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 350, Tue Nov 23 15:39:45 2004 UTC revision 2096, Fri Dec 7 17:44:44 2007 UTC
# Line 1  Line 1 
1  2004-11-16  Douglas Bates  <bates@bates1-home>  
2    
3    >>>>>> FIXME  rcond(matrix(1:6, 2,3))   gives infinite recursion !!! <<<<<<<<<<
4    
5    
6    
7    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/sparseMatrix.R (cov2cor): method for sparse matrices
10    
11            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
12    
13            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
14    
15            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
16    
17    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/Matrix.R: "generic" cov2cor() method
20    
21            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
22                    speed up Q %*% D %*% t(Q)
23            * tests/dpoMatrix.R: test nearPD()
24    
25    2007-12-05  Doug Bates and Martin Maechler
26    
27            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
28            stats::xtabs() allowing to create sparse matrices.
29    
30    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
33    
34    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
37    
38    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/LU.R: solve() method for "denseLU"
41    
42    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * DESCRIPTION (Version): 0.999375-3 preparing for release
45    
46            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
47    
48            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
49    
50    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
53              thanks to Kasper Kristensen.
54            * tests/matprod.R: regression test for that.
55    
56    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4778] R/AllGeneric.R: Check R version before defining generics for
59              primitives
60    
61    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/denseMatrix.R (rcond): method
64            * R/sparseQR.R (rcond): method, use x or t(x)
65    
66    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
69            matrices.
70            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
71    
72            * man/rcond.Rd: mention the more general definition, and add
73            example for non-square matrices.
74    
75            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
76    
77    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
80    
81    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
84            * tests/indexing.R: add new regression for the above cases.
85    
86    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * src/Mutils.h (__sun): clause for alloca.h on Solaris
89    
90    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Date, Version): 0.999375-2
93    
94    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/HBMM.R (readMM): make work for pattern matrices as well
97    
98    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4730] src/Mutils.h: declare alloca
101            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
102              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
103              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
104              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
105              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
106              methods; switch writeMM to use CHOLMOD code; repair readMM
107    
108    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
111            Oehlschlaegel's ... result type still to be discussed!
112    
113    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * man/image-methods.Rd: new, combining all image() methods
116    
117    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
120            to work via dgC...
121    
122            * R/Matrix.R (Matrix): special treatment for "table" (S3)
123    
124    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dgTMatrix.R (image): change defaults to
127                    aspect = "iso", colorkey = FALSE
128    
129    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
132            must copy its *expanded* x slot before LAPACK call.
133    
134            * tests/matprod.R: test the last days' changes.
135    
136    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
139              as well as in sources
140            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
141              Lapack call
142    
143    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
146                    ("Matrix", "matrix") which is needed in some cases.
147            Ditto for solve().
148    
149            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
150            infinite recursion in dispatch for some cases.
151    
152    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
153    
154            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
155              so pointers match
156    
157    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * DESCRIPTION (Date): set ready for release -- 0.999375-1
160    
161    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
162    
163            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
164              src/chm_common.c, src/chm_common.h: Change API for
165              numeric_as_chm_dense and N_AS_CHM_DN
166    
167    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
170            * tests/matprod.R: regr.test for it
171    
172    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
175            * tests/group-methods.R: and regression-test it
176    
177    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
178    
179            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
180              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
181              triplet_to_sparse, documentation, use typedefs
182    
183    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * man/dpoMatrix-class.Rd: added 'corMatrix' example
186    
187            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
188            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
189            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
190    
191            * R/lsparseMatrix.R: bug fix in "all" method
192            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
193    
194            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
195            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
196                    + matrix |-> nMatrix coercion
197            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
198            * man/pMatrix-class.Rd: ditto
199    
200            * R/Matrix.R (Summary): method for non-dMatrix
201    
202            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
203            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
204                    test all Summary methods.
205    
206    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
209    
210    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
213    
214            * R/pMatrix.R (t?crossprod): methods for pMatrix
215    
216    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
217    
218            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
219    
220    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
221    
222            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
223              trying to fix a subtle bug - which has been somewhere else.
224    
225    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
226    
227            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
228              solve the bug
229    
230    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * src/dgCMatrix.c (compressed_to_TMatrix):
233    
234    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/Csparse.c (Rsparse_validate): new, to have some validity
237            checking for RsparseMatrix
238            * src/dgCMatrix.c (xRMatrix_validate): ditto
239            * src/dtCMatrix.c (tRMatrix_validate): ditto
240    
241    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
242    
243            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
244              lgRMatrix
245            * [r4568] DESCRIPTION: Prepare for bug-fix release
246            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
247              for declaration of cholmod_symmetry
248    
249    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
252            release.
253    
254    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
255    
256            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
257              functions - no longer used
258            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
259              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
260              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
261              Alloca
262    
263    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
264    
265            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
266              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
267              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
268              src/t_gCMatrix_colSums.c: more R_CheckStack()s
269    
270    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
271    
272            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
273              the required amount of memory then call M_numeric_as_chm_dense.
274            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
275              (like Calloc but calling alloca)
276    
277    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
280            and extended with more sophisticated 'col.names' option.
281            * NAMESPACE: export  printSparseMatrix()
282            * man/printSpMatrix.Rd: document, incl. examples
283    
284    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
285    
286            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
287              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
288              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
289    
290    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * DESCRIPTION (Version): 0.99875-4
293    
294            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
295            some dimnames perservation.
296    
297            * R/dsTMatrix.R (t-method): keep dimnames
298            * R/dtTMatrix.R:  ditto
299    
300            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
301            and ncol(.) < 10
302    
303            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
304            from Mutils.h
305    
306            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
307            e.g. in as(<ngCMatrix>, "matrix")
308    
309    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
310    
311            * [r4529] .: Create a branch for the API changes from the 0.99875
312              series to the 0.999375 series
313            * [r4530] DESCRIPTION, inst/include/Matrix.h,
314              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
315              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
316              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
317              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
318              as_cholmod_x functions
319    
320    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
321    
322            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
323              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
324              to Comparisons
325    
326    >>>>>>> .merge-right.r4561
327    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * DESCRIPTION (Version): 0.99875-3 ready to be released.
330    
331            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
332    
333            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
334            that should also work in a future version of R.
335    
336    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
339    
340            * R/sparseVector.R: more *sparseVector coercions, notably for
341            non - double ones.
342    
343    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
346              notably the new ones building on the new .Call(.)s:
347    
348            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
349            all 4 of [dlin]gCMatrix_colSums().
350    
351    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
352    
353            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
354            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
355              result
356    
357    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/kronecker.R: fix typo (could lead to inf.recursion)
360            * test/simple.R: testing that
361    
362            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
363            method as well (which can have arguments, show() can't).
364    
365    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
366    
367            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
368              added dgCMatrix_colSums for [col,row][Sums,Means]
369    
370    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
371    
372            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
373              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
374              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
375            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
376              class
377            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
378              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
379              row names to store the levels - duh!  Added an example.
380    
381    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * src/Csparse.c (Csparse_validate): check for *repeated* entries
384            thanks to example from Christian Buchta; with a test here:
385            * tests/simple.R:
386    
387    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
390            of colSums(*, sparseResult = TRUE)
391    
392    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
395            'na.rm = FALSE' as "everywhere" else in R.
396    
397    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
398    
399            * [r4421] src/CSparse_install.sh: Modify for new organization of
400              CSparse package
401            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
402              SuiteSparse
403            * [r4426] src/Makefile: add ./UFconfig to the include path for
404              compilation
405            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
406            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
407              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
408    
409    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
412            * R/sparseMatrix.R (prSpMatrix): now gives a message about
413            suppressed column names.
414    
415    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
416    
417            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
418              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
419              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
420              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
421              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
422              Remove warnings after change to const char* CHAR
423    
424    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
425    
426            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
427              type of M_cholmod_ssmult
428    
429    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
430    
431            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
432              src/init.c: Yet another cholmod export - cholmod_ssmult
433    
434    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * NAMESPACE: exported drop0(), since
437            * man/drop0.Rd: I have seen several cases, I really wanted to use
438            it, so our users may want too.
439    
440    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * man/colSums.Rd: separately document colSums() etc, since these
443            have the extra argument 'sparseResult'.
444    
445    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
448            * man/spMatrix.Rd: docu., including examples
449    
450            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
451            in order to make colMeans() etc fast *and* correct.
452            * R/sparseVector.R (replSPvec): "[<-" functionality for
453            sparseVectors; tested in
454            * tests/simple.R:
455    
456    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
459            (very) sparse Matrices; output similar to Matlab's print().
460    
461    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
462    
463            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
464            0-based, indices (Jose Quesada <quesada@gmail.com>).
465    
466    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
467    
468            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
469    
470    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/Auxiliaries.R (sparsapply): new utility, much faster than
473            tapply1() for large sparse matrices.
474    
475    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Matrix.R (dim<-): reshape now via sparseVector.
478    
479            * R/sparseVector.R: methods and function for
480            * R/AllClass.R: new "sparseVector" class and daughters.
481            * NAMESPACE: export new classes
482    
483    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * DESCRIPTION (Version): 0.99875-1
486            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
487    
488    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
491            indexing
492            * tests/indexing.R: test set for that.
493    
494    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
497            entries.
498            * tests/indexing.R(out): add regression test for it
499    
500    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
503            name for "!" method definitions.
504    
505    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/Tsparse.R (intI): new utility, used for "[" :
508                    Cleanup up there, and fixes for duplicated indices - more TODO!
509    
510            * tests/indexing.R(out): more tests
511    
512    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
513    
514            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
515            code that is now part of the R Lapack library.
516    
517            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
518            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
519    
520    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
523    
524    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
527            up with extraneous names '0'...'<n-1>'
528    
529    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/dgTMatrix.R (mat2dgT): care about NAs
532    
533    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/kronecker.R: triangularity preserving methods
536    
537    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/kronecker.R: new file collecting kronecker() methods in one
540                    place.  Goal: become much faster!
541    
542    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
545            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
546            can be much faster.
547    
548            * tests/matprod.R: add regression tests for these (upper & lower).
549    
550    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/Matrix.R (diff): method for our Matrices.
553    
554            * R/sparseMatrix.R (isDiagonal): check dim()!
555    
556    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Matrix.R (dim<-): new method for "reshape()" built on a
559            proposal from Tamas Papp.
560    
561    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
564    
565            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
566            rather define and export  cBind() and rBind() only.
567            --> useRs *must* change code that used to have cbind()/rbind() !!
568    
569            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
570            * R/bind.Rout.save: ditto
571    
572    2007-02-16  Douglas Bates  <bates@r-project.org>
573    
574            * DESCRIPTION (Date, Version): 0.9975-11 with new date
575            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
576            const modifier on declaration of the array 'valid'
577    
578    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
579    
580            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
581    
582    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
585    
586            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
587            * tests/simple.R: test the above and some of these coercions:
588    
589            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
590                    be careful to avoid infinite recursion, using new coercions in
591            * R/ngCMatrix.R and nsC... and ntC...
592            * R/lsparseMatrix.R: ditto
593    
594            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
595    
596            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
597            * R/Rsparse.R: reactivate .Call()s
598    
599            * tests/Class+Meth.R: a bit more on actual classes
600    
601    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
604    
605    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * DESCRIPTION (Version): 0.9975-10 to upload
608    
609            * tests/Class+Meth.R (tstMatrixClass): require coercions to
610            specific classes less unconditionally.
611    
612            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
613    
614            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
615    
616            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
617            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
618            R_to_CMatrix segfaults on one platform.
619            Eliminate most coercion method to *specific* classes, and replace
620            with virtual classes coercions.
621    
622    
623    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
624    
625            * src/init.c: export the CHM...._validate() placeholders, since
626            they *are* called.
627    
628            * tests/Class+Meth.R (classCanCoerce): and starting to test
629            all as(<from>, <to>)
630    
631    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
634            * tests/indexing.R: tested now
635            * tests/indexing.Rout.save: updated
636    
637            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
638            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
639            appropriate.
640    
641            * NAMESPACE: export a trivial
642            * R/Matrix.R: drop() Matrix-method
643    
644            * R/AllClass.R: moved all prototypes to virtual super classes.
645    
646            * R/Rsparse.R: many more coercions to have less exceptions in
647            * tests/Class+Meth.R:
648    
649            * R/Ops.R (Compare): tweak for case with NA
650            * tests/simpl.R: hence another 'FIXME' eliminated
651    
652    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
655            objects.
656    
657            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
658              and more of "!", "&", "|", all, any; coercions
659    
660            * R/Rsparse.R: many coercions (which enable quite a few other
661            methods), thanks to enhancements in
662            * src/dgCMatrix.c (R_to_CMatrix): new, and
663            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
664            symmetric & triangular and ..RMatrix objects.
665    
666            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
667            renamed file from src/dsTMatrix.c;
668            now dealing with symmetric and triangular Tsparse coercions, both
669            to dense and general.
670    
671    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
674    
675            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
676            where sensible when the <numeric> is of length > 1.
677    
678    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R ([<-): for M[] <- value: fix length
681    
682    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
685            * R/ndenseMatrix.R: new coercions n* -> l*
686    
687    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
690    
691            * R/Ops.R ("Logic"): and other "Ops", many updates
692    
693    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * src/Mutils.h (SET_DimNames): new utility
696    
697            * R/Auxiliaries.R (nnzero): improved and now exported via
698    
699            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
700    
701    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/diagMatrix.R (!): fix typo.
704    
705    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/Auxiliaries.R (as_Csparse): and quite a few others:
708                    allow to pass class definition --> speedup
709            * R/sparseMatrix.R: apply the above
710    
711            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
712    
713            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
714            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
715            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
716    
717            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
718    
719            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
720            and use it for "sparse*" as well, since it's faster than the
721            as_Csparse(.) way.
722    
723    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
726    
727    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
730            as method for   M[ ij ] <- v
731            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
732    
733            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
734            FALSE answer
735    
736            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
737            * tests/indexing.R: test it, and some of the above
738    
739    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * R/Auxiliaries.R (is_duplicatedT): new utility
742    
743    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
744    
745            * src/init.c (R_init_Matrix): export cholmod_scale
746    
747    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
750            base::as.matrix to (x, ...)
751    
752    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
755            file; start using "Logic", hence
756    
757            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
758            * NAMESPACE: import and export "Logic"
759    
760    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
763            only needed previously to R version 2.5.0.
764    
765    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
768    
769            * R/Tsparse.R (replTmat): fix subassignment of triangular
770            * R/Csparse.R (replCmat): ditto
771            * tests/indexing.R: more tests, incl the above fix
772    
773    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/Auxiliaries.R (drop0): extend for non CSparse
776            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
777    
778            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
779                    use uplo correctly (!); other places: use uplo_P() macro
780    
781            * R/Csparse.R (replCmat): call diagU2N() when needed
782            * R/Tsparse.R (replTmat): ditto
783    
784            * src/dtCMatrix.c (tCMatrix_validate): new
785            * src/dtTMatrix.c (tTMatrix_validate): new, used in
786            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
787    
788            * R/diagMatrix.R (replDiag): to use in [<-
789    
790    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
793                    also more general diagU2N().
794    
795    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
798            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
799    
800    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * tests/bind.R: a few more cases
803            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
804    
805            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
806            * R/ddenseMatrix.R (cbind2/rbind2)
807            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
808            * tests/indexing.R
809            * tests/indexing.Rout.save: updated
810    
811    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
814            * tests/indexing.R
815    
816    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
819            align with proper position of "0", i.e., right for integers.
820            argument 'align' by default is "fancy".
821    
822    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
825            * R/Csparse.R: and fix "Compare" for more cases.
826            * tests/Class+Meth.R: test some of these (m == m, m != m)
827    
828    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/lsparseMatrix.R: all() and any() methods
831            * R/ldenseMatrix.R:      ditto
832            * NAMESPACE, R/Matrix.R: ditto
833    
834            * man/all-methods.Rd: document them minimally
835    
836            * tests/simple.R: add a few examples for these
837    
838    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/Tsparse.R ([): fix long standing typo in symmetric case
841            * man/dsCMatrix-class.Rd: add example exhibiting the above case
842    
843    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
844    
845            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
846            to LL before converting to a sparse matrix. (The LDL form can be
847            converted to a sparse matrix but it is implicitly a unit
848            triangular matrix and a diagonal matrix overwritten on the diagonal.)
849    
850    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
851    
852            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
853    
854    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
855    
856            * DESCRIPTION (Version): updated -> release 0.9975-7
857            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
858    
859    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
862    
863    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
864    
865            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
866            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
867            is exactly singular.
868    
869    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * DESCRIPTION (Date): updated -> release 0.9975-6
872    
873    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
876            now returns symmetric.
877    
878            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
879    
880            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
881            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
882    
883            * R/Auxiliaries.R (.type.kind): added
884    
885    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
888            running src/CSparse_install.sh
889    
890            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
891    
892    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
895            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
896    
897            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
898    
899            * tests/Class+Meth.R (tstMatrixClass): now assure
900            the (important in method programming) property :
901    
902                    ###>>  Every "Matrix" is either
903                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
904    
905                    (where "*" stands for "Matrix")
906    
907            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
908    
909            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
910            * tests/validObj.R: checks for "comparison"
911    
912            * R/sparseMatrix.R ([): improved indexing for sparse;
913                    trying to keep <symmetric>[ n, n] symmmetric
914    
915            * tests/indexing.R: indexing for logical sparse now ok
916    
917    
918    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * src/Tsparse.c: use xTsparse_validate() , and hence remove
921    
922            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
923    
924    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
927    
928            * tests/simple.R: validObject() checking the above.
929    
930            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
931            replacing both dgCMatrix_validate and lgCM*.
932    
933            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
934            fix dimnames setting in other places.
935            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
936    
937    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
940    
941            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
942            symmetry test, via
943            * R/Auxiliaries.R (.as.dgC.0.factors):
944    
945    2006-11-01  Douglas Bates  <bates@r-project.org>
946    
947            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
948            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
949            <CsparseMatrix>) added
950    
951    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * tests/matprod.R: add a variation of Harri's example
954    
955            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
956            recursive infinitely.
957    
958            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
959    
960            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
961    
962    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
965            matrix if possible; test m+m == 2*m; now test dgRMatrix.
966            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
967            satisfy the above test.
968    
969    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
972    
973            * R/dgCMatrix.R: solve(a, b="missing") based on
974            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
975            RHS = NULL.
976    
977            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
978            add more (needed) [t]crossprod() methods.
979    
980            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
981    
982            * R/Auxiliaries.R (as_CspClass): cleanup
983            (drop0): internal utility for "Csparse_drop(*, 0)"
984            (.bail.out.2): encourage active feedback
985    
986    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/dMatrix.R(Compare): new(), then slots [no validity check]
989    
990            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
991            non-valid or 'sorted' case).
992    
993            * R/dsparseMatrix.R: add "chol" method.
994            * R/ddenseMatrix.R: ditto
995    
996            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
997            * NAMESPACE (Ops)
998            * R/diagMatrix.R (diag2T): simple utility used "higher level"
999            coercion; deprecating direct lower level coercions.
1000    
1001            * R/*.R (seq): use seq_len() and seq_along() where possible.
1002    
1003    
1004    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * DESCRIPTION (Version): 0.9975-5 ready for release
1007    
1008    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1009    
1010            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1011    
1012    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/AllClass.R (corMatrix): add 'validity' check;
1015                    comment out unused "LDL" class definition
1016            * NAMESPACE: mention, but do not export "LDL" class
1017            * R/corMatrix.R: new (simple), needed for R-devel with
1018            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1019              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1020    
1021    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1022    
1023            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1024            use Rprintf and R's error handling.
1025    
1026    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1029            * tests/matprod.R: add tests for the bug fixed.
1030    
1031    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1032    
1033            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1034            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1035    
1036    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1037    
1038            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1039    
1040    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * DESCRIPTION (Version): 0.9975-3
1043    
1044            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1045            (sparse) matrices.
1046            * man/bdiag.Rd: docu + examples
1047    
1048            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1049    
1050            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1051            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1052    
1053            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1054            that result is sparse or diagonal (and not dense).
1055    
1056            * man/Subassign-methods.Rd: fix examples
1057    
1058            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1059            should always return a sparse (and not sometimes a diagonal) matrix.
1060    
1061    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1062    
1063            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1064    
1065    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1066    
1067            * DESCRIPTION (Version): 0.9975-2
1068    
1069            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1070    
1071    2006-10-02  Douglas Bates  <bates@R-project.org>
1072    
1073            * tests/dg_Matrix.R: Simplify test taking into account new code.
1074    
1075    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1078    
1079            * R/lsTMatrix.R: new files w/ missing methods
1080            * R/nsTMatrix.R:  "  'for completeness'
1081    
1082            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1083    
1084            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1085    
1086    
1087    2006-09-28  Douglas Bates  <bates@R-project.org>
1088    
1089            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1090            included.
1091    
1092            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1093            Export C-callable functions used in Zt_create in lme4.
1094    
1095    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * DESCRIPTION (Version): 0.9975-1
1098    
1099            * tests/simple.R: less checks fail; using NA, found that our
1100                    kronecker() is not base-compatible with NA's.
1101    
1102            * R/dMatrix.R: "Compare" method now implemented for all cases
1103    
1104            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1105    
1106            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1107    
1108            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1109            * src/dspMatrix.c (dspMatrix_validate): ditto
1110    
1111            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1112              including coercion to [nl]tTMatrix.
1113    
1114            * R/diagMatrix.R (show): print a header line as for other classes.
1115    
1116    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * src/Makefile.win (SUBDIRS): fix typo
1119    
1120    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1123    
1124    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1125    
1126            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1127            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1128            accept a symmetric matrix).
1129            * tests/group-methods.R: Uncomment test of crossprod applied to
1130            lsCMatrix objects.
1131    
1132    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1133    
1134            * R/AllClass.R (symmetricMatrix): add validity method (available
1135            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1136    
1137            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1138    
1139            * tests/indexing.Rout.save:
1140            * tests/indexing.R: additions, mainly for 'lsparse'
1141    
1142            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1143            case.
1144    
1145            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1146    
1147    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1150                    as 'N' (1-letter - Ok?)
1151    
1152            * tests/group-methods.R: add test for logical + NAs
1153    
1154            * R/dMatrix.R ("Compare"): fix to work with NA's
1155    
1156            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1157    
1158            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1159                    which is implemented.
1160    
1161    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * src/chm_common.c: coerce logical <-> double instead of
1164            typecasting;  needed for "l" matrix handling in cholmod.
1165    
1166            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1167    
1168            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1169            (Tsp2grNEL): other fixes needed
1170    
1171    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1172    
1173            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1174                    Matrices, since "lMatrix", also "lsparseM" can have NA
1175            * R/ndenseMatrix.R, etc: new source files
1176            * man/nsparseMatrix-classes.Rd, etc: new help files
1177            * tests/: adaptions
1178            * src/chm_common.c (chm_dense_to_SEXP): and others:
1179                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1180            * src/Csparse.c, etc: ditto
1181    
1182    2006-09-11  Douglas Bates  <bates@R-project.org>
1183    
1184            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1185            alloc_d**Matrix functions to the lme4 package.
1186    
1187    2006-09-09  Douglas Bates  <bates@R-project.org>
1188    
1189            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1190            fixed
1191    
1192    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/lMatrix.R: new
1195    
1196            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1197    
1198            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1199            * man/tcrossprod.Rd: ditto
1200    
1201    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1202    
1203            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1204            for exported functions
1205            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1206            Remove partitioning algorithms for sparse matrix reordering.  The
1207            copyright on the Metis code was problematic and the methods were
1208            rarely used.
1209            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1210            operations are now done entirely in CHOLMOD code.
1211    
1212    2006-09-06  Douglas Bates  <bates@R-project.org>
1213    
1214            * src/Mutils.h: Remove functions that are no longer used.
1215    
1216    2006-09-04  Douglas Bates  <bates@R-project.org>
1217    
1218            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1219            * src/DEPS.mkf: update
1220    
1221    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1222    
1223            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1224            * DESCRIPTION (Version): 0.9975-0
1225            (Depends): R (>= 2.4.0)
1226    
1227    2006-09-01  Douglas Bates  <bates@R-project.org>
1228    
1229            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1230    
1231    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1232    
1233            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1234            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1235    
1236            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1237    
1238    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1239    
1240            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1241            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1242            * R/dsparseMatrix.R: ditto
1243            * R/Csparse.R: ditto
1244    
1245    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * R/dMatrix.R (Compare): improve availability of "<", etc
1248            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1249    
1250    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1251    
1252            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1253            of a 0-index which was used as 1-index (..hmm)
1254    
1255            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1256    
1257            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1258            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1259            (.is.diagonal): ditto
1260    
1261            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1262    
1263            * R/Matrix.R (Matrix): also work for NA data
1264    
1265    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1266    
1267            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1268            in all cases.
1269    
1270    2006-08-27  Douglas Bates  <bates@R-project.org>
1271    
1272            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1273            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1274    
1275    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1276    
1277            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1278            subclasses of "ddenseMatrix"
1279            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1280            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1281            instead of half dozen specialized ones.
1282    
1283    2006-08-25  Douglas Bates  <bates@R-project.org>
1284    
1285            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1286            <tillard@cirad.fr> - ordering standard errors to match effects.
1287    
1288    2006-08-24  Douglas Bates  <bates@R-project.org>
1289    
1290            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1291            on R_ldl.
1292            * R/lCholCMatrix.R,
1293            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1294            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1295            * many files in ./R and ./src: Use more general version of
1296            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1297            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1298            dtpMatrix, dspMatrix and dppMatrix conversions.
1299    
1300    
1301    2006-08-23  Douglas Bates  <bates@R-project.org>
1302    
1303            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1304            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1305            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1306            dgeMatrix_crossprod (may need to do this in other places).
1307            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1308            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1309    
1310    2006-08-22  Douglas Bates  <bates@R-project.org>
1311    
1312            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1313            types of classed Matrices, matrices or numeric or logical vectors.
1314            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1315            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1316            to Mutils.h (as an inline) and change name to Matrix_check_class;
1317            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1318            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1319            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1320            * src/Csparse.c: use diag_P and uplo_P macros.
1321    
1322    2006-08-21  Douglas Bates  <bates@R-project.org>
1323    
1324            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1325            valgrind.
1326            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1327            inverses.
1328            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1329            -Wall warnings.
1330            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1331            Use dup_mMatrix_as_dgeMatrix.
1332    
1333    2006-08-20  Douglas Bates  <bates@R-project.org>
1334    
1335            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1336            * tests/sparseQR.R: Added
1337            * man/sparseQR-class.Rd: Document methods for qr.* generics
1338            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1339    
1340    2006-08-19  Douglas Bates  <bates@R-project.org>
1341    
1342            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1343            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1344            and qr.fitted.
1345            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1346            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1347    
1348    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1349    
1350            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1351            the base version has no "..." argument.
1352    
1353            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1354    
1355            * R/Matrix.R: define and
1356            * NAMESPACE: export as.numeric() and as.logical() methods.
1357                    Let's hope these do not badly slow down something...
1358            Finally export the zapsmall() method.
1359    
1360    2006-08-17  Douglas Bates  <bates@R-project.org>
1361    
1362            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1363            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1364            * src/dtCMatrix.c :Remove code that is no longer used
1365            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1366    
1367    2006-08-14  Douglas Bates  <bates@R-project.org>
1368    
1369            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1370            Csparse_to_logical and Csparse_symmetric_to_general.
1371            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1372            coercion methods between CsparseMatrix and TsparseMatrix.
1373    
1374    2006-08-14  Douglas Bates  <bates@R-project.org>
1375    
1376            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1377            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1378            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1379            possible.
1380    
1381    2006-08-12  Douglas Bates  <bates@R-project.org>
1382    
1383            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1384              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1385              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1386              generalize conversions between TsparseMatrix, CsparseMatrix,
1387              denseMatrix and matrix.  Preserve triangularity property and
1388              propagate Dimnames in the easy cases.
1389    
1390    2006-08-10  Douglas Bates  <bates@R-project.org>
1391    
1392            * src/lmer.c: adjust checks in glmer_init for S4SXP
1393            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1394            before S4SXP but for the wrong reasons.
1395    
1396    2006-08-08  Douglas Bates  <bates@R-project.org>
1397    
1398            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1399            Later modified to return the upper triangle only.
1400            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1401    
1402    2006-08-07  Douglas Bates  <bates@R-project.org>
1403    
1404            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1405            R-level conversion to a sparse symmetric class.
1406            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1407            Remove conversion to sparse symmetric classes (now done in C code).
1408    
1409    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1410    
1411            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1412            * man/band.Rd:  adapt the \dontshow{} unit test.
1413    
1414    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1415    
1416            * DESCRIPTION (Version): 0.995-14  for CRAN
1417    
1418            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1419    
1420            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1421            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1422    
1423            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1424            * R/Tsparse.R (tril, triu, band): methods
1425            * R/dgRMatrix.R (tril, ...):    ditto
1426            * man/band.Rd:                  ditto
1427    
1428    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1431                    to be up-to-date automatically.
1432    
1433    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1434    
1435            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1436    
1437            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1438            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1439            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1440            such that the S4 objects are always created by the current version
1441            of R and 'Matrix' class definitions.
1442    
1443    2006-08-01  Douglas Bates  <bates@R-project.org>
1444    
1445            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1446            inst/external/test3comp.rda: Added warnings for convergence on
1447            boundary and test cases.
1448    
1449            * src/lmer.c (mer_postVar): Modified to return the variances that
1450            are marginal to the fixed effects, not conditional on them (which
1451            is what the bVar slot contents represent).
1452    
1453    2006-07-31  Douglas Bates  <bates@R-project.org>
1454    
1455            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1456            function which calls the C function mer_hat_trace2.
1457    
1458            * man/ranef.Rd: Include description of "postVar" argument and
1459            producing a caterpillar plot.
1460    
1461    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1462    
1463            * NAMESPACE:    change  "correlation" to "corMatrix"
1464            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1465            * R/dpoMatrix.R: ditto
1466            * R/lmer.R:      ditto
1467    
1468    2006-07-28  Douglas Bates  <bates@R-project.org>
1469    
1470            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1471            RZXinv slot's contents into a separate internal function that can
1472            be used in mer_hat_trace.
1473    
1474    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1475    
1476            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1477            via new smart
1478            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1479            utility functions.
1480    
1481    
1482    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1483    
1484            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1485            matrices when appropriate; band() even symmetric ones.
1486            (replCmat): extend to potentially all "CsparseMatrix"
1487            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1488            allow subassignment for special sparse matrices.
1489    
1490            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1491    
1492            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1493            argument; in glmer_*(): print only if(verbose).
1494    
1495            speed-optimize a few places by moving REAL(.) out of loops.
1496    
1497            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1498    
1499    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1500    
1501            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1502                    since that wrongly triggers also for M[ logi , ]
1503    
1504            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1505            a symmetric matrix that results in a non-symmetric one.
1506            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1507    
1508            * R/dMatrix.R: make round(M) work as round(M, 0)
1509    
1510            * R/dgTMatrix.R (image): coordinate system and axis now use
1511            1-based indices, not 0-based ones.
1512    
1513            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1514            * tests/indexing.R: test it.
1515    
1516            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1517            * man/isSymmetric-methods.Rd: and document it.
1518    
1519            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1520            * man/SparseM-conv.Rd: docu them
1521    
1522            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1523                    for 'SparseM' conversions
1524    
1525    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1526    
1527            * R/Matrix.R (head): added head() and tail() methods.
1528    
1529    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1530    
1531            * DESCRIPTION (Version): 0.995-12 released to CRAN
1532    
1533    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1534    
1535            * tests/simple.R: add check for correct dsT -> dgT coercion;
1536                    add check for correct printing of symmetric sparse matrices.
1537    
1538            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1539            for sparse symmetric matrices.
1540    
1541            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1542            diagonal twice.
1543    
1544    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1545    
1546            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1547            being applied to the x slot (detected by Brian Ripley).
1548    
1549    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1550    
1551            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1552    
1553            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1554    
1555    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1556    
1557            * src/lgCMatrix.c (lgCMatrix_diag): new function
1558            * R/lgCMatrix.R (diag): for new method
1559    
1560            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1561                 ==> construction of illegal "*gTMatrix" via new() should
1562                 now be much less easy:
1563            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1564    
1565            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1566                    directly.
1567            * man/Matrix.Rd: documents it.
1568    
1569    2006-07-06  Douglas Bates  <bates@R-project.org>
1570    
1571            * src/pedigree.c (pedigree_inbreeding): Correction in
1572            initialization.  This function is not currently being used and is
1573            not fully tested.
1574    
1575            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1576            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1577            objects.  Modified validity check on pedigree objects to account
1578            for nonparallel patterns of missingness of parents.
1579    
1580            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1581            class.
1582    
1583    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1584    
1585            * R/pMatrix.R: coercion pMatrix -> Tsparse
1586    
1587    2006-06-12  Douglas Bates  <bates@R-project.org>
1588    
1589            * DESCRIPTION (Version): 0.995-11 released to CRAN
1590    
1591            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1592            the output from mcmcsamp.
1593    
1594    2006-06-10  Douglas Bates  <bates@R-project.org>
1595    
1596            * R/lmer.R (simulestimate): added C code for calculating the trace
1597            of the hat matrix.
1598    
1599    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1600    
1601            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1602            classes.
1603            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1604    
1605    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1606    
1607            * R/dgTMatrix.R (colSums): etc. All four of
1608            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1609            all "Matrices".
1610    
1611    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1612    
1613            * R/lmer.R (panel.ci): Add a reference line at zero and a
1614            background grid to the qqmath plot of ranef.lmer.
1615    
1616    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1617    
1618            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1619            grouping factors to be specified in the formula as (1|foo/bar).
1620    
1621    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1622    
1623            * R/lmer.R (findbars and others): Change check of is.numeric to
1624            !is.language to resolve the bug reported by Jacob Wegelin.
1625    
1626            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1627            code to evaluate inbreeding coefficients without calculating T,
1628            based on code in Sargolzaei and Iwaisaki's paper.
1629    
1630    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1631    
1632            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1633            generic and mer methods for isNested and denomDF. This denomDF was
1634            an attempt to emulate that in lme but I don't think that makes
1635            sense.  Use the trace of the hat matrix instead.
1636    
1637    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1638    
1639            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1640            the C code depending on a slot structure that's no longer valid.
1641            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1642    
1643    
1644    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1645    
1646            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1647            of lowerTriMatrix generic and methods to tril (also upper to triu)
1648            and added a general band extractor.
1649    
1650    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1651    
1652            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1653            allowable range with NAs. Added a corresponding check in the
1654            validity check for the pedigree class.
1655    
1656            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1657            crossprod methods now inherits from symmetricMatrix.
1658    
1659    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1660    
1661            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1662            generics lowerTriMatrix and upperTriMatrix along with methods for
1663            the Csparse virtual class.  Also added a C function Csparse_band
1664            that implements these methods by calling cholmod_band.
1665    
1666    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1667    
1668            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1669            erased when it was NULL.  This led to invalid subselections!
1670    
1671    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1672    
1673            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1674            in method for "t" so as not to lose the unit diagonal property.
1675    
1676    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1677    
1678            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1679            and methods.  This is now an option to the ranef method for the
1680            mer class.
1681    
1682            * src/cs_utils.c: Ensure that the nz component is -1 for a
1683            compressed column-oriented matrix.  Minor formatting cleanup.
1684    
1685            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1686            objects.
1687    
1688    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1689    
1690            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1691            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1692    
1693    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1694    
1695            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1696            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1697    
1698            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1699            for the dtCMatrix class.
1700    
1701    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1702    
1703            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1704            and methods for it.
1705    
1706    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1707    
1708            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1709            arguments, such that M %*% 1:6 now works
1710            * Tests/matprod.R: test the above
1711    
1712    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1713    
1714            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1715            the ranef.lmer class.
1716    
1717            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1718            methods to extract the posterior variances from the bVar slot.
1719    
1720    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1721    
1722            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1723            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1724    
1725            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1726            * tests/simple: (extended)
1727    
1728            * R/sparseMatrix.R (isTriangular): now using much improved
1729            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1730    
1731    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1732    
1733            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1734            (problem report from Franklin Parlamis).  This should be done
1735            generally.
1736    
1737    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1738    
1739            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1740            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1741            update the plot methods.
1742    
1743    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1744    
1745            * R/lmer.R (resid and ranef methods):  Added methods for the
1746            "residuals" and "resid" generic but only for linear mixed model
1747            fits.  Changed the ranef method to return a list of data frames so
1748            that the plot methods now work.
1749    
1750    2006-03-16  Douglas Bates  <bates@bates2>
1751    
1752            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1753            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1754    
1755            * DESCRIPTION (Date): New release
1756    
1757    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1758    
1759            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1760    
1761            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1762            * man/KNex.Rd: and other help files
1763            * tests/*.R: several ones needed adaption
1764            * inst/doc/Comparisons.Rnw: ditto
1765    
1766    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1767    
1768            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1769    
1770            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1771    
1772    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1773    
1774            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1775    
1776            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1777    
1778    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1779    
1780            * R/dMatrix.R: enable things like  M [ M < 10 ]
1781            * R/dgeMatrix.R: implement it
1782    
1783    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1784    
1785            * R/AllClass.R: define "summary.mer" and "*.lmer"
1786            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1787            * R/lmer.R (show): now works with summary()
1788    
1789    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1790    
1791            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1792            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1793                    support the above
1794    
1795    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1796    
1797            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1798            Use glmFit$prior.weights for weights in a glmm.
1799            Allow an option usePQL = FALSE to skip the PQL steps for the
1800            Laplace method (and, in time, the AGQ method).
1801    
1802            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1803            into a separate function internal_mer_Xfactor to be able to call
1804            it from internal_bhat.
1805    
1806    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1807    
1808            * tests/Class+Meth.R (tstMatrixClass): function for much better
1809            testing; now again of all actual classes.
1810    
1811            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1812                    use macros and define make_d_matrix_* and make_i_matrix_*
1813                    where _i_ is for the ldense routines:
1814    
1815            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1816            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1817    
1818            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1819    
1820    
1821    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1822    
1823            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1824                    many different kinds of matrices.
1825            * R/*.R: quite a few new methods were needed for R CMD check with
1826                    new Matrix().  Very good for users playing around.
1827    
1828    
1829    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1830    
1831            * src/dgeMatrix.c (dMatrix_validate): new
1832            * src/Mutils.c (dense_nonpacked_validate): new
1833    
1834            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1835    
1836    
1837    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1838    
1839            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1840    
1841    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1842    
1843            * DESCRIPTION (Version): 0.99-6 released to CRAN
1844    
1845            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1846            segfault in cases with multiple non-nested grouping factors.
1847    
1848    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1849    
1850            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1851                    (Depends): also on 'utils'
1852    
1853            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1854            * R/diagMatrix.R (Diagonal): constructor and methods for
1855            diagonal matrices
1856    
1857            * R/ltTMatrix.R: new "minimal methods"
1858    
1859    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1860    
1861            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1862            all methods (and help files).
1863    
1864    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1865    
1866            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1867                    for case (dimn.  op  no_dimn.)
1868    
1869    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1870    
1871            * DESCRIPTION (Version): 0.99-2  released to CRAN
1872    
1873    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1874    
1875            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1876            by Julian Faraway.
1877    
1878    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1879    
1880            * R/Auxiliaries.R (try_as): new utility
1881            * R/sparseMatrix.R: use try_as() in coercion to original class
1882    
1883    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1884    
1885            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1886    
1887    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1888    
1889            * R/Auxiliaries.R (dimNamesCheck): added
1890    
1891            * R/Matrix.R (as.array), (as.vector): new
1892    
1893    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1894    
1895            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1896                    default.
1897            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1898                    "pMatrix" now contains "sparseMatrix"
1899    
1900    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1901    
1902            * tests/Class+Meth.R: new tests; t(t(m)) == m
1903    
1904            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1905    
1906            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1907            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1908    
1909            * R/dspMatrix.R: typo in "t" method
1910    
1911    2005-09-18  Douglas Bates  <bates@wisc.edu>
1912    
1913            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1914            * R/Tsparse.R: instead of R/gTMatrix.R
1915            * R/Csparse.R: new
1916            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1917            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1918            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1919                            via cholmod
1920    
1921    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1922    
1923            * R/Auxiliaries.R (non0ind): new function using new C code
1924            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1925    
1926    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1927    
1928            * src/chm_common.h: header file required by all C sources that
1929            call CHOLMOD functions.  It defines a cholmod_common structure
1930            called 'c' whose address is passed as the last argument to
1931            (virtually) every CHOLMOD function.
1932    
1933            * src/Pattern.c: Simple example of the use of CHOLMOD.
1934    
1935            * src/init.c: initialize and finalize the cholmod_common structure.
1936    
1937            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1938            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1939    
1940    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1941    
1942            * inst/test-tools.R: new file collecting the utility functions used
1943                    in ./tests/*.R
1944    
1945            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1946            * R/Matrix.R (cbind2): methods for NULL and missing
1947    
1948    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1949    
1950            * R/AllClass.R: new "index" class for "[" and "[<-":
1951                    First cut at "symmetricMatrix" and "triangularMatrix"
1952            * R/gTMatrix.R (.ind.prep): new function;
1953                    Logical and character indexing now work too.
1954            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1955            * tests/indexing.R: new, including *.Rout.save
1956            * tests/dgTMatrix.R: new
1957    
1958    2005-08-29  Douglas Bates  <bates@wisc.edu>
1959    
1960            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1961            indicator pos not being updated.  Also enforced upper triangular
1962            for symmetric case.  Need to coerce edges component of elements of
1963            edge list - grr! (Why don't they define their classes cleanly?)
1964    
1965    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1966    
1967            * R/Matrix.R:  added first "[<-" methods; not yet functional
1968            * R/denseMatrix.R: ditto
1969            * man/Subassign-methods.Rd: new help file for these
1970    
1971    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1972    
1973            * DESCRIPTION (Version): 0.98-6
1974    
1975            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1976            matrices.
1977    
1978    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1979    
1980            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1981                    as( <logical>, "matrix")
1982    
1983            * R/pMatrix.R: coercion to "lgTMatrix"
1984    
1985            * R/gTMatrix.R: new virtual class to define "[" methods for.
1986            * man/gTMatrix-class.Rd:
1987            * General slight re-organization of where "[" methods are defined.
1988              more to come.
1989    
1990    2005-08-18  Douglas Bates  <bates@wisc.edu>
1991    
1992            * DESCRIPTION (Version): 0.98-5  released to CRAN
1993    
1994            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1995            * .....
1996    
1997    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1998    
1999            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
2000            or glmer objects.
2001    
2002    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2003    
2004            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
2005    
2006    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
2007    
2008            * R/HBMM.R: finish re-writing R-only code.
2009    
2010    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
2011    
2012            * man/externalFormats.Rd: move documentation for writeHB and
2013            writeMM here.
2014    
2015            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
2016            (suggested by Paul Roecker).
2017    
2018            * tests/validObj.R (assertError): Comment out test that is failing
2019            after recent changes in r-devel.
2020    
2021    
2022    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2023    
2024            * R/AllClass.R: intermediate virtual class "denseMatrix"
2025            * man/denseMatrix-class.Rd
2026            * NAMESPACE: export it, and also export
2027            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
2028    
2029    2005-08-10  Douglas Bates  <bates@wisc.edu>
2030    
2031            * DESCRIPTION (Version): 0.98-3 to CRAN
2032    
2033            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
2034            matrix_solve code (which was really, really wrong).
2035    
2036    2005-08-07  Douglas Bates  <bates@wisc.edu>
2037    
2038            * DESCRIPTION (Version): 0.98-2
2039    
2040            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
2041    
2042            * R/lmer.R (abbrvNms): new
2043            * R/lmer.R (mcmcsamp): allow transformed parameters
2044            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
2045            for the Harwell-Boeing and the MatrixMarket formats.
2046    
2047    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
2048    
2049            * man/dtrMatrix-class.Rd: add examples
2050            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
2051    
2052            * TODO: note the dtpMatrix (docu) bug
2053    
2054            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
2055            in order to ensure that new as.matrix() is used by old functions,
2056            e.g., svd(), qr(), eigen(), dist(),..;
2057                  apply(), also matplot() or pairs().
2058    
2059    
2060    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2061    
2062            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
2063              add comments about 'control' / lmerControl() arguments
2064    
2065    2005-07-27  Douglas Bates  <bates@wisc.edu>
2066    
2067            * man/sleepstudy.Rd: Added the sleep data set.
2068            * DESCRIPTION (Version): 0.98-1  released to CRAN
2069    
2070    2005-07-12  Douglas Bates  <bates@wisc.edu>
2071            * man/sleepstudy.Rd: Added the sleep data set.
2072    
2073            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
2074            .Call calls that were producing spurious output.
2075    
2076    2005-07-05  Douglas Bates  <bates@wisc.edu>
2077    
2078            * R/lmer.R (lmer): stored updated variance component estimates in
2079            mer object for the generalized model.  (Bug reported by Renaud
2080            Lancelot).
2081    
2082    2005-07-03  Douglas Bates  <bates@wisc.edu>
2083    
2084            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2085            unidimensional case.
2086    
2087    2005-06-08  Douglas Bates  <bates@wisc.edu>
2088    
2089            * DESCRIPTION (Version): 0.96-1
2090    
2091            * moved  lmer-class' R and C code moved from lme4 to here
2092    
2093    2005-06-04  Douglas Bates  <bates@wisc.edu>
2094    
2095            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2096            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2097    
2098    2005-06-02  Douglas Bates  <bates@wisc.edu>
2099    
2100            * src/Makefile.win: Forgot to update this when Makefile changed.
2101    
2102    2005-05-11  Douglas Bates  <bates@wisc.edu>
2103    
2104            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2105            bug reported by Kurt Hornik and Michael Hahsler.
2106    
2107    2005-05-10  Douglas Bates  <bates@wisc.edu>
2108    
2109            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2110            logical sparse matrices.  These will also be used in the symbolic
2111            analysis for lmer objects.
2112    
2113            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2114            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
2115    
2116    2005-05-06  Douglas Bates  <bates@wisc.edu>
2117    
2118            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2119            colMeans, colSums, rowMeans and rowSums.
2120    
2121    2005-04-18  Douglas Bates  <bates@wisc.edu>
2122    
2123            * src/lgCMatrix.[ch]: code for _validate method and stub for
2124            multiplication operation.
2125    
2126            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2127            to dgetrs.
2128    
2129            * src/init.c: Fix cut-and-paste error in definition of
2130            dgeMatrix_matrix_solve
2131    
2132            * src/{many files}: Tighten code by using ALLOC_SLOT.
2133    
2134    2005-04-15  Douglas Bates  <bates@wisc.edu>
2135    
2136            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2137    
2138            * DESCRIPTION: Eliminate import of stats.
2139    
2140    
2141    2005-04-06  Douglas Bates  <bates@wisc.edu>
2142    
2143            * R/AllClass.R : add logical sparse matrix classes
2144    
2145    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2146    
2147            * R/dgTMatrix.R: add "[" method for triplet matrices
2148            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2149    
2150    2005-03-31  Douglas Bates  <bates@wisc.edu>
2151    
2152            * DESCRIPTION (Version): release 0.95-5 to CRAN
2153    
2154            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2155            * R/sparseMatrix.R: %*%, crossprod()
2156            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2157            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2158            * src/lmer.c (lmer_fitted): fix thinko
2159    
2160    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2161    
2162            * R/AllClass.R: add two virtual sparse classes ``on top''
2163    
2164    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2165    
2166            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2167                    correspondingly fix examples and tests/ since new()
2168                    doesn't work for virtual classes.
2169    
2170    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2171    
2172            * R/Matrix.R (as.matrix): method and one for unname()
2173            * tests/dpoMatrix.R: tests should now be less platform dependent;
2174              also run for R 2.1.0; using as.matrix()
2175    
2176    2005-03-15  Douglas Bates  <bates@wisc.edu>
2177    
2178            * R/pMatrix.R: "pMatrix" class added
2179            * ....
2180    
2181    2005-03-14  Douglas Bates  <bates@wisc.edu>
2182    
2183            * R/dtpMatrix.R: Add unpack method and an example.
2184    
2185            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2186            of general symmetric matrices and associated S4 methods.
2187    
2188    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
2189            +
2190    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2191    
2192            * R/dgeMatrix.R (setAs): and many other files: more coercion,
2193              crossprod() and "%*%" methods added; tests, too.
2194            * tests/matprod.R: new, for testing these
2195    
2196    2005-03-03  Douglas Bates  <bates@wisc.edu>
2197    
2198            * src/lmer.c (lmer_fitted): Added.
2199    
2200    2005-03-02  Douglas Bates  <bates@wisc.edu>
2201    
2202            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2203    
2204    2005-02-28  Douglas Bates  <bates@wisc.edu>
2205    
2206            * src/*.c,po/,inst/po: Internationalization and localization of
2207            the package.
2208    
2209            * src/ldl.[ch]: Removed these as their contents are referenced in the
2210            R_ldl.c file.
2211    
2212            * src/flame.[ch]: Removed these source files.
2213    
2214            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2215    
2216            * src/LU.[ch],src/init.c: absorb in factorizations
2217    
2218            * src/Mutils.h: prepare for internationalization
2219    
2220            * src/cblas.h: move the enum definitions to Mutils.h and remove
2221            this file
2222    
2223    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2224    
2225            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2226    
2227            * R/dtrMatrix.R: fix t() method
2228    
2229            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2230            * NAMESPACE: export them (and import generics from "methods")
2231            * tests/group-methods.R : and test them.
2232    
2233            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2234            border case
2235    
2236    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
2237    
2238            * DESCRIPTION (Version): 0.95-2  released to CRAN
2239    
2240            * src/dgBCMatrix.c:
2241            * src/lmer.c: many changes
2242            * ...
2243    
2244    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
2245    
2246            * R/Matrix.R: add more sophisticated show() method.
2247    
2248    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
2249    
2250            * */* : almost complete reorganization of classes.
2251    
2252    2005-01-26  Douglas Bates  <bates@wisc.edu>
2253    
2254            * R/AllGeneric.R: Added matrix exponential generic expm and a method
2255            for the geMatrix class.
2256    
2257    2005-01-24  Douglas Bates  <bates@wisc.edu>
2258    
2259            * src/Makefile (clean): Remove *.a and *.so
2260    
2261            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2262    
2263    2005-01-23  Douglas Bates  <bates@wisc.edu>
2264    
2265            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
2266            had an effect in cases with more than 2 grouping factors.
2267    
2268    2005-01-03  Douglas Bates  <bates@wisc.edu>
2269    
2270            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2271    
2272    2004-12-23  Douglas Bates  <bates@wisc.edu>
2273    
2274            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2275            and R_useDynamicSymbols (suggested by B.D.Ripley).
2276    
2277    2004-12-14  Douglas Bates  <bates@wisc.edu>
2278    
2279            * R/sscMatrix.R: Add determinant methods
2280    
2281            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2282            for tripletMatrix to matrix.
2283    
2284    2004-12-13  Douglas Bates  <bates@wisc.edu>
2285    
2286            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2287            no longer used.
2288    
2289            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2290            with dynamic allocation of scratch arrays.
2291    
2292            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2293            for multivariate random effects with multiple grouping factors.
2294            Fixes part but not all of #15.
2295    
2296    2004-12-03  Douglas Bates  <bates@wisc.edu>
2297    
2298            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2299            scalar grouping factors corrected.
2300    
2301    2004-11-29  Douglas Bates  <bates@wisc.edu>
2302    
2303            * src/bCrosstab.c: remove diag_update which is no longer used
2304    
2305    2004-11-16  Douglas Bates  <bates@wisc.edu>
2306    
2307          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
2308          .h file can be included.          .h file can be included.
2309    
2310  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
2311    
2312          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2313          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
2314    
2315          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
2316    
2317  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
2318    
2319          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
2320    
2321  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
2322    
2323          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
2324    
2325  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
2326    
2327          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2328    
2329  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
2330    
2331          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2332    
2333  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
2334    
2335          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
2336          routines.          routines.
2337    
2338  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
2339    
2340          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2341    
2342  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
2343    
2344          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2345    

Legend:
Removed from v.350  
changed lines
  Added in v.2096

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