ops)
1303            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1304            coercion; deprecating direct lower level coercions.
1305    
1306            * R/*.R (seq): use seq_len() and seq_along() where possible.
1307    
1308    
1309    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1310    
1311            * DESCRIPTION (Version): 0.9975-5 ready for release
1312    
1313    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1314    
1315            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1316    
1317    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1318    
1319            * R/AllClass.R (corMatrix): add 'validity' check;
1320                    comment out unused "LDL" class definition
1321            * NAMESPACE: mention, but do not export "LDL" class
1322            * R/corMatrix.R: new (simple), needed for R-devel with
1323            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1324              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1325    
1326    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1327    
1328            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1329            use Rprintf and R's error handling.
1330    
1331    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1332    
1333            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1334            * tests/matprod.R: add tests for the bug fixed.
1335    
1336    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1337    
1338            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1339            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1340    
1341    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1342    
1343            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1344    
1345    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1346    
1347            * DESCRIPTION (Version): 0.9975-3
1348    
1349            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1350            (sparse) matrices.
1351            * man/bdiag.Rd: docu + examples
1352    
1353            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1354    
1355            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1356            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1357    
1358            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1359            that result is sparse or diagonal (and not dense).
1360    
1361            * man/Subassign-methods.Rd: fix examples
1362    
1363            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1364            should always return a sparse (and not sometimes a diagonal) matrix.
1365    
1366    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1367    
1368            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1369    
1370    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1371    
1372            * DESCRIPTION (Version): 0.9975-2
1373    
1374            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1375    
1376    2006-10-02  Douglas Bates  <bates@R-project.org>
1377    
1378            * tests/dg_Matrix.R: Simplify test taking into account new code.
1379    
1380    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1381    
1382            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1383    
1384            * R/lsTMatrix.R: new files w/ missing methods
1385            * R/nsTMatrix.R:  "  'for completeness'
1386    
1387            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1388    
1389            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1390    
1391    
1392    2006-09-28  Douglas Bates  <bates@R-project.org>
1393    
1394            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1395            included.
1396    
1397            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1398            Export C-callable functions used in Zt_create in lme4.
1399    
1400    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1401    
1402            * DESCRIPTION (Version): 0.9975-1
1403    
1404            * tests/simple.R: less checks fail; using NA, found that our
1405                    kronecker() is not base-compatible with NA's.
1406    
1407            * R/dMatrix.R: "Compare" method now implemented for all cases
1408    
1409            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1410    
1411            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1412    
1413            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1414            * src/dspMatrix.c (dspMatrix_validate): ditto
1415    
1416            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1417              including coercion to [nl]tTMatrix.
1418    
1419            * R/diagMatrix.R (show): print a header line as for other classes.
1420    
1421    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1422    
1423            * src/Makefile.win (SUBDIRS): fix typo
1424    
1425    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1426    
1427            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1428    
1429    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1430    
1431            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1432            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1433            accept a symmetric matrix).
1434            * tests/group-methods.R: Uncomment test of crossprod applied to
1435            lsCMatrix objects.
1436    
1437    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1438    
1439            * R/AllClass.R (symmetricMatrix): add validity method (available
1440            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1441    
1442            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1443    
1444            * tests/indexing.Rout.save:
1445            * tests/indexing.R: additions, mainly for 'lsparse'
1446    
1447            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1448            case.
1449    
1450            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1451    
1452    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1453    
1454            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1455                    as 'N' (1-letter - Ok?)
1456    
1457            * tests/group-methods.R: add test for logical + NAs
1458    
1459            * R/dMatrix.R ("Compare"): fix to work with NA's
1460    
1461            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1462    
1463            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1464                    which is implemented.
1465    
1466    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1467    
1468            * src/chm_common.c: coerce logical <-> double instead of
1469            typecasting;  needed for "l" matrix handling in cholmod.
1470    
1471            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1472    
1473            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1474            (Tsp2grNEL): other fixes needed
1475    
1476    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1477    
1478            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1479                    Matrices, since "lMatrix", also "lsparseM" can have NA
1480            * R/ndenseMatrix.R, etc: new source files
1481            * man/nsparseMatrix-classes.Rd, etc: new help files
1482            * tests/: adaptions
1483            * src/chm_common.c (chm_dense_to_SEXP): and others:
1484                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1485            * src/Csparse.c, etc: ditto
1486    
1487    2006-09-11  Douglas Bates  <bates@R-project.org>
1488    
1489            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1490            alloc_d**Matrix functions to the lme4 package.
1491    
1492    2006-09-09  Douglas Bates  <bates@R-project.org>
1493    
1494            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1495            fixed
1496    
1497    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1498    
1499            * R/lMatrix.R: new
1500    
1501            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1502    
1503            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1504            * man/tcrossprod.Rd: ditto
1505    
1506    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1507    
1508            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1509            for exported functions
1510            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1511            Remove partitioning algorithms for sparse matrix reordering.  The
1512            copyright on the Metis code was problematic and the methods were
1513            rarely used.
1514            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1515            operations are now done entirely in CHOLMOD code.
1516    
1517    2006-09-06  Douglas Bates  <bates@R-project.org>
1518    
1519            * src/Mutils.h: Remove functions that are no longer used.
1520    
1521    2006-09-04  Douglas Bates  <bates@R-project.org>
1522    
1523            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1524            * src/DEPS.mkf: update
1525    
1526    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1527    
1528            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1529            * DESCRIPTION (Version): 0.9975-0
1530            (Depends): R (>= 2.4.0)
1531    
1532    2006-09-01  Douglas Bates  <bates@R-project.org>
1533    
1534            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1535    
1536    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1537    
1538            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1539            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1540    
1541            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1542    
1543    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1544    
1545            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1546            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1547            * R/dsparseMatrix.R: ditto
1548            * R/Csparse.R: ditto
1549    
1550    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1551    
1552            * R/dMatrix.R (Compare): improve availability of "<", etc
1553            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1554    
1555    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1556    
1557            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1558            of a 0-index which was used as 1-index (..hmm)
1559    
1560            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1561    
1562            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1563            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1564            (.is.diagonal): ditto
1565    
1566            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1567    
1568            * R/Matrix.R (Matrix): also work for NA data
1569    
1570    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1571    
1572            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1573            in all cases.
1574    
1575    2006-08-27  Douglas Bates  <bates@R-project.org>
1576    
1577            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1578            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1579    
1580    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1581    
1582            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1583            subclasses of "ddenseMatrix"
1584            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1585            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1586            instead of half dozen specialized ones.
1587    
1588    2006-08-25  Douglas Bates  <bates@R-project.org>
1589    
1590            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1591            <tillard@cirad.fr> - ordering standard errors to match effects.
1592    
1593    2006-08-24  Douglas Bates  <bates@R-project.org>
1594    
1595            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1596            on R_ldl.
1597            * R/lCholCMatrix.R,
1598            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1599            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1600            * many files in ./R and ./src: Use more general version of
1601            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1602            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1603            dtpMatrix, dspMatrix and dppMatrix conversions.
1604    
1605    
1606    2006-08-23  Douglas Bates  <bates@R-project.org>
1607    
1608            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1609            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1610            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1611            dgeMatrix_crossprod (may need to do this in other places).
1612            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1613            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1614    
1615    2006-08-22  Douglas Bates  <bates@R-project.org>
1616    
1617            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1618            types of classed Matrices, matrices or numeric or logical vectors.
1619            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1620            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1621            to Mutils.h (as an inline) and change name to Matrix_check_class;
1622            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1623            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1624            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1625            * src/Csparse.c: use diag_P and uplo_P macros.
1626    
1627    2006-08-21  Douglas Bates  <bates@R-project.org>
1628    
1629            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1630            valgrind.
1631            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1632            inverses.
1633            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1634            -Wall warnings.
1635            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1636            Use dup_mMatrix_as_dgeMatrix.
1637    
1638    2006-08-20  Douglas Bates  <bates@R-project.org>
1639    
1640            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1641            * tests/sparseQR.R: Added
1642            * man/sparseQR-class.Rd: Document methods for qr.* generics
1643            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1644    
1645    2006-08-19  Douglas Bates  <bates@R-project.org>
1646    
1647            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1648            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1649            and qr.fitted.
1650            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1651            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1652    
1653    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1654    
1655            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1656            the base version has no "..." argument.
1657    
1658            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1659    
1660            * R/Matrix.R: define and
1661            * NAMESPACE: export as.numeric() and as.logical() methods.
1662                    Let's hope these do not badly slow down something...
1663            Finally export the zapsmall() method.
1664    
1665    2006-08-17  Douglas Bates  <bates@R-project.org>
1666    
1667            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1668            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1669            * src/dtCMatrix.c :Remove code that is no longer used
1670            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1671    
1672    2006-08-14  Douglas Bates  <bates@R-project.org>
1673    
1674            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1675            Csparse_to_logical and Csparse_symmetric_to_general.
1676            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1677            coercion methods between CsparseMatrix and TsparseMatrix.
1678    
1679    2006-08-14  Douglas Bates  <bates@R-project.org>
1680    
1681            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1682            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1683            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1684            possible.
1685    
1686    2006-08-12  Douglas Bates  <bates@R-project.org>
1687    
1688            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1689              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1690              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1691              generalize conversions between TsparseMatrix, CsparseMatrix,
1692              denseMatrix and matrix.  Preserve triangularity property and
1693              propagate Dimnames in the easy cases.
1694    
1695    2006-08-10  Douglas Bates  <bates@R-project.org>
1696    
1697            * src/lmer.c: adjust checks in glmer_init for S4SXP
1698            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1699            before S4SXP but for the wrong reasons.
1700    
1701  2006-08-08  Douglas Bates  <bates@R-project.org>  2006-08-08  Douglas Bates  <bates@R-project.org>
1702    
1703          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.

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