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 1405, Mon Aug 21 14:43:00 2006 UTC revision 2157, Tue Mar 25 15:00:01 2008 UTC
# Line 1  Line 1 
1    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version,Date): 0.999375-8
4    
5            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
6    
7            * inst/test-tools.R (isValid): new utility, used much in
8            * tests/simple.R:
9    
10            * man/BunchKaufman-methods.Rd: added too
11    
12    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/dsyMatrix.R: add BunchKaufman() methods.
15            * R/dspMatrix.R:
16    
17            * src/init.c: add dsyMatrix_trf
18    
19    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
20    
21            * DESCRIPTION (Version): release 0.999375-7
22            * src/CHMfactor.c (CHMfactor_update): fix
23    
24    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
27            internal_chm_factor().
28    
29            * R/AllGeneric.R: do *not* define a "chol" generic
30                    (but rather use the implicit one *without* making pivot
31                    part of the signature)
32            * R/*.R: drop the 'pivot' from chol's signature and make
33                    'pivot=FALSE' a default argument of method definitions.
34    
35            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
36            version of Matrix
37    
38    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
41    
42            * R/sparseMatrix.R (is.na): new simple method
43            * R/denseMatrix.R (is.na): ditto.
44    
45            * R/diagMatrix.R (.symDiagonal): newly exported utility.
46    
47            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
48    
49            * src/UFsparse_download.sh: -->
50            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
51    
52    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
55            functionality; barely tested in
56            * tests/factorizing.R
57    
58            * src/Csparse.c (diag_tC): new functionality to enable faster
59            determinant(<dsCMatrix>, .) in
60            * R/dsCMatrix.R
61    
62    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
63    
64            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
65              src/CHMfactor.c, src/CHMfactor.h,
66              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
67              Log-determinant of the parent matrix from a CHMfactor object as
68              chm_factor_ldetL2; documentation and support
69    
70    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
73    
74    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
77            warning.
78    
79    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
82    
83            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
84              <diagonal> o <sparse_triangular>
85              setAs(., "nMatrix") added.
86    
87            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
88    
89            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
90                    new argument 'checkDense = FALSE'.
91    
92    
93    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
96            back-permutation of the matrix exponential.
97    
98            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
99    
100            * DESCRIPTION (Date,Version): ready to release 0.999375-5
101    
102            * tests/simple.R: testing diagN2U
103    
104    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Auxiliaries.R (diagN2U): interface to
107    
108            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
109    
110            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
111    
112    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/chm_common.c (chm_diagN2U): new utility.
115    
116            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
117            make use of chm_diagN2U() and hence now preserve triangularity and
118            unit-triangularity.
119    
120            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
121    
122    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
125    
126            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
127            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
128    
129            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
130    
131            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
132    
133            * src/chm_common.c (AS_CHM_FINISH): add note about problem
134            for triangular (diag = "U").
135    
136    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
139            * R/bind.R:  .Call(dense_to_Csparse, *)
140    
141    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Matrix.R (Matrix): no longer use coercions to specific classes
144                    (since we are discouraging them in user code).
145    
146            * tests/*.R: also replaces coercions to specific classes by
147            coercions to super classes.
148    
149            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
150    
151    
152    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
155    
156            * src/dense.c (dense_band): generalized from ddense_band
157    
158            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
159              now for "denseMatrix" (instead of just "ddense*"); much
160              simplified setMethod()s for these.
161    
162            * src/dense.c (dense_to_symmetric): generalized from ddense_*
163    
164    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
167            version of as(*, "symmetricMatric").
168    
169            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
170            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
171    
172    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R (subset.ij): utility, as first step to faster
175               M [ <ij-matrix> ] indexing.
176    
177            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
178    
179            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
180            for more efficient symmpart() and skewpart() methods.
181    
182            * src/Mutils.c (equal_string_vectors): utility
183    
184            * src/dense.c (ddense_to_symmetric): new function used in
185    
186            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
187    
188            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
189            order to match the generic (and evade .local(..)).
190    
191            * R/dsCMatrix.R: dgC -> dsC: use C code!
192    
193            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
194            as per TODO
195    
196            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
197    
198            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
199    
200    
201    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
204    
205            * R/Auxiliaries.R (non0.i): take out of non0ind
206    
207            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
208            make tril(), triu(), band() work for "matrix" and all "dense*"
209    
210            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
211            * tests/simple.R: test the fix above
212    
213            * R/sparseMatrix.R ([): simplification: no coerce to <general>
214                    before we use as(., <Tsparse>)[...] anyway
215    
216            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
217    
218            * R/triangularMatrix.R (isTriangular): methods for all subclasses
219            instead of "triangularMatrix" -- just to disambiguate
220    
221    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
224            * tests/indexing.R: example that fails above
225    
226    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
229            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
230                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
231    
232            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
233            * src/Tsparse.h, init.c: ditto
234            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
235                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
236            * R/sparseMatrix.R (isTriangular): hence simplified
237    
238    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Ops.R (.Arith.Csparse): new utility factored out of former
241              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
242    
243    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
246    
247            * inst/test-tools.R (isOrthogonal): new function; also file restructured
248    
249    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
252            coercion to "nMatrix" and "pMatrix"
253    
254            * R/AllClass.R: "Schur" class;  "number" class union
255            * man/number-class.Rd:
256            * man/Schur-class.Rd:
257    
258            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
259            (.simpleSchur): Schur() method for diagonal matrices
260            (.triSchur):    Schur() method for triangular matrices
261            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
262    
263    
264    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
267    
268    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
271                    in order to ensure 'system = *' is not lost;
272                    formals()$system instead of cut&paste.
273            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
274    
275    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * DESCRIPTION (Date): make ready for release --> 0.999375-4
278    
279            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
280    
281    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
284                    and hence does as.vector(.).
285            * man/pMatrix-class.Rd: docs
286            * R/sparseMatrix.R: fix for printing "integer sparse"
287    
288            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
289    
290            * R/Matrix.R and others: use "exact" function argument list for
291                    both "["   : (x, i,j, ..., drop)
292                    and  "[<-" : (x, i,j, ..., value)
293    
294            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
295            * R/Tsparse.R (replTmat):    ditto
296            * R/diagMatrix.R (replDiag): ditto
297            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
298            * tests/indexing.R: testing the above
299    
300    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/sparseMatrix.R (cov2cor): method for sparse matrices
303    
304            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
305    
306            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
307    
308            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
309    
310    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Matrix.R: "generic" cov2cor() method
313    
314            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
315                    speed up Q %*% D %*% t(Q)
316            * tests/dpoMatrix.R: test nearPD()
317    
318    2007-12-05  Doug Bates and Martin Maechler
319    
320            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
321            stats::xtabs() allowing to create sparse matrices.
322    
323    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
326    
327    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
330    
331    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/LU.R: solve() method for "denseLU"
334    
335    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * DESCRIPTION (Version): 0.999375-3 preparing for release
338    
339            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
340    
341            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
342    
343    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
346              thanks to Kasper Kristensen.
347            * tests/matprod.R: regression test for that.
348    
349    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
350    
351            * [r4778] R/AllGeneric.R: Check R version before defining generics for
352              primitives
353    
354    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/denseMatrix.R (rcond): method
357            * R/sparseQR.R (rcond): method, use x or t(x)
358    
359    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
362            matrices.
363            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
364    
365            * man/rcond.Rd: mention the more general definition, and add
366            example for non-square matrices.
367    
368            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
369    
370    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
373    
374    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
377            * tests/indexing.R: add new regression for the above cases.
378    
379    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/Mutils.h (__sun): clause for alloca.h on Solaris
382    
383    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * DESCRIPTION (Date, Version): 0.999375-2
386    
387    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/HBMM.R (readMM): make work for pattern matrices as well
390    
391    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
392    
393            * [r4730] src/Mutils.h: declare alloca
394            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
395              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
396              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
397              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
398              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
399              methods; switch writeMM to use CHOLMOD code; repair readMM
400    
401    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
404            Oehlschlaegel's ... result type still to be discussed!
405    
406    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * man/image-methods.Rd: new, combining all image() methods
409    
410    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
413            to work via dgC...
414    
415            * R/Matrix.R (Matrix): special treatment for "table" (S3)
416    
417    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/dgTMatrix.R (image): change defaults to
420                    aspect = "iso", colorkey = FALSE
421    
422    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
425            must copy its *expanded* x slot before LAPACK call.
426    
427            * tests/matprod.R: test the last days' changes.
428    
429    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
430    
431            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
432              as well as in sources
433            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
434              Lapack call
435    
436    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
439                    ("Matrix", "matrix") which is needed in some cases.
440            Ditto for solve().
441    
442            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
443            infinite recursion in dispatch for some cases.
444    
445    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
446    
447            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
448              so pointers match
449    
450    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * DESCRIPTION (Date): set ready for release -- 0.999375-1
453    
454    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
455    
456            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
457              src/chm_common.c, src/chm_common.h: Change API for
458              numeric_as_chm_dense and N_AS_CHM_DN
459    
460    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
463            * tests/matprod.R: regr.test for it
464    
465    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
468            * tests/group-methods.R: and regression-test it
469    
470    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
471    
472            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
473              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
474              triplet_to_sparse, documentation, use typedefs
475    
476    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * man/dpoMatrix-class.Rd: added 'corMatrix' example
479    
480            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
481            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
482            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
483    
484            * R/lsparseMatrix.R: bug fix in "all" method
485            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
486    
487            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
488            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
489                    + matrix |-> nMatrix coercion
490            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
491            * man/pMatrix-class.Rd: ditto
492    
493            * R/Matrix.R (Summary): method for non-dMatrix
494    
495            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
496            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
497                    test all Summary methods.
498    
499    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
502    
503    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
506    
507            * R/pMatrix.R (t?crossprod): methods for pMatrix
508    
509    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
510    
511            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
512    
513    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
514    
515            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
516              trying to fix a subtle bug - which has been somewhere else.
517    
518    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
519    
520            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
521              solve the bug
522    
523    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * src/dgCMatrix.c (compressed_to_TMatrix):
526    
527    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * src/Csparse.c (Rsparse_validate): new, to have some validity
530            checking for RsparseMatrix
531            * src/dgCMatrix.c (xRMatrix_validate): ditto
532            * src/dtCMatrix.c (tRMatrix_validate): ditto
533    
534    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
535    
536            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
537              lgRMatrix
538            * [r4568] DESCRIPTION: Prepare for bug-fix release
539            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
540              for declaration of cholmod_symmetry
541    
542    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
545            release.
546    
547    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
548    
549            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
550              functions - no longer used
551            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
552              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
553              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
554              Alloca
555    
556    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
557    
558            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
559              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
560              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
561              src/t_gCMatrix_colSums.c: more R_CheckStack()s
562    
563    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
564    
565            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
566              the required amount of memory then call M_numeric_as_chm_dense.
567            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
568              (like Calloc but calling alloca)
569    
570    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
573            and extended with more sophisticated 'col.names' option.
574            * NAMESPACE: export  printSparseMatrix()
575            * man/printSpMatrix.Rd: document, incl. examples
576    
577    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
578    
579            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
580              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
581              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
582    
583    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * DESCRIPTION (Version): 0.99875-4
586    
587            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
588            some dimnames perservation.
589    
590            * R/dsTMatrix.R (t-method): keep dimnames
591            * R/dtTMatrix.R:  ditto
592    
593            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
594            and ncol(.) < 10
595    
596            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
597            from Mutils.h
598    
599            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
600            e.g. in as(<ngCMatrix>, "matrix")
601    
602    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
603    
604            * [r4529] .: Create a branch for the API changes from the 0.99875
605              series to the 0.999375 series
606            * [r4530] DESCRIPTION, inst/include/Matrix.h,
607              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
608              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
609              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
610              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
611              as_cholmod_x functions
612    
613    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
614    
615            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
616              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
617              to Comparisons
618    
619    >>>>>>> .merge-right.r4561
620    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * DESCRIPTION (Version): 0.99875-3 ready to be released.
623    
624            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
625    
626            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
627            that should also work in a future version of R.
628    
629    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
632    
633            * R/sparseVector.R: more *sparseVector coercions, notably for
634            non - double ones.
635    
636    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
639              notably the new ones building on the new .Call(.)s:
640    
641            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
642            all 4 of [dlin]gCMatrix_colSums().
643    
644    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
645    
646            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
647            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
648              result
649    
650    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/kronecker.R: fix typo (could lead to inf.recursion)
653            * test/simple.R: testing that
654    
655            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
656            method as well (which can have arguments, show() can't).
657    
658    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
659    
660            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
661              added dgCMatrix_colSums for [col,row][Sums,Means]
662    
663    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
664    
665            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
666              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
667              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
668            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
669              class
670            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
671              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
672              row names to store the levels - duh!  Added an example.
673    
674    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * src/Csparse.c (Csparse_validate): check for *repeated* entries
677            thanks to example from Christian Buchta; with a test here:
678            * tests/simple.R:
679    
680    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
683            of colSums(*, sparseResult = TRUE)
684    
685    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
688            'na.rm = FALSE' as "everywhere" else in R.
689    
690    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
691    
692            * [r4421] src/CSparse_install.sh: Modify for new organization of
693              CSparse package
694            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
695              SuiteSparse
696            * [r4426] src/Makefile: add ./UFconfig to the include path for
697              compilation
698            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
699            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
700              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
701    
702    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
705            * R/sparseMatrix.R (prSpMatrix): now gives a message about
706            suppressed column names.
707    
708    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
709    
710            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
711              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
712              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
713              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
714              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
715              Remove warnings after change to const char* CHAR
716    
717    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
718    
719            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
720              type of M_cholmod_ssmult
721    
722    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
723    
724            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
725              src/init.c: Yet another cholmod export - cholmod_ssmult
726    
727    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * NAMESPACE: exported drop0(), since
730            * man/drop0.Rd: I have seen several cases, I really wanted to use
731            it, so our users may want too.
732    
733    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * man/colSums.Rd: separately document colSums() etc, since these
736            have the extra argument 'sparseResult'.
737    
738    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
741            * man/spMatrix.Rd: docu., including examples
742    
743            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
744            in order to make colMeans() etc fast *and* correct.
745            * R/sparseVector.R (replSPvec): "[<-" functionality for
746            sparseVectors; tested in
747            * tests/simple.R:
748    
749    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
752            (very) sparse Matrices; output similar to Matlab's print().
753    
754    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
757            0-based, indices (Jose Quesada <quesada@gmail.com>).
758    
759    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
760    
761            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
762    
763    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/Auxiliaries.R (sparsapply): new utility, much faster than
766            tapply1() for large sparse matrices.
767    
768    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/Matrix.R (dim<-): reshape now via sparseVector.
771    
772            * R/sparseVector.R: methods and function for
773            * R/AllClass.R: new "sparseVector" class and daughters.
774            * NAMESPACE: export new classes
775    
776    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * DESCRIPTION (Version): 0.99875-1
779            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
780    
781    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
784            indexing
785            * tests/indexing.R: test set for that.
786    
787    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
790            entries.
791            * tests/indexing.R(out): add regression test for it
792    
793    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
796            name for "!" method definitions.
797    
798    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Tsparse.R (intI): new utility, used for "[" :
801                    Cleanup up there, and fixes for duplicated indices - more TODO!
802    
803            * tests/indexing.R(out): more tests
804    
805    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
806    
807            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
808            code that is now part of the R Lapack library.
809    
810            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
811            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
812    
813    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
816    
817    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
820            up with extraneous names '0'...'<n-1>'
821    
822    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/dgTMatrix.R (mat2dgT): care about NAs
825    
826    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/kronecker.R: triangularity preserving methods
829    
830    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/kronecker.R: new file collecting kronecker() methods in one
833                    place.  Goal: become much faster!
834    
835    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
838            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
839            can be much faster.
840    
841            * tests/matprod.R: add regression tests for these (upper & lower).
842    
843    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * R/Matrix.R (diff): method for our Matrices.
846    
847            * R/sparseMatrix.R (isDiagonal): check dim()!
848    
849    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * R/Matrix.R (dim<-): new method for "reshape()" built on a
852            proposal from Tamas Papp.
853    
854    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
857    
858            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
859            rather define and export  cBind() and rBind() only.
860            --> useRs *must* change code that used to have cbind()/rbind() !!
861    
862            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
863            * R/bind.Rout.save: ditto
864    
865    2007-02-16  Douglas Bates  <bates@r-project.org>
866    
867            * DESCRIPTION (Date, Version): 0.9975-11 with new date
868            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
869            const modifier on declaration of the array 'valid'
870    
871    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
872    
873            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
874    
875    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
878    
879            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
880            * tests/simple.R: test the above and some of these coercions:
881    
882            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
883                    be careful to avoid infinite recursion, using new coercions in
884            * R/ngCMatrix.R and nsC... and ntC...
885            * R/lsparseMatrix.R: ditto
886    
887            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
888    
889            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
890            * R/Rsparse.R: reactivate .Call()s
891    
892            * tests/Class+Meth.R: a bit more on actual classes
893    
894    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
895    
896            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
897    
898    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
900            * DESCRIPTION (Version): 0.9975-10 to upload
901    
902            * tests/Class+Meth.R (tstMatrixClass): require coercions to
903            specific classes less unconditionally.
904    
905            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
906    
907            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
908    
909            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
910            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
911            R_to_CMatrix segfaults on one platform.
912            Eliminate most coercion method to *specific* classes, and replace
913            with virtual classes coercions.
914    
915    
916    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
917    
918            * src/init.c: export the CHM...._validate() placeholders, since
919            they *are* called.
920    
921            * tests/Class+Meth.R (classCanCoerce): and starting to test
922            all as(<from>, <to>)
923    
924    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
927            * tests/indexing.R: tested now
928            * tests/indexing.Rout.save: updated
929    
930            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
931            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
932            appropriate.
933    
934            * NAMESPACE: export a trivial
935            * R/Matrix.R: drop() Matrix-method
936    
937            * R/AllClass.R: moved all prototypes to virtual super classes.
938    
939            * R/Rsparse.R: many more coercions to have less exceptions in
940            * tests/Class+Meth.R:
941    
942            * R/Ops.R (Compare): tweak for case with NA
943            * tests/simpl.R: hence another 'FIXME' eliminated
944    
945    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
948            objects.
949    
950            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
951              and more of "!", "&", "|", all, any; coercions
952    
953            * R/Rsparse.R: many coercions (which enable quite a few other
954            methods), thanks to enhancements in
955            * src/dgCMatrix.c (R_to_CMatrix): new, and
956            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
957            symmetric & triangular and ..RMatrix objects.
958    
959            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
960            renamed file from src/dsTMatrix.c;
961            now dealing with symmetric and triangular Tsparse coercions, both
962            to dense and general.
963    
964    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
967    
968            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
969            where sensible when the <numeric> is of length > 1.
970    
971    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * R/Matrix.R ([<-): for M[] <- value: fix length
974    
975    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
978            * R/ndenseMatrix.R: new coercions n* -> l*
979    
980    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
983    
984            * R/Ops.R ("Logic"): and other "Ops", many updates
985    
986    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * src/Mutils.h (SET_DimNames): new utility
989    
990            * R/Auxiliaries.R (nnzero): improved and now exported via
991    
992            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
993    
994    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/diagMatrix.R (!): fix typo.
997    
998    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1001                    allow to pass class definition --> speedup
1002            * R/sparseMatrix.R: apply the above
1003    
1004            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1005    
1006            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1007            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1008            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1009    
1010            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1011    
1012            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1013            and use it for "sparse*" as well, since it's faster than the
1014            as_Csparse(.) way.
1015    
1016    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1019    
1020    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1023            as method for   M[ ij ] <- v
1024            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1025    
1026            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1027            FALSE answer
1028    
1029            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1030            * tests/indexing.R: test it, and some of the above
1031    
1032    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * R/Auxiliaries.R (is_duplicatedT): new utility
1035    
1036    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1037    
1038            * src/init.c (R_init_Matrix): export cholmod_scale
1039    
1040    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1043            base::as.matrix to (x, ...)
1044    
1045    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1046    
1047            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1048            file; start using "Logic", hence
1049    
1050            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1051            * NAMESPACE: import and export "Logic"
1052    
1053    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1054    
1055            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1056            only needed previously to R version 2.5.0.
1057    
1058    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1059    
1060            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1061    
1062            * R/Tsparse.R (replTmat): fix subassignment of triangular
1063            * R/Csparse.R (replCmat): ditto
1064            * tests/indexing.R: more tests, incl the above fix
1065    
1066    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1067    
1068            * R/Auxiliaries.R (drop0): extend for non CSparse
1069            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1070    
1071            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1072                    use uplo correctly (!); other places: use uplo_P() macro
1073    
1074            * R/Csparse.R (replCmat): call diagU2N() when needed
1075            * R/Tsparse.R (replTmat): ditto
1076    
1077            * src/dtCMatrix.c (tCMatrix_validate): new
1078            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1079            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1080    
1081            * R/diagMatrix.R (replDiag): to use in [<-
1082    
1083    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1086                    also more general diagU2N().
1087    
1088    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1091            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1092    
1093    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095            * tests/bind.R: a few more cases
1096            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1097    
1098            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1099            * R/ddenseMatrix.R (cbind2/rbind2)
1100            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1101            * tests/indexing.R
1102            * tests/indexing.Rout.save: updated
1103    
1104    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1105    
1106            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1107            * tests/indexing.R
1108    
1109    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1112            align with proper position of "0", i.e., right for integers.
1113            argument 'align' by default is "fancy".
1114    
1115    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1116    
1117            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1118            * R/Csparse.R: and fix "Compare" for more cases.
1119            * tests/Class+Meth.R: test some of these (m == m, m != m)
1120    
1121    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/lsparseMatrix.R: all() and any() methods
1124            * R/ldenseMatrix.R:      ditto
1125            * NAMESPACE, R/Matrix.R: ditto
1126    
1127            * man/all-methods.Rd: document them minimally
1128    
1129            * tests/simple.R: add a few examples for these
1130    
1131    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1132    
1133            * R/Tsparse.R ([): fix long standing typo in symmetric case
1134            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1135    
1136    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1137    
1138            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1139            to LL before converting to a sparse matrix. (The LDL form can be
1140            converted to a sparse matrix but it is implicitly a unit
1141            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1142    
1143    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1144    
1145            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1146    
1147    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1148    
1149            * DESCRIPTION (Version): updated -> release 0.9975-7
1150            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1151    
1152    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1153    
1154            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1155    
1156    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1157    
1158            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1159            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1160            is exactly singular.
1161    
1162    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * DESCRIPTION (Date): updated -> release 0.9975-6
1165    
1166    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1169            now returns symmetric.
1170    
1171            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1172    
1173            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1174            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1175    
1176            * R/Auxiliaries.R (.type.kind): added
1177    
1178    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1181            running src/CSparse_install.sh
1182    
1183            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1184    
1185    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1188            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1189    
1190            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1191    
1192            * tests/Class+Meth.R (tstMatrixClass): now assure
1193            the (important in method programming) property :
1194    
1195                    ###>>  Every "Matrix" is either
1196                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1197    
1198                    (where "*" stands for "Matrix")
1199    
1200            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1201    
1202            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1203            * tests/validObj.R: checks for "comparison"
1204    
1205            * R/sparseMatrix.R ([): improved indexing for sparse;
1206                    trying to keep <symmetric>[ n, n] symmmetric
1207    
1208            * tests/indexing.R: indexing for logical sparse now ok
1209    
1210    
1211    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1212    
1213            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1214    
1215            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1216    
1217    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1218    
1219            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1220    
1221            * tests/simple.R: validObject() checking the above.
1222    
1223            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1224            replacing both dgCMatrix_validate and lgCM*.
1225    
1226            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1227            fix dimnames setting in other places.
1228            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1229    
1230    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1231    
1232            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1233    
1234            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1235            symmetry test, via
1236            * R/Auxiliaries.R (.as.dgC.0.factors):
1237    
1238    2006-11-01  Douglas Bates  <bates@r-project.org>
1239    
1240            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1241            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1242            <CsparseMatrix>) added
1243    
1244    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1245    
1246            * tests/matprod.R: add a variation of Harri's example
1247    
1248            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1249            recursive infinitely.
1250    
1251            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1252    
1253            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1254    
1255    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1256    
1257            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1258            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1259            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1260            satisfy the above test.
1261    
1262    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1263    
1264            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1265    
1266            * R/dgCMatrix.R: solve(a, b="missing") based on
1267            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1268            RHS = NULL.
1269    
1270            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1271            add more (needed) [t]crossprod() methods.
1272    
1273            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1274    
1275            * R/Auxiliaries.R (as_CspClass): cleanup
1276            (drop0): internal utility for "Csparse_drop(*, 0)"
1277            (.bail.out.2): encourage active feedback
1278    
1279    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1282    
1283            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1284            non-valid or 'sorted' case).
1285    
1286            * R/dsparseMatrix.R: add "chol" method.
1287            * R/ddenseMatrix.R: ditto
1288    
1289            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1290            * NAMESPACE (Ops)
1291            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1292            coercion; deprecating direct lower level coercions.
1293    
1294            * R/*.R (seq): use seq_len() and seq_along() where possible.
1295    
1296    
1297    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1298    
1299            * DESCRIPTION (Version): 0.9975-5 ready for release
1300    
1301    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1302    
1303            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1304    
1305    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * R/AllClass.R (corMatrix): add 'validity' check;
1308                    comment out unused "LDL" class definition
1309            * NAMESPACE: mention, but do not export "LDL" class
1310            * R/corMatrix.R: new (simple), needed for R-devel with
1311            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1312              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1313    
1314    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1315    
1316            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1317            use Rprintf and R's error handling.
1318    
1319    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1320    
1321            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1322            * tests/matprod.R: add tests for the bug fixed.
1323    
1324    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1325    
1326            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1327            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1328    
1329    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1330    
1331            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1332    
1333    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1334    
1335            * DESCRIPTION (Version): 0.9975-3
1336    
1337            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1338            (sparse) matrices.
1339            * man/bdiag.Rd: docu + examples
1340    
1341            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1342    
1343            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1344            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1345    
1346            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1347            that result is sparse or diagonal (and not dense).
1348    
1349            * man/Subassign-methods.Rd: fix examples
1350    
1351            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1352            should always return a sparse (and not sometimes a diagonal) matrix.
1353    
1354    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1355    
1356            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1357    
1358    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1359    
1360            * DESCRIPTION (Version): 0.9975-2
1361    
1362            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1363    
1364    2006-10-02  Douglas Bates  <bates@R-project.org>
1365    
1366            * tests/dg_Matrix.R: Simplify test taking into account new code.
1367    
1368    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1369    
1370            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1371    
1372            * R/lsTMatrix.R: new files w/ missing methods
1373            * R/nsTMatrix.R:  "  'for completeness'
1374    
1375            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1376    
1377            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1378    
1379    
1380    2006-09-28  Douglas Bates  <bates@R-project.org>
1381    
1382            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1383            included.
1384    
1385            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1386            Export C-callable functions used in Zt_create in lme4.
1387    
1388    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * DESCRIPTION (Version): 0.9975-1
1391    
1392            * tests/simple.R: less checks fail; using NA, found that our
1393                    kronecker() is not base-compatible with NA's.
1394    
1395            * R/dMatrix.R: "Compare" method now implemented for all cases
1396    
1397            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1398    
1399            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1400    
1401            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1402            * src/dspMatrix.c (dspMatrix_validate): ditto
1403    
1404            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1405              including coercion to [nl]tTMatrix.
1406    
1407            * R/diagMatrix.R (show): print a header line as for other classes.
1408    
1409    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1410    
1411            * src/Makefile.win (SUBDIRS): fix typo
1412    
1413    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1414    
1415            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1416    
1417    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1418    
1419            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1420            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1421            accept a symmetric matrix).
1422            * tests/group-methods.R: Uncomment test of crossprod applied to
1423            lsCMatrix objects.
1424    
1425    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1426    
1427            * R/AllClass.R (symmetricMatrix): add validity method (available
1428            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1429    
1430            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1431    
1432            * tests/indexing.Rout.save:
1433            * tests/indexing.R: additions, mainly for 'lsparse'
1434    
1435            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1436            case.
1437    
1438            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1439    
1440    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1441    
1442            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1443                    as 'N' (1-letter - Ok?)
1444    
1445            * tests/group-methods.R: add test for logical + NAs
1446    
1447            * R/dMatrix.R ("Compare"): fix to work with NA's
1448    
1449            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1450    
1451            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1452                    which is implemented.
1453    
1454    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1455    
1456            * src/chm_common.c: coerce logical <-> double instead of
1457            typecasting;  needed for "l" matrix handling in cholmod.
1458    
1459            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1460    
1461            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1462            (Tsp2grNEL): other fixes needed
1463    
1464    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1465    
1466            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1467                    Matrices, since "lMatrix", also "lsparseM" can have NA
1468            * R/ndenseMatrix.R, etc: new source files
1469            * man/nsparseMatrix-classes.Rd, etc: new help files
1470            * tests/: adaptions
1471            * src/chm_common.c (chm_dense_to_SEXP): and others:
1472                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1473            * src/Csparse.c, etc: ditto
1474    
1475    2006-09-11  Douglas Bates  <bates@R-project.org>
1476    
1477            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1478            alloc_d**Matrix functions to the lme4 package.
1479    
1480    2006-09-09  Douglas Bates  <bates@R-project.org>
1481    
1482            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1483            fixed
1484    
1485    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1486    
1487            * R/lMatrix.R: new
1488    
1489            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1490    
1491            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1492            * man/tcrossprod.Rd: ditto
1493    
1494    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1495    
1496            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1497            for exported functions
1498            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1499            Remove partitioning algorithms for sparse matrix reordering.  The
1500            copyright on the Metis code was problematic and the methods were
1501            rarely used.
1502            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1503            operations are now done entirely in CHOLMOD code.
1504    
1505    2006-09-06  Douglas Bates  <bates@R-project.org>
1506    
1507            * src/Mutils.h: Remove functions that are no longer used.
1508    
1509    2006-09-04  Douglas Bates  <bates@R-project.org>
1510    
1511            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1512            * src/DEPS.mkf: update
1513    
1514    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1515    
1516            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1517            * DESCRIPTION (Version): 0.9975-0
1518            (Depends): R (>= 2.4.0)
1519    
1520    2006-09-01  Douglas Bates  <bates@R-project.org>
1521    
1522            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1523    
1524    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1525    
1526            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1527            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1528    
1529            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1530    
1531    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1532    
1533            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1534            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1535            * R/dsparseMatrix.R: ditto
1536            * R/Csparse.R: ditto
1537    
1538    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1539    
1540            * R/dMatrix.R (Compare): improve availability of "<", etc
1541            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1542    
1543    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1544    
1545            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1546            of a 0-index which was used as 1-index (..hmm)
1547    
1548            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1549    
1550            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1551            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1552            (.is.diagonal): ditto
1553    
1554            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1555    
1556            * R/Matrix.R (Matrix): also work for NA data
1557    
1558    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1559    
1560            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1561            in all cases.
1562    
1563    2006-08-27  Douglas Bates  <bates@R-project.org>
1564    
1565            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1566            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1567    
1568    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1569    
1570            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1571            subclasses of "ddenseMatrix"
1572            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1573            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1574            instead of half dozen specialized ones.
1575    
1576    2006-08-25  Douglas Bates  <bates@R-project.org>
1577    
1578            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1579            <tillard@cirad.fr> - ordering standard errors to match effects.
1580    
1581    2006-08-24  Douglas Bates  <bates@R-project.org>
1582    
1583            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1584            on R_ldl.
1585            * R/lCholCMatrix.R,
1586            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1587            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1588            * many files in ./R and ./src: Use more general version of
1589            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1590            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1591            dtpMatrix, dspMatrix and dppMatrix conversions.
1592    
1593    
1594    2006-08-23  Douglas Bates  <bates@R-project.org>
1595    
1596            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1597            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1598            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1599            dgeMatrix_crossprod (may need to do this in other places).
1600            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1601            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1602    
1603    2006-08-22  Douglas Bates  <bates@R-project.org>
1604    
1605            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1606            types of classed Matrices, matrices or numeric or logical vectors.
1607            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1608            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1609            to Mutils.h (as an inline) and change name to Matrix_check_class;
1610            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1611            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1612            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1613            * src/Csparse.c: use diag_P and uplo_P macros.
1614    
1615  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
1616    
1617          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1618          valgrind.          valgrind.
1619            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1620            inverses.
1621            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1622            -Wall warnings.
1623            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1624            Use dup_mMatrix_as_dgeMatrix.
1625    
1626  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
1627    

Legend:
Removed from v.1405  
changed lines
  Added in v.2157

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