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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1707, Thu Dec 21 08:03:05 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/bind.R: a few more cases
4            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
5    
6            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
7            * R/ddenseMatrix.R (cbind2/rbind2)
8            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
9            * tests/indexing.R
10            * tests/indexing.Rout.save: updated
11    
12    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
15            * tests/indexing.R
16    
17    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
20            align with proper position of "0", i.e., right for integers.
21            argument 'align' by default is "fancy".
22    
23    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
26            * R/Csparse.R: and fix "Compare" for more cases.
27            * tests/Class+Meth.R: test some of these (m == m, m != m)
28    
29    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/lsparseMatrix.R: all() and any() methods
32            * R/ldenseMatrix.R:      ditto
33            * NAMESPACE, R/Matrix.R: ditto
34    
35            * man/all-methods.Rd: document them minimally
36    
37            * tests/simple.R: add a few examples for these
38    
39    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Tsparse.R ([): fix long standing typo in symmetric case
42            * man/dsCMatrix-class.Rd: add example exhibiting the above case
43    
44    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
45    
46            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
47            to LL before converting to a sparse matrix. (The LDL form can be
48            converted to a sparse matrix but it is implicitly a unit
49            triangular matrix and a diagonal matrix overwritten on the diagonal.)
50    
51    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
54    
55    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * DESCRIPTION (Version): updated -> release 0.9975-7
58            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
59    
60    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
63    
64    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
67            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
68            is exactly singular.
69    
70    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Date): updated -> release 0.9975-6
73    
74    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
77            now returns symmetric.
78    
79            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
80    
81            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
82            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
83    
84            * R/Auxiliaries.R (.type.kind): added
85    
86    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
89            running src/CSparse_install.sh
90    
91            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
92    
93    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
96            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
97    
98            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
99    
100            * tests/Class+Meth.R (tstMatrixClass): now assure
101            the (important in method programming) property :
102    
103                    ###>>  Every "Matrix" is either
104                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
105    
106                    (where "*" stands for "Matrix")
107    
108            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
109    
110            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
111            * tests/validObj.R: checks for "comparison"
112    
113            * R/sparseMatrix.R ([): improved indexing for sparse;
114                    trying to keep <symmetric>[ n, n] symmmetric
115    
116            * tests/indexing.R: indexing for logical sparse now ok
117    
118    
119    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * src/Tsparse.c: use xTsparse_validate() , and hence remove
122    
123            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
124    
125    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
128    
129            * tests/simple.R: validObject() checking the above.
130    
131            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
132            replacing both dgCMatrix_validate and lgCM*.
133    
134            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
135            fix dimnames setting in other places.
136            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
137    
138    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
141    
142            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
143            symmetry test, via
144            * R/Auxiliaries.R (.as.dgC.0.factors):
145    
146    2006-11-01  Douglas Bates  <bates@r-project.org>
147    
148            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
149            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
150            <CsparseMatrix>) added
151    
152    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * tests/matprod.R: add a variation of Harri's example
155    
156            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
157            recursive infinitely.
158    
159            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
160    
161            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
162    
163    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
166            matrix if possible; test m+m == 2*m; now test dgRMatrix.
167            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
168            satisfy the above test.
169    
170    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
173    
174            * R/dgCMatrix.R: solve(a, b="missing") based on
175            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
176            RHS = NULL.
177    
178            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
179            add more (needed) [t]crossprod() methods.
180    
181            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
182    
183            * R/Auxiliaries.R (as_CspClass): cleanup
184            (drop0): internal utility for "Csparse_drop(*, 0)"
185            (.bail.out.2): encourage active feedback
186    
187    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/dMatrix.R(Compare): new(), then slots [no validity check]
190    
191            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
192            non-valid or 'sorted' case).
193    
194            * R/dsparseMatrix.R: add "chol" method.
195            * R/ddenseMatrix.R: ditto
196    
197            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
198            * NAMESPACE (Ops)
199            * R/diagMatrix.R (diag2T): simple utility used "higher level"
200            coercion; deprecating direct lower level coercions.
201    
202            * R/*.R (seq): use seq_len() and seq_along() where possible.
203    
204    
205    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * DESCRIPTION (Version): 0.9975-5 ready for release
208    
209    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
210    
211            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
212    
213    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/AllClass.R (corMatrix): add 'validity' check;
216                    comment out unused "LDL" class definition
217            * NAMESPACE: mention, but do not export "LDL" class
218            * R/corMatrix.R: new (simple), needed for R-devel with
219            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
220              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
221    
222    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
225            use Rprintf and R's error handling.
226    
227    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
230            * tests/matprod.R: add tests for the bug fixed.
231    
232    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
235            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
236    
237    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
240    
241    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION (Version): 0.9975-3
244    
245            * R/diagMatrix.R (bdiag): new function constructing block diagonal
246            (sparse) matrices.
247            * man/bdiag.Rd: docu + examples
248    
249            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
250    
251            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
252            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
253    
254            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
255            that result is sparse or diagonal (and not dense).
256    
257            * man/Subassign-methods.Rd: fix examples
258    
259            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
260            should always return a sparse (and not sometimes a diagonal) matrix.
261    
262    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
265    
266    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
267    
268            * DESCRIPTION (Version): 0.9975-2
269    
270            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
271    
272    2006-10-02  Douglas Bates  <bates@R-project.org>
273    
274            * tests/dg_Matrix.R: Simplify test taking into account new code.
275    
276    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
279    
280            * R/lsTMatrix.R: new files w/ missing methods
281            * R/nsTMatrix.R:  "  'for completeness'
282    
283            * tests/Class+Meth.R: a bit less 'not.ok.classes'
284    
285            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
286    
287    
288    2006-09-28  Douglas Bates  <bates@R-project.org>
289    
290            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
291            included.
292    
293            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
294            Export C-callable functions used in Zt_create in lme4.
295    
296    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * DESCRIPTION (Version): 0.9975-1
299    
300            * tests/simple.R: less checks fail; using NA, found that our
301                    kronecker() is not base-compatible with NA's.
302    
303            * R/dMatrix.R: "Compare" method now implemented for all cases
304    
305            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
306    
307            * man/dtpMatrix-class.Rd: mention length of 'x' slot
308    
309            * src/dtpMatrix.c (dtpMatrix_validate): fix check
310            * src/dspMatrix.c (dspMatrix_validate): ditto
311    
312            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
313              including coercion to [nl]tTMatrix.
314    
315            * R/diagMatrix.R (show): print a header line as for other classes.
316    
317    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * src/Makefile.win (SUBDIRS): fix typo
320    
321    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
324    
325    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
326    
327            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
328            symmetric and y missing in R code using %*% (cholmod_aat doesn't
329            accept a symmetric matrix).
330            * tests/group-methods.R: Uncomment test of crossprod applied to
331            lsCMatrix objects.
332    
333    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/AllClass.R (symmetricMatrix): add validity method (available
336            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
337    
338            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
339    
340            * tests/indexing.Rout.save:
341            * tests/indexing.R: additions, mainly for 'lsparse'
342    
343            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
344            case.
345    
346            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
347    
348    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
351                    as 'N' (1-letter - Ok?)
352    
353            * tests/group-methods.R: add test for logical + NAs
354    
355            * R/dMatrix.R ("Compare"): fix to work with NA's
356    
357            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
358    
359            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
360                    which is implemented.
361    
362    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * src/chm_common.c: coerce logical <-> double instead of
365            typecasting;  needed for "l" matrix handling in cholmod.
366    
367            * tests/other-pkgs.R (graph): small extension in "graph" checks.
368    
369            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
370            (Tsp2grNEL): other fixes needed
371    
372    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
375                    Matrices, since "lMatrix", also "lsparseM" can have NA
376            * R/ndenseMatrix.R, etc: new source files
377            * man/nsparseMatrix-classes.Rd, etc: new help files
378            * tests/: adaptions
379            * src/chm_common.c (chm_dense_to_SEXP): and others:
380                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
381            * src/Csparse.c, etc: ditto
382    
383    2006-09-11  Douglas Bates  <bates@R-project.org>
384    
385            * src/Mutils.[ch],init.c inst/include/*.h: Move the
386            alloc_d**Matrix functions to the lme4 package.
387    
388    2006-09-09  Douglas Bates  <bates@R-project.org>
389    
390            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
391            fixed
392    
393    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/lMatrix.R: new
396    
397            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
398    
399            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
400            * man/tcrossprod.Rd: ditto
401    
402    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
403    
404            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
405            for exported functions
406            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
407            Remove partitioning algorithms for sparse matrix reordering.  The
408            copyright on the Metis code was problematic and the methods were
409            rarely used.
410            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
411            operations are now done entirely in CHOLMOD code.
412    
413    2006-09-06  Douglas Bates  <bates@R-project.org>
414    
415            * src/Mutils.h: Remove functions that are no longer used.
416    
417    2006-09-04  Douglas Bates  <bates@R-project.org>
418    
419            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
420            * src/DEPS.mkf: update
421    
422    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * created branches/Matrix-for-R-2.3.x;  on trunk: do
425            * DESCRIPTION (Version): 0.9975-0
426            (Depends): R (>= 2.4.0)
427    
428    2006-09-01  Douglas Bates  <bates@R-project.org>
429    
430            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
431    
432    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
435            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
436    
437            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
438    
439    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
442            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
443            * R/dsparseMatrix.R: ditto
444            * R/Csparse.R: ditto
445    
446    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/dMatrix.R (Compare): improve availability of "<", etc
449            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
450    
451    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
454            of a 0-index which was used as 1-index (..hmm)
455    
456            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
457    
458            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
459            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
460            (.is.diagonal): ditto
461    
462            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
463    
464            * R/Matrix.R (Matrix): also work for NA data
465    
466    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
469            in all cases.
470    
471    2006-08-27  Douglas Bates  <bates@R-project.org>
472    
473            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
474            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
475    
476    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
479            subclasses of "ddenseMatrix"
480            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
481            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
482            instead of half dozen specialized ones.
483    
484    2006-08-25  Douglas Bates  <bates@R-project.org>
485    
486            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
487            <tillard@cirad.fr> - ordering standard errors to match effects.
488    
489    2006-08-24  Douglas Bates  <bates@R-project.org>
490    
491            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
492            on R_ldl.
493            * R/lCholCMatrix.R,
494            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
495            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
496            * many files in ./R and ./src: Use more general version of
497            dup_mMatrix_as_dgeMatrix to simplify method definitions.
498            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
499            dtpMatrix, dspMatrix and dppMatrix conversions.
500    
501    
502    2006-08-23  Douglas Bates  <bates@R-project.org>
503    
504            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
505            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
506            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
507            dgeMatrix_crossprod (may need to do this in other places).
508            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
509            generic and method for dsCMatrix.  Use CHOLMOD for chol().
510    
511    2006-08-22  Douglas Bates  <bates@R-project.org>
512    
513            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
514            types of classed Matrices, matrices or numeric or logical vectors.
515            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
516            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
517            to Mutils.h (as an inline) and change name to Matrix_check_class;
518            fixes in as_cholmod_factor and chm_factor_to_SEXP.
519            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
520            dsCMatrix_matrix_solve.  Comment out vestigial functions.
521            * src/Csparse.c: use diag_P and uplo_P macros.
522    
523    2006-08-21  Douglas Bates  <bates@R-project.org>
524    
525            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
526            valgrind.
527            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
528            inverses.
529            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
530            -Wall warnings.
531            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
532            Use dup_mMatrix_as_dgeMatrix.
533    
534    2006-08-20  Douglas Bates  <bates@R-project.org>
535    
536            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
537            * tests/sparseQR.R: Added
538            * man/sparseQR-class.Rd: Document methods for qr.* generics
539            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
540    
541    2006-08-19  Douglas Bates  <bates@R-project.org>
542    
543            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
544            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
545            and qr.fitted.
546            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
547            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
548    
549    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
552            the base version has no "..." argument.
553    
554            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
555    
556            * R/Matrix.R: define and
557            * NAMESPACE: export as.numeric() and as.logical() methods.
558                    Let's hope these do not badly slow down something...
559            Finally export the zapsmall() method.
560    
561    2006-08-17  Douglas Bates  <bates@R-project.org>
562    
563            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
564            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
565            * src/dtCMatrix.c :Remove code that is no longer used
566            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
567    
568    2006-08-14  Douglas Bates  <bates@R-project.org>
569    
570            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
571            Csparse_to_logical and Csparse_symmetric_to_general.
572            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
573            coercion methods between CsparseMatrix and TsparseMatrix.
574    
575    2006-08-14  Douglas Bates  <bates@R-project.org>
576    
577            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
578            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
579            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
580            possible.
581    
582    2006-08-12  Douglas Bates  <bates@R-project.org>
583    
584            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
585              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
586              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
587              generalize conversions between TsparseMatrix, CsparseMatrix,
588              denseMatrix and matrix.  Preserve triangularity property and
589              propagate Dimnames in the easy cases.
590    
591    2006-08-10  Douglas Bates  <bates@R-project.org>
592    
593            * src/lmer.c: adjust checks in glmer_init for S4SXP
594            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
595            before S4SXP but for the wrong reasons.
596    
597    2006-08-08  Douglas Bates  <bates@R-project.org>
598    
599            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
600            Later modified to return the upper triangle only.
601            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
602    
603    2006-08-07  Douglas Bates  <bates@R-project.org>
604    
605            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
606            R-level conversion to a sparse symmetric class.
607            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
608            Remove conversion to sparse symmetric classes (now done in C code).
609    
610    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
613            * man/band.Rd:  adapt the \dontshow{} unit test.
614    
615    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * DESCRIPTION (Version): 0.995-14  for CRAN
618    
619            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
620    
621            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
622            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
623    
624            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
625            * R/Tsparse.R (tril, triu, band): methods
626            * R/dgRMatrix.R (tril, ...):    ditto
627            * man/band.Rd:                  ditto
628    
629    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Matrix.R (head, tail): directly use utils:::head.matrix
632                    to be up-to-date automatically.
633    
634    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
637    
638            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
639            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
640            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
641            such that the S4 objects are always created by the current version
642            of R and 'Matrix' class definitions.
643    
644    2006-08-01  Douglas Bates  <bates@R-project.org>
645    
646            * R/lmer.R (LMEoptimize method), tests/lmer.R,
647            inst/external/test3comp.rda: Added warnings for convergence on
648            boundary and test cases.
649    
650            * src/lmer.c (mer_postVar): Modified to return the variances that
651            are marginal to the fixed effects, not conditional on them (which
652            is what the bVar slot contents represent).
653    
654    2006-07-31  Douglas Bates  <bates@R-project.org>
655    
656            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
657            function which calls the C function mer_hat_trace2.
658    
659            * man/ranef.Rd: Include description of "postVar" argument and
660            producing a caterpillar plot.
661    
662    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * NAMESPACE:    change  "correlation" to "corMatrix"
665            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
666            * R/dpoMatrix.R: ditto
667            * R/lmer.R:      ditto
668    
669    2006-07-28  Douglas Bates  <bates@R-project.org>
670    
671            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
672            RZXinv slot's contents into a separate internal function that can
673            be used in mer_hat_trace.
674    
675    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
678            via new smart
679            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
680            utility functions.
681    
682    
683    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/Csparse.R (tril, triu, band): do return *triangular* classed
686            matrices when appropriate; band() even symmetric ones.
687            (replCmat): extend to potentially all "CsparseMatrix"
688            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
689            allow subassignment for special sparse matrices.
690    
691            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
692    
693            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
694            argument; in glmer_*(): print only if(verbose).
695    
696            speed-optimize a few places by moving REAL(.) out of loops.
697    
698            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
699    
700    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
703                    since that wrongly triggers also for M[ logi , ]
704    
705            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
706            a symmetric matrix that results in a non-symmetric one.
707            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
708    
709            * R/dMatrix.R: make round(M) work as round(M, 0)
710    
711            * R/dgTMatrix.R (image): coordinate system and axis now use
712            1-based indices, not 0-based ones.
713    
714            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
715            * tests/indexing.R: test it.
716    
717            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
718            * man/isSymmetric-methods.Rd: and document it.
719    
720            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
721            * man/SparseM-conv.Rd: docu them
722    
723            * tests/other-pkgs.R: renamed from tests/graph.R and add example
724                    for 'SparseM' conversions
725    
726    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
727    
728            * R/Matrix.R (head): added head() and tail() methods.
729    
730    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * DESCRIPTION (Version): 0.995-12 released to CRAN
733    
734    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * tests/simple.R: add check for correct dsT -> dgT coercion;
737                    add check for correct printing of symmetric sparse matrices.
738    
739            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
740            for sparse symmetric matrices.
741    
742            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
743            diagonal twice.
744    
745    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
746    
747            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
748            being applied to the x slot (detected by Brian Ripley).
749    
750    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
753    
754            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
755    
756    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * src/lgCMatrix.c (lgCMatrix_diag): new function
759            * R/lgCMatrix.R (diag): for new method
760    
761            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
762                 ==> construction of illegal "*gTMatrix" via new() should
763                 now be much less easy:
764            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
765    
766            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
767                    directly.
768            * man/Matrix.Rd: documents it.
769    
770    2006-07-06  Douglas Bates  <bates@R-project.org>
771    
772            * src/pedigree.c (pedigree_inbreeding): Correction in
773            initialization.  This function is not currently being used and is
774            not fully tested.
775    
776            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
777            Introduced the glmer class.  Added code for mcmcmsamp on glmer
778            objects.  Modified validity check on pedigree objects to account
779            for nonparallel patterns of missingness of parents.
780    
781            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
782            class.
783    
784    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/pMatrix.R: coercion pMatrix -> Tsparse
787    
788    2006-06-12  Douglas Bates  <bates@R-project.org>
789    
790            * DESCRIPTION (Version): 0.995-11 released to CRAN
791    
792            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
793            the output from mcmcsamp.
794    
795    2006-06-10  Douglas Bates  <bates@R-project.org>
796    
797            * R/lmer.R (simulestimate): added C code for calculating the trace
798            of the hat matrix.
799    
800    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
803            classes.
804            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
805    
806    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * R/dgTMatrix.R (colSums): etc. All four of
809            colSums(), rowSums(), colMeans(), rowMeans() now should work for
810            all "Matrices".
811    
812    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
813    
814            * R/lmer.R (panel.ci): Add a reference line at zero and a
815            background grid to the qqmath plot of ranef.lmer.
816    
817    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
818    
819            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
820            grouping factors to be specified in the formula as (1|foo/bar).
821    
822    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
823    
824            * R/lmer.R (findbars and others): Change check of is.numeric to
825            !is.language to resolve the bug reported by Jacob Wegelin.
826    
827            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
828            code to evaluate inbreeding coefficients without calculating T,
829            based on code in Sargolzaei and Iwaisaki's paper.
830    
831    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
832    
833            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
834            generic and mer methods for isNested and denomDF. This denomDF was
835            an attempt to emulate that in lme but I don't think that makes
836            sense.  Use the trace of the hat matrix instead.
837    
838    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
841            the C code depending on a slot structure that's no longer valid.
842            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
843    
844    
845    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
846    
847            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
848            of lowerTriMatrix generic and methods to tril (also upper to triu)
849            and added a general band extractor.
850    
851    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
852    
853            * R/pedigree.R (pedigree): Replace sire and dam values outside the
854            allowable range with NAs. Added a corresponding check in the
855            validity check for the pedigree class.
856    
857            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
858            crossprod methods now inherits from symmetricMatrix.
859    
860    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
861    
862            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
863            generics lowerTriMatrix and upperTriMatrix along with methods for
864            the Csparse virtual class.  Also added a C function Csparse_band
865            that implements these methods by calling cholmod_band.
866    
867    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
870            erased when it was NULL.  This led to invalid subselections!
871    
872    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
873    
874            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
875            in method for "t" so as not to lose the unit diagonal property.
876    
877    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
878    
879            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
880            and methods.  This is now an option to the ranef method for the
881            mer class.
882    
883            * src/cs_utils.c: Ensure that the nz component is -1 for a
884            compressed column-oriented matrix.  Minor formatting cleanup.
885    
886            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
887            objects.
888    
889    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
892            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
893    
894    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
895    
896            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
897            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
898    
899            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
900            for the dtCMatrix class.
901    
902    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
903    
904            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
905            and methods for it.
906    
907    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
908    
909            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
910            arguments, such that M %*% 1:6 now works
911            * Tests/matprod.R: test the above
912    
913    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
914    
915            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
916            the ranef.lmer class.
917    
918            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
919            methods to extract the posterior variances from the bVar slot.
920    
921    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
922    
923            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
924            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
925    
926            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
927            * tests/simple: (extended)
928    
929            * R/sparseMatrix.R (isTriangular): now using much improved
930            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
931    
932    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
933    
934            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
935            (problem report from Franklin Parlamis).  This should be done
936            generally.
937    
938    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
939    
940            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
941            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
942            update the plot methods.
943    
944    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
945    
946            * R/lmer.R (resid and ranef methods):  Added methods for the
947            "residuals" and "resid" generic but only for linear mixed model
948            fits.  Changed the ranef method to return a list of data frames so
949            that the plot methods now work.
950    
951    2006-03-16  Douglas Bates  <bates@bates2>
952    
953            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
954            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
955    
956            * DESCRIPTION (Date): New release
957    
958    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
961    
962            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
963            * man/KNex.Rd: and other help files
964            * tests/*.R: several ones needed adaption
965            * inst/doc/Comparisons.Rnw: ditto
966    
967    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
968    
969            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
970    
971            * tests/indexing.R: tests for new [<- methods for sparse matrices.
972    
973    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
976    
977            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
978    
979    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * R/dMatrix.R: enable things like  M [ M < 10 ]
982            * R/dgeMatrix.R: implement it
983    
984    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
985    
986            * R/AllClass.R: define "summary.mer" and "*.lmer"
987            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
988            * R/lmer.R (show): now works with summary()
989    
990    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
993            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
994                    support the above
995    
996    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
997    
998            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
999            Use glmFit$prior.weights for weights in a glmm.
1000            Allow an option usePQL = FALSE to skip the PQL steps for the
1001            Laplace method (and, in time, the AGQ method).
1002    
1003            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1004            into a separate function internal_mer_Xfactor to be able to call
1005            it from internal_bhat.
1006    
1007    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * tests/Class+Meth.R (tstMatrixClass): function for much better
1010            testing; now again of all actual classes.
1011    
1012            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1013                    use macros and define make_d_matrix_* and make_i_matrix_*
1014                    where _i_ is for the ldense routines:
1015    
1016            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1017            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1018    
1019            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1020    
1021    
1022    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1025                    many different kinds of matrices.
1026            * R/*.R: quite a few new methods were needed for R CMD check with
1027                    new Matrix().  Very good for users playing around.
1028    
1029    
1030    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * src/dgeMatrix.c (dMatrix_validate): new
1033            * src/Mutils.c (dense_nonpacked_validate): new
1034    
1035            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1036    
1037    
1038    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1039    
1040            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1041    
1042    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1043    
1044            * DESCRIPTION (Version): 0.99-6 released to CRAN
1045    
1046            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1047            segfault in cases with multiple non-nested grouping factors.
1048    
1049    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1052                    (Depends): also on 'utils'
1053    
1054            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1055            * R/diagMatrix.R (Diagonal): constructor and methods for
1056            diagonal matrices
1057    
1058            * R/ltTMatrix.R: new "minimal methods"
1059    
1060    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1063            all methods (and help files).
1064    
1065    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1068                    for case (dimn.  op  no_dimn.)
1069    
1070    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1071    
1072            * DESCRIPTION (Version): 0.99-2  released to CRAN
1073    
1074    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1075    
1076            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1077            by Julian Faraway.
1078    
1079    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/Auxiliaries.R (try_as): new utility
1082            * R/sparseMatrix.R: use try_as() in coercion to original class
1083    
1084    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1087    
1088    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * R/Auxiliaries.R (dimNamesCheck): added
1091    
1092            * R/Matrix.R (as.array), (as.vector): new
1093    
1094    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1097                    default.
1098            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1099                    "pMatrix" now contains "sparseMatrix"
1100    
1101    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * tests/Class+Meth.R: new tests; t(t(m)) == m
1104    
1105            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1106    
1107            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1108            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1109    
1110            * R/dspMatrix.R: typo in "t" method
1111    
1112    2005-09-18  Douglas Bates  <bates@wisc.edu>
1113    
1114            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1115            * R/Tsparse.R: instead of R/gTMatrix.R
1116            * R/Csparse.R: new
1117            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1118            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1119            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1120                            via cholmod
1121    
1122    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1123    
1124            * R/Auxiliaries.R (non0ind): new function using new C code
1125            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1126    
1127    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1128    
1129            * src/chm_common.h: header file required by all C sources that
1130            call CHOLMOD functions.  It defines a cholmod_common structure
1131            called 'c' whose address is passed as the last argument to
1132            (virtually) every CHOLMOD function.
1133    
1134            * src/Pattern.c: Simple example of the use of CHOLMOD.
1135    
1136            * src/init.c: initialize and finalize the cholmod_common structure.
1137    
1138            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1139            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1140    
1141    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1142    
1143            * inst/test-tools.R: new file collecting the utility functions used
1144                    in ./tests/*.R
1145    
1146            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1147            * R/Matrix.R (cbind2): methods for NULL and missing
1148    
1149    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/AllClass.R: new "index" class for "[" and "[<-":
1152                    First cut at "symmetricMatrix" and "triangularMatrix"
1153            * R/gTMatrix.R (.ind.prep): new function;
1154                    Logical and character indexing now work too.
1155            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1156            * tests/indexing.R: new, including *.Rout.save
1157            * tests/dgTMatrix.R: new
1158    
1159    2005-08-29  Douglas Bates  <bates@wisc.edu>
1160    
1161            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1162            indicator pos not being updated.  Also enforced upper triangular
1163            for symmetric case.  Need to coerce edges component of elements of
1164            edge list - grr! (Why don't they define their classes cleanly?)
1165    
1166    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/Matrix.R:  added first "[<-" methods; not yet functional
1169            * R/denseMatrix.R: ditto
1170            * man/Subassign-methods.Rd: new help file for these
1171    
1172    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * DESCRIPTION (Version): 0.98-6
1175    
1176            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1177            matrices.
1178    
1179    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1182                    as( <logical>, "matrix")
1183    
1184            * R/pMatrix.R: coercion to "lgTMatrix"
1185    
1186            * R/gTMatrix.R: new virtual class to define "[" methods for.
1187            * man/gTMatrix-class.Rd:
1188            * General slight re-organization of where "[" methods are defined.
1189              more to come.
1190    
1191    2005-08-18  Douglas Bates  <bates@wisc.edu>
1192    
1193            * DESCRIPTION (Version): 0.98-5  released to CRAN
1194    
1195            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1196            * .....
1197    
1198    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1199    
1200            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1201            or glmer objects.
1202    
1203    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1204    
1205            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1206    
1207    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1208    
1209            * R/HBMM.R: finish re-writing R-only code.
1210    
1211    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1212    
1213            * man/externalFormats.Rd: move documentation for writeHB and
1214            writeMM here.
1215    
1216            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1217            (suggested by Paul Roecker).
1218    
1219            * tests/validObj.R (assertError): Comment out test that is failing
1220            after recent changes in r-devel.
1221    
1222    
1223    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225            * R/AllClass.R: intermediate virtual class "denseMatrix"
1226            * man/denseMatrix-class.Rd
1227            * NAMESPACE: export it, and also export
1228            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1229    
1230    2005-08-10  Douglas Bates  <bates@wisc.edu>
1231    
1232            * DESCRIPTION (Version): 0.98-3 to CRAN
1233    
1234            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1235            matrix_solve code (which was really, really wrong).
1236    
1237    2005-08-07  Douglas Bates  <bates@wisc.edu>
1238    
1239            * DESCRIPTION (Version): 0.98-2
1240    
1241            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1242    
1243            * R/lmer.R (abbrvNms): new
1244            * R/lmer.R (mcmcsamp): allow transformed parameters
1245            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1246            for the Harwell-Boeing and the MatrixMarket formats.
1247    
1248    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1249    
1250            * man/dtrMatrix-class.Rd: add examples
1251            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1252    
1253            * TODO: note the dtpMatrix (docu) bug
1254    
1255            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1256            in order to ensure that new as.matrix() is used by old functions,
1257            e.g., svd(), qr(), eigen(), dist(),..;
1258                  apply(), also matplot() or pairs().
1259    
1260    
1261    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1262    
1263            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1264              add comments about 'control' / lmerControl() arguments
1265    
1266    2005-07-27  Douglas Bates  <bates@wisc.edu>
1267    
1268            * man/sleepstudy.Rd: Added the sleep data set.
1269            * DESCRIPTION (Version): 0.98-1  released to CRAN
1270    
1271    2005-07-12  Douglas Bates  <bates@wisc.edu>
1272            * man/sleepstudy.Rd: Added the sleep data set.
1273    
1274            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1275            .Call calls that were producing spurious output.
1276    
1277    2005-07-05  Douglas Bates  <bates@wisc.edu>
1278    
1279            * R/lmer.R (lmer): stored updated variance component estimates in
1280            mer object for the generalized model.  (Bug reported by Renaud
1281            Lancelot).
1282    
1283    2005-07-03  Douglas Bates  <bates@wisc.edu>
1284    
1285            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1286            unidimensional case.
1287    
1288    2005-06-08  Douglas Bates  <bates@wisc.edu>
1289    
1290            * DESCRIPTION (Version): 0.96-1
1291    
1292            * moved  lmer-class' R and C code moved from lme4 to here
1293    
1294    2005-06-04  Douglas Bates  <bates@wisc.edu>
1295    
1296            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1297            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1298    
1299    2005-06-02  Douglas Bates  <bates@wisc.edu>
1300    
1301            * src/Makefile.win: Forgot to update this when Makefile changed.
1302    
1303    2005-05-11  Douglas Bates  <bates@wisc.edu>
1304    
1305            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1306            bug reported by Kurt Hornik and Michael Hahsler.
1307    
1308    2005-05-10  Douglas Bates  <bates@wisc.edu>
1309    
1310            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1311            logical sparse matrices.  These will also be used in the symbolic
1312            analysis for lmer objects.
1313    
1314            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1315            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1316    
1317    2005-05-06  Douglas Bates  <bates@wisc.edu>
1318    
1319            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1320            colMeans, colSums, rowMeans and rowSums.
1321    
1322    2005-04-18  Douglas Bates  <bates@wisc.edu>
1323    
1324            * src/lgCMatrix.[ch]: code for _validate method and stub for
1325            multiplication operation.
1326    
1327            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1328            to dgetrs.
1329    
1330            * src/init.c: Fix cut-and-paste error in definition of
1331            dgeMatrix_matrix_solve
1332    
1333            * src/{many files}: Tighten code by using ALLOC_SLOT.
1334    
1335    2005-04-15  Douglas Bates  <bates@wisc.edu>
1336    
1337            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1338    
1339            * DESCRIPTION: Eliminate import of stats.
1340    
1341    
1342    2005-04-06  Douglas Bates  <bates@wisc.edu>
1343    
1344            * R/AllClass.R : add logical sparse matrix classes
1345    
1346    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1347    
1348            * R/dgTMatrix.R: add "[" method for triplet matrices
1349            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1350    
1351    2005-03-31  Douglas Bates  <bates@wisc.edu>
1352    
1353            * DESCRIPTION (Version): release 0.95-5 to CRAN
1354    
1355            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1356            * R/sparseMatrix.R: %*%, crossprod()
1357            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1358            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1359            * src/lmer.c (lmer_fitted): fix thinko
1360    
1361    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1362    
1363            * R/AllClass.R: add two virtual sparse classes ``on top''
1364    
1365    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1366    
1367            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1368                    correspondingly fix examples and tests/ since new()
1369                    doesn't work for virtual classes.
1370    
1371    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1372    
1373            * R/Matrix.R (as.matrix): method and one for unname()
1374            * tests/dpoMatrix.R: tests should now be less platform dependent;
1375              also run for R 2.1.0; using as.matrix()
1376    
1377    2005-03-15  Douglas Bates  <bates@wisc.edu>
1378    
1379            * R/pMatrix.R: "pMatrix" class added
1380            * ....
1381    
1382    2005-03-14  Douglas Bates  <bates@wisc.edu>
1383    
1384            * R/dtpMatrix.R: Add unpack method and an example.
1385    
1386            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1387            of general symmetric matrices and associated S4 methods.
1388    
1389    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1390            +
1391    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1392    
1393            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1394              crossprod() and "%*%" methods added; tests, too.
1395            * tests/matprod.R: new, for testing these
1396    
1397    2005-03-03  Douglas Bates  <bates@wisc.edu>
1398    
1399            * src/lmer.c (lmer_fitted): Added.
1400    
1401    2005-03-02  Douglas Bates  <bates@wisc.edu>
1402    
1403            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1404    
1405    2005-02-28  Douglas Bates  <bates@wisc.edu>
1406    
1407            * src/*.c,po/,inst/po: Internationalization and localization of
1408            the package.
1409    
1410            * src/ldl.[ch]: Removed these as their contents are referenced in the
1411            R_ldl.c file.
1412    
1413            * src/flame.[ch]: Removed these source files.
1414    
1415            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1416    
1417            * src/LU.[ch],src/init.c: absorb in factorizations
1418    
1419            * src/Mutils.h: prepare for internationalization
1420    
1421            * src/cblas.h: move the enum definitions to Mutils.h and remove
1422            this file
1423    
1424    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1425    
1426            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1427    
1428            * R/dtrMatrix.R: fix t() method
1429    
1430            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1431            * NAMESPACE: export them (and import generics from "methods")
1432            * tests/group-methods.R : and test them.
1433    
1434            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1435            border case
1436    
1437    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1438    
1439            * DESCRIPTION (Version): 0.95-2  released to CRAN
1440    
1441            * src/dgBCMatrix.c:
1442            * src/lmer.c: many changes
1443            * ...
1444    
1445    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1446    
1447            * R/Matrix.R: add more sophisticated show() method.
1448    
1449    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1450    
1451            * */* : almost complete reorganization of classes.
1452    
1453    2005-01-26  Douglas Bates  <bates@wisc.edu>
1454    
1455            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1456            for the geMatrix class.
1457    
1458    2005-01-24  Douglas Bates  <bates@wisc.edu>
1459    
1460            * src/Makefile (clean): Remove *.a and *.so
1461    
1462            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1463    
1464    2005-01-23  Douglas Bates  <bates@wisc.edu>
1465    
1466            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1467            had an effect in cases with more than 2 grouping factors.
1468    
1469    2005-01-03  Douglas Bates  <bates@wisc.edu>
1470    
1471            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1472    
1473    2004-12-23  Douglas Bates  <bates@wisc.edu>
1474    
1475            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1476            and R_useDynamicSymbols (suggested by B.D.Ripley).
1477    
1478    2004-12-14  Douglas Bates  <bates@wisc.edu>
1479    
1480          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1481    
1482          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1483          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1484    
1485  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1486    
1487          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1488          no longer used.          no longer used.
# Line 17  Line 1494 
1494          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1495          Fixes part but not all of #15.          Fixes part but not all of #15.
1496    
1497  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1498    
1499          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1500          scalar grouping factors corrected.          scalar grouping factors corrected.
1501    
1502  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1503    
1504          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1505    
1506  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1507    
1508          * 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
1509          .h file can be included.          .h file can be included.
1510    
1511  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1512    
1513          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1514          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1515    
1516          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1517    
1518  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1519    
1520          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1521    
1522  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1523    
1524          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1525    
1526  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1527    
1528          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1529    
1530  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1531    
1532          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1533    
1534  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1535    
1536          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1537          routines.          routines.
1538    
1539  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1540    
1541          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1542    
1543  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1544    
1545          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1546    

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