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 1351, Mon Aug 7 16:51:14 2006 UTC revision 2105, Tue Jan 15 10:16:29 2008 UTC
# Line 1  Line 1 
1    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
4                    in order to ensure 'system = *' is not lost;
5                    formals()$system instead of cut&paste.
6            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
7    
8    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * DESCRIPTION (Date): make ready for release --> 0.999375-4
11    
12            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
13    
14    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
17                    and hence does as.vector(.).
18            * man/pMatrix-class.Rd: docs
19            * R/sparseMatrix.R: fix for printing "integer sparse"
20    
21            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
22    
23            * R/Matrix.R and others: use "exact" function argument list for
24                    both "["   : (x, i,j, ..., drop)
25                    and  "[<-" : (x, i,j, ..., value)
26    
27            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
28            * R/Tsparse.R (replTmat):    ditto
29            * R/diagMatrix.R (replDiag): ditto
30            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
31            * tests/indexing.R: testing the above
32    
33    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/sparseMatrix.R (cov2cor): method for sparse matrices
36    
37            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
38    
39            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
40    
41            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
42    
43    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/Matrix.R: "generic" cov2cor() method
46    
47            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
48                    speed up Q %*% D %*% t(Q)
49            * tests/dpoMatrix.R: test nearPD()
50    
51    2007-12-05  Doug Bates and Martin Maechler
52    
53            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
54            stats::xtabs() allowing to create sparse matrices.
55    
56    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
59    
60    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
63    
64    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/LU.R: solve() method for "denseLU"
67    
68    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * DESCRIPTION (Version): 0.999375-3 preparing for release
71    
72            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
73    
74            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
75    
76    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
79              thanks to Kasper Kristensen.
80            * tests/matprod.R: regression test for that.
81    
82    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
83    
84            * [r4778] R/AllGeneric.R: Check R version before defining generics for
85              primitives
86    
87    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/denseMatrix.R (rcond): method
90            * R/sparseQR.R (rcond): method, use x or t(x)
91    
92    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
95            matrices.
96            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
97    
98            * man/rcond.Rd: mention the more general definition, and add
99            example for non-square matrices.
100    
101            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
102    
103    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
106    
107    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
110            * tests/indexing.R: add new regression for the above cases.
111    
112    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/Mutils.h (__sun): clause for alloca.h on Solaris
115    
116    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * DESCRIPTION (Date, Version): 0.999375-2
119    
120    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/HBMM.R (readMM): make work for pattern matrices as well
123    
124    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4730] src/Mutils.h: declare alloca
127            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
128              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
129              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
130              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
131              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
132              methods; switch writeMM to use CHOLMOD code; repair readMM
133    
134    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
137            Oehlschlaegel's ... result type still to be discussed!
138    
139    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * man/image-methods.Rd: new, combining all image() methods
142    
143    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
146            to work via dgC...
147    
148            * R/Matrix.R (Matrix): special treatment for "table" (S3)
149    
150    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/dgTMatrix.R (image): change defaults to
153                    aspect = "iso", colorkey = FALSE
154    
155    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
158            must copy its *expanded* x slot before LAPACK call.
159    
160            * tests/matprod.R: test the last days' changes.
161    
162    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
163    
164            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
165              as well as in sources
166            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
167              Lapack call
168    
169    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
172                    ("Matrix", "matrix") which is needed in some cases.
173            Ditto for solve().
174    
175            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
176            infinite recursion in dispatch for some cases.
177    
178    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
179    
180            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
181              so pointers match
182    
183    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Date): set ready for release -- 0.999375-1
186    
187    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
190              src/chm_common.c, src/chm_common.h: Change API for
191              numeric_as_chm_dense and N_AS_CHM_DN
192    
193    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
196            * tests/matprod.R: regr.test for it
197    
198    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
201            * tests/group-methods.R: and regression-test it
202    
203    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
204    
205            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
206              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
207              triplet_to_sparse, documentation, use typedefs
208    
209    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * man/dpoMatrix-class.Rd: added 'corMatrix' example
212    
213            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
214            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
215            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
216    
217            * R/lsparseMatrix.R: bug fix in "all" method
218            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
219    
220            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
221            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
222                    + matrix |-> nMatrix coercion
223            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
224            * man/pMatrix-class.Rd: ditto
225    
226            * R/Matrix.R (Summary): method for non-dMatrix
227    
228            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
229            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
230                    test all Summary methods.
231    
232    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
235    
236    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
239    
240            * R/pMatrix.R (t?crossprod): methods for pMatrix
241    
242    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
245    
246    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
247    
248            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
249              trying to fix a subtle bug - which has been somewhere else.
250    
251    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
252    
253            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
254              solve the bug
255    
256    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * src/dgCMatrix.c (compressed_to_TMatrix):
259    
260    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * src/Csparse.c (Rsparse_validate): new, to have some validity
263            checking for RsparseMatrix
264            * src/dgCMatrix.c (xRMatrix_validate): ditto
265            * src/dtCMatrix.c (tRMatrix_validate): ditto
266    
267    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
268    
269            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
270              lgRMatrix
271            * [r4568] DESCRIPTION: Prepare for bug-fix release
272            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
273              for declaration of cholmod_symmetry
274    
275    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
278            release.
279    
280    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
281    
282            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
283              functions - no longer used
284            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
285              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
286              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
287              Alloca
288    
289    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
290    
291            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
292              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
293              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
294              src/t_gCMatrix_colSums.c: more R_CheckStack()s
295    
296    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
297    
298            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
299              the required amount of memory then call M_numeric_as_chm_dense.
300            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
301              (like Calloc but calling alloca)
302    
303    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
306            and extended with more sophisticated 'col.names' option.
307            * NAMESPACE: export  printSparseMatrix()
308            * man/printSpMatrix.Rd: document, incl. examples
309    
310    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
311    
312            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
313              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
314              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
315    
316    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * DESCRIPTION (Version): 0.99875-4
319    
320            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
321            some dimnames perservation.
322    
323            * R/dsTMatrix.R (t-method): keep dimnames
324            * R/dtTMatrix.R:  ditto
325    
326            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
327            and ncol(.) < 10
328    
329            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
330            from Mutils.h
331    
332            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
333            e.g. in as(<ngCMatrix>, "matrix")
334    
335    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
336    
337            * [r4529] .: Create a branch for the API changes from the 0.99875
338              series to the 0.999375 series
339            * [r4530] DESCRIPTION, inst/include/Matrix.h,
340              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
341              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
342              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
343              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
344              as_cholmod_x functions
345    
346    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
347    
348            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
349              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
350              to Comparisons
351    
352    >>>>>>> .merge-right.r4561
353    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Version): 0.99875-3 ready to be released.
356    
357            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
358    
359            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
360            that should also work in a future version of R.
361    
362    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
365    
366            * R/sparseVector.R: more *sparseVector coercions, notably for
367            non - double ones.
368    
369    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
372              notably the new ones building on the new .Call(.)s:
373    
374            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
375            all 4 of [dlin]gCMatrix_colSums().
376    
377    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
378    
379            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
380            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
381              result
382    
383    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/kronecker.R: fix typo (could lead to inf.recursion)
386            * test/simple.R: testing that
387    
388            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
389            method as well (which can have arguments, show() can't).
390    
391    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
392    
393            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
394              added dgCMatrix_colSums for [col,row][Sums,Means]
395    
396    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
397    
398            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
399              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
400              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
401            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
402              class
403            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
404              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
405              row names to store the levels - duh!  Added an example.
406    
407    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * src/Csparse.c (Csparse_validate): check for *repeated* entries
410            thanks to example from Christian Buchta; with a test here:
411            * tests/simple.R:
412    
413    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
416            of colSums(*, sparseResult = TRUE)
417    
418    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
421            'na.rm = FALSE' as "everywhere" else in R.
422    
423    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
424    
425            * [r4421] src/CSparse_install.sh: Modify for new organization of
426              CSparse package
427            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
428              SuiteSparse
429            * [r4426] src/Makefile: add ./UFconfig to the include path for
430              compilation
431            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
432            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
433              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
434    
435    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
438            * R/sparseMatrix.R (prSpMatrix): now gives a message about
439            suppressed column names.
440    
441    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
442    
443            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
444              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
445              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
446              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
447              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
448              Remove warnings after change to const char* CHAR
449    
450    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
451    
452            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
453              type of M_cholmod_ssmult
454    
455    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
456    
457            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
458              src/init.c: Yet another cholmod export - cholmod_ssmult
459    
460    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * NAMESPACE: exported drop0(), since
463            * man/drop0.Rd: I have seen several cases, I really wanted to use
464            it, so our users may want too.
465    
466    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * man/colSums.Rd: separately document colSums() etc, since these
469            have the extra argument 'sparseResult'.
470    
471    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
474            * man/spMatrix.Rd: docu., including examples
475    
476            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
477            in order to make colMeans() etc fast *and* correct.
478            * R/sparseVector.R (replSPvec): "[<-" functionality for
479            sparseVectors; tested in
480            * tests/simple.R:
481    
482    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
485            (very) sparse Matrices; output similar to Matlab's print().
486    
487    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
488    
489            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
490            0-based, indices (Jose Quesada <quesada@gmail.com>).
491    
492    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
493    
494            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
495    
496    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Auxiliaries.R (sparsapply): new utility, much faster than
499            tapply1() for large sparse matrices.
500    
501    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/Matrix.R (dim<-): reshape now via sparseVector.
504    
505            * R/sparseVector.R: methods and function for
506            * R/AllClass.R: new "sparseVector" class and daughters.
507            * NAMESPACE: export new classes
508    
509    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * DESCRIPTION (Version): 0.99875-1
512            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
513    
514    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
517            indexing
518            * tests/indexing.R: test set for that.
519    
520    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
523            entries.
524            * tests/indexing.R(out): add regression test for it
525    
526    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
529            name for "!" method definitions.
530    
531    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/Tsparse.R (intI): new utility, used for "[" :
534                    Cleanup up there, and fixes for duplicated indices - more TODO!
535    
536            * tests/indexing.R(out): more tests
537    
538    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
539    
540            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
541            code that is now part of the R Lapack library.
542    
543            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
544            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
545    
546    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
549    
550    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
553            up with extraneous names '0'...'<n-1>'
554    
555    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/dgTMatrix.R (mat2dgT): care about NAs
558    
559    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/kronecker.R: triangularity preserving methods
562    
563    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/kronecker.R: new file collecting kronecker() methods in one
566                    place.  Goal: become much faster!
567    
568    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
571            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
572            can be much faster.
573    
574            * tests/matprod.R: add regression tests for these (upper & lower).
575    
576    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/Matrix.R (diff): method for our Matrices.
579    
580            * R/sparseMatrix.R (isDiagonal): check dim()!
581    
582    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Matrix.R (dim<-): new method for "reshape()" built on a
585            proposal from Tamas Papp.
586    
587    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
590    
591            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
592            rather define and export  cBind() and rBind() only.
593            --> useRs *must* change code that used to have cbind()/rbind() !!
594    
595            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
596            * R/bind.Rout.save: ditto
597    
598    2007-02-16  Douglas Bates  <bates@r-project.org>
599    
600            * DESCRIPTION (Date, Version): 0.9975-11 with new date
601            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
602            const modifier on declaration of the array 'valid'
603    
604    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
605    
606            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
607    
608    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
611    
612            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
613            * tests/simple.R: test the above and some of these coercions:
614    
615            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
616                    be careful to avoid infinite recursion, using new coercions in
617            * R/ngCMatrix.R and nsC... and ntC...
618            * R/lsparseMatrix.R: ditto
619    
620            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
621    
622            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
623            * R/Rsparse.R: reactivate .Call()s
624    
625            * tests/Class+Meth.R: a bit more on actual classes
626    
627    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
628    
629            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
630    
631    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * DESCRIPTION (Version): 0.9975-10 to upload
634    
635            * tests/Class+Meth.R (tstMatrixClass): require coercions to
636            specific classes less unconditionally.
637    
638            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
639    
640            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
641    
642            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
643            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
644            R_to_CMatrix segfaults on one platform.
645            Eliminate most coercion method to *specific* classes, and replace
646            with virtual classes coercions.
647    
648    
649    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
650    
651            * src/init.c: export the CHM...._validate() placeholders, since
652            they *are* called.
653    
654            * tests/Class+Meth.R (classCanCoerce): and starting to test
655            all as(<from>, <to>)
656    
657    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
660            * tests/indexing.R: tested now
661            * tests/indexing.Rout.save: updated
662    
663            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
664            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
665            appropriate.
666    
667            * NAMESPACE: export a trivial
668            * R/Matrix.R: drop() Matrix-method
669    
670            * R/AllClass.R: moved all prototypes to virtual super classes.
671    
672            * R/Rsparse.R: many more coercions to have less exceptions in
673            * tests/Class+Meth.R:
674    
675            * R/Ops.R (Compare): tweak for case with NA
676            * tests/simpl.R: hence another 'FIXME' eliminated
677    
678    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
681            objects.
682    
683            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
684              and more of "!", "&", "|", all, any; coercions
685    
686            * R/Rsparse.R: many coercions (which enable quite a few other
687            methods), thanks to enhancements in
688            * src/dgCMatrix.c (R_to_CMatrix): new, and
689            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
690            symmetric & triangular and ..RMatrix objects.
691    
692            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
693            renamed file from src/dsTMatrix.c;
694            now dealing with symmetric and triangular Tsparse coercions, both
695            to dense and general.
696    
697    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
700    
701            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
702            where sensible when the <numeric> is of length > 1.
703    
704    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * R/Matrix.R ([<-): for M[] <- value: fix length
707    
708    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
711            * R/ndenseMatrix.R: new coercions n* -> l*
712    
713    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
716    
717            * R/Ops.R ("Logic"): and other "Ops", many updates
718    
719    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * src/Mutils.h (SET_DimNames): new utility
722    
723            * R/Auxiliaries.R (nnzero): improved and now exported via
724    
725            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
726    
727    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/diagMatrix.R (!): fix typo.
730    
731    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/Auxiliaries.R (as_Csparse): and quite a few others:
734                    allow to pass class definition --> speedup
735            * R/sparseMatrix.R: apply the above
736    
737            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
738    
739            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
740            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
741            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
742    
743            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
744    
745            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
746            and use it for "sparse*" as well, since it's faster than the
747            as_Csparse(.) way.
748    
749    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
752    
753    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
756            as method for   M[ ij ] <- v
757            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
758    
759            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
760            FALSE answer
761    
762            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
763            * tests/indexing.R: test it, and some of the above
764    
765    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/Auxiliaries.R (is_duplicatedT): new utility
768    
769    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
770    
771            * src/init.c (R_init_Matrix): export cholmod_scale
772    
773    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
776            base::as.matrix to (x, ...)
777    
778    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
781            file; start using "Logic", hence
782    
783            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
784            * NAMESPACE: import and export "Logic"
785    
786    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
789            only needed previously to R version 2.5.0.
790    
791    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
794    
795            * R/Tsparse.R (replTmat): fix subassignment of triangular
796            * R/Csparse.R (replCmat): ditto
797            * tests/indexing.R: more tests, incl the above fix
798    
799    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/Auxiliaries.R (drop0): extend for non CSparse
802            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
803    
804            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
805                    use uplo correctly (!); other places: use uplo_P() macro
806    
807            * R/Csparse.R (replCmat): call diagU2N() when needed
808            * R/Tsparse.R (replTmat): ditto
809    
810            * src/dtCMatrix.c (tCMatrix_validate): new
811            * src/dtTMatrix.c (tTMatrix_validate): new, used in
812            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
813    
814            * R/diagMatrix.R (replDiag): to use in [<-
815    
816    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
819                    also more general diagU2N().
820    
821    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
824            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
825    
826    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * tests/bind.R: a few more cases
829            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
830    
831            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
832            * R/ddenseMatrix.R (cbind2/rbind2)
833            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
834            * tests/indexing.R
835            * tests/indexing.Rout.save: updated
836    
837    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
838    
839            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
840            * tests/indexing.R
841    
842    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
845            align with proper position of "0", i.e., right for integers.
846            argument 'align' by default is "fancy".
847    
848    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
851            * R/Csparse.R: and fix "Compare" for more cases.
852            * tests/Class+Meth.R: test some of these (m == m, m != m)
853    
854    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/lsparseMatrix.R: all() and any() methods
857            * R/ldenseMatrix.R:      ditto
858            * NAMESPACE, R/Matrix.R: ditto
859    
860            * man/all-methods.Rd: document them minimally
861    
862            * tests/simple.R: add a few examples for these
863    
864    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * R/Tsparse.R ([): fix long standing typo in symmetric case
867            * man/dsCMatrix-class.Rd: add example exhibiting the above case
868    
869    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
870    
871            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
872            to LL before converting to a sparse matrix. (The LDL form can be
873            converted to a sparse matrix but it is implicitly a unit
874            triangular matrix and a diagonal matrix overwritten on the diagonal.)
875    
876    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
877    
878            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
879    
880    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
881    
882            * DESCRIPTION (Version): updated -> release 0.9975-7
883            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
884    
885    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
888    
889    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
890    
891            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
892            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
893            is exactly singular.
894    
895    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * DESCRIPTION (Date): updated -> release 0.9975-6
898    
899    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
902            now returns symmetric.
903    
904            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
905    
906            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
907            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
908    
909            * R/Auxiliaries.R (.type.kind): added
910    
911    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
914            running src/CSparse_install.sh
915    
916            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
917    
918    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
921            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
922    
923            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
924    
925            * tests/Class+Meth.R (tstMatrixClass): now assure
926            the (important in method programming) property :
927    
928                    ###>>  Every "Matrix" is either
929                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
930    
931                    (where "*" stands for "Matrix")
932    
933            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
934    
935            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
936            * tests/validObj.R: checks for "comparison"
937    
938            * R/sparseMatrix.R ([): improved indexing for sparse;
939                    trying to keep <symmetric>[ n, n] symmmetric
940    
941            * tests/indexing.R: indexing for logical sparse now ok
942    
943    
944    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * src/Tsparse.c: use xTsparse_validate() , and hence remove
947    
948            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
949    
950    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
953    
954            * tests/simple.R: validObject() checking the above.
955    
956            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
957            replacing both dgCMatrix_validate and lgCM*.
958    
959            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
960            fix dimnames setting in other places.
961            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
962    
963    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
966    
967            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
968            symmetry test, via
969            * R/Auxiliaries.R (.as.dgC.0.factors):
970    
971    2006-11-01  Douglas Bates  <bates@r-project.org>
972    
973            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
974            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
975            <CsparseMatrix>) added
976    
977    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * tests/matprod.R: add a variation of Harri's example
980    
981            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
982            recursive infinitely.
983    
984            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
985    
986            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
987    
988    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
991            matrix if possible; test m+m == 2*m; now test dgRMatrix.
992            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
993            satisfy the above test.
994    
995    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
998    
999            * R/dgCMatrix.R: solve(a, b="missing") based on
1000            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1001            RHS = NULL.
1002    
1003            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1004            add more (needed) [t]crossprod() methods.
1005    
1006            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1007    
1008            * R/Auxiliaries.R (as_CspClass): cleanup
1009            (drop0): internal utility for "Csparse_drop(*, 0)"
1010            (.bail.out.2): encourage active feedback
1011    
1012    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1015    
1016            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1017            non-valid or 'sorted' case).
1018    
1019            * R/dsparseMatrix.R: add "chol" method.
1020            * R/ddenseMatrix.R: ditto
1021    
1022            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1023            * NAMESPACE (Ops)
1024            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1025            coercion; deprecating direct lower level coercions.
1026    
1027            * R/*.R (seq): use seq_len() and seq_along() where possible.
1028    
1029    
1030    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * DESCRIPTION (Version): 0.9975-5 ready for release
1033    
1034    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1035    
1036            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1037    
1038    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1039    
1040            * R/AllClass.R (corMatrix): add 'validity' check;
1041                    comment out unused "LDL" class definition
1042            * NAMESPACE: mention, but do not export "LDL" class
1043            * R/corMatrix.R: new (simple), needed for R-devel with
1044            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1045              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1046    
1047    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1048    
1049            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1050            use Rprintf and R's error handling.
1051    
1052    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1053    
1054            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1055            * tests/matprod.R: add tests for the bug fixed.
1056    
1057    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1058    
1059            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1060            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1061    
1062    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1063    
1064            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1065    
1066    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1067    
1068            * DESCRIPTION (Version): 0.9975-3
1069    
1070            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1071            (sparse) matrices.
1072            * man/bdiag.Rd: docu + examples
1073    
1074            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1075    
1076            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1077            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1078    
1079            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1080            that result is sparse or diagonal (and not dense).
1081    
1082            * man/Subassign-methods.Rd: fix examples
1083    
1084            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1085            should always return a sparse (and not sometimes a diagonal) matrix.
1086    
1087    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1088    
1089            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1090    
1091    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1092    
1093            * DESCRIPTION (Version): 0.9975-2
1094    
1095            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1096    
1097    2006-10-02  Douglas Bates  <bates@R-project.org>
1098    
1099            * tests/dg_Matrix.R: Simplify test taking into account new code.
1100    
1101    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1104    
1105            * R/lsTMatrix.R: new files w/ missing methods
1106            * R/nsTMatrix.R:  "  'for completeness'
1107    
1108            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1109    
1110            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1111    
1112    
1113    2006-09-28  Douglas Bates  <bates@R-project.org>
1114    
1115            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1116            included.
1117    
1118            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1119            Export C-callable functions used in Zt_create in lme4.
1120    
1121    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * DESCRIPTION (Version): 0.9975-1
1124    
1125            * tests/simple.R: less checks fail; using NA, found that our
1126                    kronecker() is not base-compatible with NA's.
1127    
1128            * R/dMatrix.R: "Compare" method now implemented for all cases
1129    
1130            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1131    
1132            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1133    
1134            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1135            * src/dspMatrix.c (dspMatrix_validate): ditto
1136    
1137            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1138              including coercion to [nl]tTMatrix.
1139    
1140            * R/diagMatrix.R (show): print a header line as for other classes.
1141    
1142    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1143    
1144            * src/Makefile.win (SUBDIRS): fix typo
1145    
1146    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1149    
1150    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1151    
1152            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1153            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1154            accept a symmetric matrix).
1155            * tests/group-methods.R: Uncomment test of crossprod applied to
1156            lsCMatrix objects.
1157    
1158    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * R/AllClass.R (symmetricMatrix): add validity method (available
1161            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1162    
1163            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1164    
1165            * tests/indexing.Rout.save:
1166            * tests/indexing.R: additions, mainly for 'lsparse'
1167    
1168            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1169            case.
1170    
1171            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1172    
1173    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1174    
1175            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1176                    as 'N' (1-letter - Ok?)
1177    
1178            * tests/group-methods.R: add test for logical + NAs
1179    
1180            * R/dMatrix.R ("Compare"): fix to work with NA's
1181    
1182            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1183    
1184            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1185                    which is implemented.
1186    
1187    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1188    
1189            * src/chm_common.c: coerce logical <-> double instead of
1190            typecasting;  needed for "l" matrix handling in cholmod.
1191    
1192            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1193    
1194            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1195            (Tsp2grNEL): other fixes needed
1196    
1197    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1200                    Matrices, since "lMatrix", also "lsparseM" can have NA
1201            * R/ndenseMatrix.R, etc: new source files
1202            * man/nsparseMatrix-classes.Rd, etc: new help files
1203            * tests/: adaptions
1204            * src/chm_common.c (chm_dense_to_SEXP): and others:
1205                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1206            * src/Csparse.c, etc: ditto
1207    
1208    2006-09-11  Douglas Bates  <bates@R-project.org>
1209    
1210            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1211            alloc_d**Matrix functions to the lme4 package.
1212    
1213    2006-09-09  Douglas Bates  <bates@R-project.org>
1214    
1215            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1216            fixed
1217    
1218    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * R/lMatrix.R: new
1221    
1222            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1223    
1224            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1225            * man/tcrossprod.Rd: ditto
1226    
1227    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1228    
1229            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1230            for exported functions
1231            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1232            Remove partitioning algorithms for sparse matrix reordering.  The
1233            copyright on the Metis code was problematic and the methods were
1234            rarely used.
1235            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1236            operations are now done entirely in CHOLMOD code.
1237    
1238    2006-09-06  Douglas Bates  <bates@R-project.org>
1239    
1240            * src/Mutils.h: Remove functions that are no longer used.
1241    
1242    2006-09-04  Douglas Bates  <bates@R-project.org>
1243    
1244            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1245            * src/DEPS.mkf: update
1246    
1247    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1248    
1249            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1250            * DESCRIPTION (Version): 0.9975-0
1251            (Depends): R (>= 2.4.0)
1252    
1253    2006-09-01  Douglas Bates  <bates@R-project.org>
1254    
1255            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1256    
1257    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1258    
1259            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1260            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1261    
1262            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1263    
1264    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1265    
1266            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1267            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1268            * R/dsparseMatrix.R: ditto
1269            * R/Csparse.R: ditto
1270    
1271    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1272    
1273            * R/dMatrix.R (Compare): improve availability of "<", etc
1274            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1275    
1276    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1277    
1278            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1279            of a 0-index which was used as 1-index (..hmm)
1280    
1281            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1282    
1283            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1284            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1285            (.is.diagonal): ditto
1286    
1287            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1288    
1289            * R/Matrix.R (Matrix): also work for NA data
1290    
1291    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1294            in all cases.
1295    
1296    2006-08-27  Douglas Bates  <bates@R-project.org>
1297    
1298            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1299            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1300    
1301    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1302    
1303            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1304            subclasses of "ddenseMatrix"
1305            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1306            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1307            instead of half dozen specialized ones.
1308    
1309    2006-08-25  Douglas Bates  <bates@R-project.org>
1310    
1311            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1312            <tillard@cirad.fr> - ordering standard errors to match effects.
1313    
1314    2006-08-24  Douglas Bates  <bates@R-project.org>
1315    
1316            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1317            on R_ldl.
1318            * R/lCholCMatrix.R,
1319            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1320            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1321            * many files in ./R and ./src: Use more general version of
1322            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1323            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1324            dtpMatrix, dspMatrix and dppMatrix conversions.
1325    
1326    
1327    2006-08-23  Douglas Bates  <bates@R-project.org>
1328    
1329            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1330            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1331            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1332            dgeMatrix_crossprod (may need to do this in other places).
1333            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1334            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1335    
1336    2006-08-22  Douglas Bates  <bates@R-project.org>
1337    
1338            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1339            types of classed Matrices, matrices or numeric or logical vectors.
1340            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1341            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1342            to Mutils.h (as an inline) and change name to Matrix_check_class;
1343            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1344            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1345            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1346            * src/Csparse.c: use diag_P and uplo_P macros.
1347    
1348    2006-08-21  Douglas Bates  <bates@R-project.org>
1349    
1350            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1351            valgrind.
1352            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1353            inverses.
1354            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1355            -Wall warnings.
1356            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1357            Use dup_mMatrix_as_dgeMatrix.
1358    
1359    2006-08-20  Douglas Bates  <bates@R-project.org>
1360    
1361            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1362            * tests/sparseQR.R: Added
1363            * man/sparseQR-class.Rd: Document methods for qr.* generics
1364            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1365    
1366    2006-08-19  Douglas Bates  <bates@R-project.org>
1367    
1368            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1369            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1370            and qr.fitted.
1371            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1372            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1373    
1374    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1375    
1376            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1377            the base version has no "..." argument.
1378    
1379            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1380    
1381            * R/Matrix.R: define and
1382            * NAMESPACE: export as.numeric() and as.logical() methods.
1383                    Let's hope these do not badly slow down something...
1384            Finally export the zapsmall() method.
1385    
1386    2006-08-17  Douglas Bates  <bates@R-project.org>
1387    
1388            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1389            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1390            * src/dtCMatrix.c :Remove code that is no longer used
1391            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1392    
1393    2006-08-14  Douglas Bates  <bates@R-project.org>
1394    
1395            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1396            Csparse_to_logical and Csparse_symmetric_to_general.
1397            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1398            coercion methods between CsparseMatrix and TsparseMatrix.
1399    
1400    2006-08-14  Douglas Bates  <bates@R-project.org>
1401    
1402            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1403            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1404            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1405            possible.
1406    
1407    2006-08-12  Douglas Bates  <bates@R-project.org>
1408    
1409            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1410              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1411              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1412              generalize conversions between TsparseMatrix, CsparseMatrix,
1413              denseMatrix and matrix.  Preserve triangularity property and
1414              propagate Dimnames in the easy cases.
1415    
1416    2006-08-10  Douglas Bates  <bates@R-project.org>
1417    
1418            * src/lmer.c: adjust checks in glmer_init for S4SXP
1419            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1420            before S4SXP but for the wrong reasons.
1421    
1422    2006-08-08  Douglas Bates  <bates@R-project.org>
1423    
1424            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1425            Later modified to return the upper triangle only.
1426            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1427    
1428    2006-08-07  Douglas Bates  <bates@R-project.org>
1429    
1430            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1431            R-level conversion to a sparse symmetric class.
1432            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1433            Remove conversion to sparse symmetric classes (now done in C code).
1434    
1435  2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1436    
1437          * R/dgCMatrix.R: disable old crossprod and tcrossprod methods          * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
# Line 14  Line 1448 
1448    
1449          * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new          * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1450          * R/Tsparse.R (tril, triu, band): methods          * R/Tsparse.R (tril, triu, band): methods
1451          * R/dgRMatrix.R (tril, ...):    dito          * R/dgRMatrix.R (tril, ...):    ditto
1452          * man/band.Rd:                  dito          * man/band.Rd:                  ditto
1453    
1454  2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1455    
# Line 54  Line 1488 
1488    
1489          * NAMESPACE:    change  "correlation" to "corMatrix"          * NAMESPACE:    change  "correlation" to "corMatrix"
1490          * R/AllClass.R: to avoid clash with S3 class in 'nlme'.          * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1491          * R/dpoMatrix.R: dito          * R/dpoMatrix.R: ditto
1492          * R/lmer.R:      dito          * R/lmer.R:      ditto
1493    
1494  2006-07-28  Douglas Bates  <bates@R-project.org>  2006-07-28  Douglas Bates  <bates@R-project.org>
1495    
# Line 230  Line 1664 
1664    
1665          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1666          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
1667          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1668    
1669    
1670  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 353  Line 1787 
1787          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1788          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1789          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1790          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1791    
1792  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1793    
# Line 557  Line 1991 
1991  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1992    
1993          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1994          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1995          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1996    
1997  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

Legend:
Removed from v.1351  
changed lines
  Added in v.2105

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