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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1705, Sat Dec 16 12:37:25 2006 UTC
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1    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
4            align with proper position of "0", i.e., right for integers.
5            argument 'align' by default is "fancy".
6    
7    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
10            * R/Csparse.R: and fix "Compare" for more cases.
11            * tests/Class+Meth.R: test some of these (m == m, m != m)
12    
13    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/lsparseMatrix.R: all() and any() methods
16            * R/ldenseMatrix.R:      ditto
17            * NAMESPACE, R/Matrix.R: ditto
18    
19            * man/all-methods.Rd: document them minimally
20    
21            * tests/simple.R: add a few examples for these
22    
23    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R ([): fix long standing typo in symmetric case
26            * man/dsCMatrix-class.Rd: add example exhibiting the above case
27    
28    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
31            to LL before converting to a sparse matrix. (The LDL form can be
32            converted to a sparse matrix but it is implicitly a unit
33            triangular matrix and a diagonal matrix overwritten on the diagonal.)
34    
35    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
38    
39    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
40    
41            * DESCRIPTION (Version): updated -> release 0.9975-7
42            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
43    
44    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
47    
48    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
49    
50            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
51            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
52            is exactly singular.
53    
54    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Date): updated -> release 0.9975-6
57    
58    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
61            now returns symmetric.
62    
63            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
64    
65            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
66            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
67    
68            * R/Auxiliaries.R (.type.kind): added
69    
70    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
73            running src/CSparse_install.sh
74    
75            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
76    
77    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
80            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
81    
82            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
83    
84            * tests/Class+Meth.R (tstMatrixClass): now assure
85            the (important in method programming) property :
86    
87                    ###>>  Every "Matrix" is either
88                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
89    
90                    (where "*" stands for "Matrix")
91    
92            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
93    
94            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
95            * tests/validObj.R: checks for "comparison"
96    
97            * R/sparseMatrix.R ([): improved indexing for sparse;
98                    trying to keep <symmetric>[ n, n] symmmetric
99    
100            * tests/indexing.R: indexing for logical sparse now ok
101    
102    
103    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * src/Tsparse.c: use xTsparse_validate() , and hence remove
106    
107            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
108    
109    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
112    
113            * tests/simple.R: validObject() checking the above.
114    
115            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
116            replacing both dgCMatrix_validate and lgCM*.
117    
118            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
119            fix dimnames setting in other places.
120            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
121    
122    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
125    
126            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
127            symmetry test, via
128            * R/Auxiliaries.R (.as.dgC.0.factors):
129    
130    2006-11-01  Douglas Bates  <bates@r-project.org>
131    
132            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
133            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
134            <CsparseMatrix>) added
135    
136    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * tests/matprod.R: add a variation of Harri's example
139    
140            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
141            recursive infinitely.
142    
143            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
144    
145            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
146    
147    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
150            matrix if possible; test m+m == 2*m; now test dgRMatrix.
151            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
152            satisfy the above test.
153    
154    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
157    
158            * R/dgCMatrix.R: solve(a, b="missing") based on
159            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
160            RHS = NULL.
161    
162            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
163            add more (needed) [t]crossprod() methods.
164    
165            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
166    
167            * R/Auxiliaries.R (as_CspClass): cleanup
168            (drop0): internal utility for "Csparse_drop(*, 0)"
169            (.bail.out.2): encourage active feedback
170    
171    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dMatrix.R(Compare): new(), then slots [no validity check]
174    
175            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
176            non-valid or 'sorted' case).
177    
178            * R/dsparseMatrix.R: add "chol" method.
179            * R/ddenseMatrix.R: ditto
180    
181            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
182            * NAMESPACE (Ops)
183            * R/diagMatrix.R (diag2T): simple utility used "higher level"
184            coercion; deprecating direct lower level coercions.
185    
186            * R/*.R (seq): use seq_len() and seq_along() where possible.
187    
188    
189    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * DESCRIPTION (Version): 0.9975-5 ready for release
192    
193    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
196    
197    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/AllClass.R (corMatrix): add 'validity' check;
200                    comment out unused "LDL" class definition
201            * NAMESPACE: mention, but do not export "LDL" class
202            * R/corMatrix.R: new (simple), needed for R-devel with
203            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
204              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
205    
206    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
209            use Rprintf and R's error handling.
210    
211    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
214            * tests/matprod.R: add tests for the bug fixed.
215    
216    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
217    
218            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
219            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
220    
221    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
222    
223            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
224    
225    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * DESCRIPTION (Version): 0.9975-3
228    
229            * R/diagMatrix.R (bdiag): new function constructing block diagonal
230            (sparse) matrices.
231            * man/bdiag.Rd: docu + examples
232    
233            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
234    
235            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
236            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
237    
238            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
239            that result is sparse or diagonal (and not dense).
240    
241            * man/Subassign-methods.Rd: fix examples
242    
243            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
244            should always return a sparse (and not sometimes a diagonal) matrix.
245    
246    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
249    
250    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * DESCRIPTION (Version): 0.9975-2
253    
254            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
255    
256    2006-10-02  Douglas Bates  <bates@R-project.org>
257    
258            * tests/dg_Matrix.R: Simplify test taking into account new code.
259    
260    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
263    
264            * R/lsTMatrix.R: new files w/ missing methods
265            * R/nsTMatrix.R:  "  'for completeness'
266    
267            * tests/Class+Meth.R: a bit less 'not.ok.classes'
268    
269            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
270    
271    
272    2006-09-28  Douglas Bates  <bates@R-project.org>
273    
274            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
275            included.
276    
277            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
278            Export C-callable functions used in Zt_create in lme4.
279    
280    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Version): 0.9975-1
283    
284            * tests/simple.R: less checks fail; using NA, found that our
285                    kronecker() is not base-compatible with NA's.
286    
287            * R/dMatrix.R: "Compare" method now implemented for all cases
288    
289            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
290    
291            * man/dtpMatrix-class.Rd: mention length of 'x' slot
292    
293            * src/dtpMatrix.c (dtpMatrix_validate): fix check
294            * src/dspMatrix.c (dspMatrix_validate): ditto
295    
296            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
297              including coercion to [nl]tTMatrix.
298    
299            * R/diagMatrix.R (show): print a header line as for other classes.
300    
301    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/Makefile.win (SUBDIRS): fix typo
304    
305    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
308    
309    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
310    
311            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
312            symmetric and y missing in R code using %*% (cholmod_aat doesn't
313            accept a symmetric matrix).
314            * tests/group-methods.R: Uncomment test of crossprod applied to
315            lsCMatrix objects.
316    
317    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/AllClass.R (symmetricMatrix): add validity method (available
320            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
321    
322            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
323    
324            * tests/indexing.Rout.save:
325            * tests/indexing.R: additions, mainly for 'lsparse'
326    
327            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
328            case.
329    
330            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
331    
332    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
335                    as 'N' (1-letter - Ok?)
336    
337            * tests/group-methods.R: add test for logical + NAs
338    
339            * R/dMatrix.R ("Compare"): fix to work with NA's
340    
341            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
342    
343            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
344                    which is implemented.
345    
346    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * src/chm_common.c: coerce logical <-> double instead of
349            typecasting;  needed for "l" matrix handling in cholmod.
350    
351            * tests/other-pkgs.R (graph): small extension in "graph" checks.
352    
353            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
354            (Tsp2grNEL): other fixes needed
355    
356    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
359                    Matrices, since "lMatrix", also "lsparseM" can have NA
360            * R/ndenseMatrix.R, etc: new source files
361            * man/nsparseMatrix-classes.Rd, etc: new help files
362            * tests/: adaptions
363            * src/chm_common.c (chm_dense_to_SEXP): and others:
364                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
365            * src/Csparse.c, etc: ditto
366    
367    2006-09-11  Douglas Bates  <bates@R-project.org>
368    
369            * src/Mutils.[ch],init.c inst/include/*.h: Move the
370            alloc_d**Matrix functions to the lme4 package.
371    
372    2006-09-09  Douglas Bates  <bates@R-project.org>
373    
374            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
375            fixed
376    
377    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/lMatrix.R: new
380    
381            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
382    
383            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
384            * man/tcrossprod.Rd: ditto
385    
386    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
389            for exported functions
390            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
391            Remove partitioning algorithms for sparse matrix reordering.  The
392            copyright on the Metis code was problematic and the methods were
393            rarely used.
394            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
395            operations are now done entirely in CHOLMOD code.
396    
397    2006-09-06  Douglas Bates  <bates@R-project.org>
398    
399            * src/Mutils.h: Remove functions that are no longer used.
400    
401    2006-09-04  Douglas Bates  <bates@R-project.org>
402    
403            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
404            * src/DEPS.mkf: update
405    
406    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * created branches/Matrix-for-R-2.3.x;  on trunk: do
409            * DESCRIPTION (Version): 0.9975-0
410            (Depends): R (>= 2.4.0)
411    
412    2006-09-01  Douglas Bates  <bates@R-project.org>
413    
414            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
415    
416    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
419            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
420    
421            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
422    
423    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
426            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
427            * R/dsparseMatrix.R: ditto
428            * R/Csparse.R: ditto
429    
430    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/dMatrix.R (Compare): improve availability of "<", etc
433            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
434    
435    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
438            of a 0-index which was used as 1-index (..hmm)
439    
440            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
441    
442            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
443            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
444            (.is.diagonal): ditto
445    
446            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
447    
448            * R/Matrix.R (Matrix): also work for NA data
449    
450    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
453            in all cases.
454    
455    2006-08-27  Douglas Bates  <bates@R-project.org>
456    
457            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
458            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
459    
460    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
463            subclasses of "ddenseMatrix"
464            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
465            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
466            instead of half dozen specialized ones.
467    
468    2006-08-25  Douglas Bates  <bates@R-project.org>
469    
470            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
471            <tillard@cirad.fr> - ordering standard errors to match effects.
472    
473    2006-08-24  Douglas Bates  <bates@R-project.org>
474    
475            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
476            on R_ldl.
477            * R/lCholCMatrix.R,
478            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
479            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
480            * many files in ./R and ./src: Use more general version of
481            dup_mMatrix_as_dgeMatrix to simplify method definitions.
482            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
483            dtpMatrix, dspMatrix and dppMatrix conversions.
484    
485    
486    2006-08-23  Douglas Bates  <bates@R-project.org>
487    
488            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
489            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
490            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
491            dgeMatrix_crossprod (may need to do this in other places).
492            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
493            generic and method for dsCMatrix.  Use CHOLMOD for chol().
494    
495    2006-08-22  Douglas Bates  <bates@R-project.org>
496    
497            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
498            types of classed Matrices, matrices or numeric or logical vectors.
499            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
500            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
501            to Mutils.h (as an inline) and change name to Matrix_check_class;
502            fixes in as_cholmod_factor and chm_factor_to_SEXP.
503            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
504            dsCMatrix_matrix_solve.  Comment out vestigial functions.
505            * src/Csparse.c: use diag_P and uplo_P macros.
506    
507    2006-08-21  Douglas Bates  <bates@R-project.org>
508    
509            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
510            valgrind.
511            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
512            inverses.
513            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
514            -Wall warnings.
515            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
516            Use dup_mMatrix_as_dgeMatrix.
517    
518    2006-08-20  Douglas Bates  <bates@R-project.org>
519    
520            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
521            * tests/sparseQR.R: Added
522            * man/sparseQR-class.Rd: Document methods for qr.* generics
523            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
524    
525    2006-08-19  Douglas Bates  <bates@R-project.org>
526    
527            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
528            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
529            and qr.fitted.
530            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
531            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
532    
533    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
536            the base version has no "..." argument.
537    
538            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
539    
540            * R/Matrix.R: define and
541            * NAMESPACE: export as.numeric() and as.logical() methods.
542                    Let's hope these do not badly slow down something...
543            Finally export the zapsmall() method.
544    
545    2006-08-17  Douglas Bates  <bates@R-project.org>
546    
547            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
548            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
549            * src/dtCMatrix.c :Remove code that is no longer used
550            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
551    
552    2006-08-14  Douglas Bates  <bates@R-project.org>
553    
554            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
555            Csparse_to_logical and Csparse_symmetric_to_general.
556            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
557            coercion methods between CsparseMatrix and TsparseMatrix.
558    
559    2006-08-14  Douglas Bates  <bates@R-project.org>
560    
561            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
562            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
563            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
564            possible.
565    
566    2006-08-12  Douglas Bates  <bates@R-project.org>
567    
568            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
569              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
570              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
571              generalize conversions between TsparseMatrix, CsparseMatrix,
572              denseMatrix and matrix.  Preserve triangularity property and
573              propagate Dimnames in the easy cases.
574    
575    2006-08-10  Douglas Bates  <bates@R-project.org>
576    
577            * src/lmer.c: adjust checks in glmer_init for S4SXP
578            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
579            before S4SXP but for the wrong reasons.
580    
581    2006-08-08  Douglas Bates  <bates@R-project.org>
582    
583            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
584            Later modified to return the upper triangle only.
585            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
586    
587    2006-08-07  Douglas Bates  <bates@R-project.org>
588    
589            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
590            R-level conversion to a sparse symmetric class.
591            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
592            Remove conversion to sparse symmetric classes (now done in C code).
593    
594    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
597            * man/band.Rd:  adapt the \dontshow{} unit test.
598    
599    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * DESCRIPTION (Version): 0.995-14  for CRAN
602    
603            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
604    
605            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
606            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
607    
608            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
609            * R/Tsparse.R (tril, triu, band): methods
610            * R/dgRMatrix.R (tril, ...):    ditto
611            * man/band.Rd:                  ditto
612    
613    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/Matrix.R (head, tail): directly use utils:::head.matrix
616                    to be up-to-date automatically.
617    
618    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
621    
622            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
623            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
624            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
625            such that the S4 objects are always created by the current version
626            of R and 'Matrix' class definitions.
627    
628    2006-08-01  Douglas Bates  <bates@R-project.org>
629    
630            * R/lmer.R (LMEoptimize method), tests/lmer.R,
631            inst/external/test3comp.rda: Added warnings for convergence on
632            boundary and test cases.
633    
634            * src/lmer.c (mer_postVar): Modified to return the variances that
635            are marginal to the fixed effects, not conditional on them (which
636            is what the bVar slot contents represent).
637    
638    2006-07-31  Douglas Bates  <bates@R-project.org>
639    
640            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
641            function which calls the C function mer_hat_trace2.
642    
643            * man/ranef.Rd: Include description of "postVar" argument and
644            producing a caterpillar plot.
645    
646    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * NAMESPACE:    change  "correlation" to "corMatrix"
649            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
650            * R/dpoMatrix.R: ditto
651            * R/lmer.R:      ditto
652    
653    2006-07-28  Douglas Bates  <bates@R-project.org>
654    
655            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
656            RZXinv slot's contents into a separate internal function that can
657            be used in mer_hat_trace.
658    
659    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
662            via new smart
663            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
664            utility functions.
665    
666    
667    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/Csparse.R (tril, triu, band): do return *triangular* classed
670            matrices when appropriate; band() even symmetric ones.
671            (replCmat): extend to potentially all "CsparseMatrix"
672            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
673            allow subassignment for special sparse matrices.
674    
675            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
676    
677            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
678            argument; in glmer_*(): print only if(verbose).
679    
680            speed-optimize a few places by moving REAL(.) out of loops.
681    
682            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
683    
684    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
687                    since that wrongly triggers also for M[ logi , ]
688    
689            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
690            a symmetric matrix that results in a non-symmetric one.
691            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
692    
693            * R/dMatrix.R: make round(M) work as round(M, 0)
694    
695            * R/dgTMatrix.R (image): coordinate system and axis now use
696            1-based indices, not 0-based ones.
697    
698            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
699            * tests/indexing.R: test it.
700    
701            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
702            * man/isSymmetric-methods.Rd: and document it.
703    
704            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
705            * man/SparseM-conv.Rd: docu them
706    
707            * tests/other-pkgs.R: renamed from tests/graph.R and add example
708                    for 'SparseM' conversions
709    
710    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
711    
712            * R/Matrix.R (head): added head() and tail() methods.
713    
714    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * DESCRIPTION (Version): 0.995-12 released to CRAN
717    
718    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * tests/simple.R: add check for correct dsT -> dgT coercion;
721                    add check for correct printing of symmetric sparse matrices.
722    
723            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
724            for sparse symmetric matrices.
725    
726            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
727            diagonal twice.
728    
729    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
730    
731            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
732            being applied to the x slot (detected by Brian Ripley).
733    
734    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
737    
738            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
739    
740    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * src/lgCMatrix.c (lgCMatrix_diag): new function
743            * R/lgCMatrix.R (diag): for new method
744    
745            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
746                 ==> construction of illegal "*gTMatrix" via new() should
747                 now be much less easy:
748            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
749    
750            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
751                    directly.
752            * man/Matrix.Rd: documents it.
753    
754    2006-07-06  Douglas Bates  <bates@R-project.org>
755    
756            * src/pedigree.c (pedigree_inbreeding): Correction in
757            initialization.  This function is not currently being used and is
758            not fully tested.
759    
760            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
761            Introduced the glmer class.  Added code for mcmcmsamp on glmer
762            objects.  Modified validity check on pedigree objects to account
763            for nonparallel patterns of missingness of parents.
764    
765            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
766            class.
767    
768    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/pMatrix.R: coercion pMatrix -> Tsparse
771    
772    2006-06-12  Douglas Bates  <bates@R-project.org>
773    
774            * DESCRIPTION (Version): 0.995-11 released to CRAN
775    
776            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
777            the output from mcmcsamp.
778    
779    2006-06-10  Douglas Bates  <bates@R-project.org>
780    
781            * R/lmer.R (simulestimate): added C code for calculating the trace
782            of the hat matrix.
783    
784    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
787            classes.
788            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
789    
790    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/dgTMatrix.R (colSums): etc. All four of
793            colSums(), rowSums(), colMeans(), rowMeans() now should work for
794            all "Matrices".
795    
796    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
797    
798            * R/lmer.R (panel.ci): Add a reference line at zero and a
799            background grid to the qqmath plot of ranef.lmer.
800    
801    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
802    
803            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
804            grouping factors to be specified in the formula as (1|foo/bar).
805    
806    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
807    
808            * R/lmer.R (findbars and others): Change check of is.numeric to
809            !is.language to resolve the bug reported by Jacob Wegelin.
810    
811            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
812            code to evaluate inbreeding coefficients without calculating T,
813            based on code in Sargolzaei and Iwaisaki's paper.
814    
815    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
816    
817            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
818            generic and mer methods for isNested and denomDF. This denomDF was
819            an attempt to emulate that in lme but I don't think that makes
820            sense.  Use the trace of the hat matrix instead.
821    
822    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
825            the C code depending on a slot structure that's no longer valid.
826            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
827    
828    
829    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
830    
831            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
832            of lowerTriMatrix generic and methods to tril (also upper to triu)
833            and added a general band extractor.
834    
835    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
836    
837            * R/pedigree.R (pedigree): Replace sire and dam values outside the
838            allowable range with NAs. Added a corresponding check in the
839            validity check for the pedigree class.
840    
841            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
842            crossprod methods now inherits from symmetricMatrix.
843    
844    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
845    
846            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
847            generics lowerTriMatrix and upperTriMatrix along with methods for
848            the Csparse virtual class.  Also added a C function Csparse_band
849            that implements these methods by calling cholmod_band.
850    
851    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
854            erased when it was NULL.  This led to invalid subselections!
855    
856    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
857    
858            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
859            in method for "t" so as not to lose the unit diagonal property.
860    
861    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
862    
863            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
864            and methods.  This is now an option to the ranef method for the
865            mer class.
866    
867            * src/cs_utils.c: Ensure that the nz component is -1 for a
868            compressed column-oriented matrix.  Minor formatting cleanup.
869    
870            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
871            objects.
872    
873    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
876            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
877    
878    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
879    
880            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
881            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
882    
883            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
884            for the dtCMatrix class.
885    
886    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
887    
888            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
889            and methods for it.
890    
891    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
894            arguments, such that M %*% 1:6 now works
895            * Tests/matprod.R: test the above
896    
897    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
898    
899            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
900            the ranef.lmer class.
901    
902            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
903            methods to extract the posterior variances from the bVar slot.
904    
905    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
908            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
909    
910            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
911            * tests/simple: (extended)
912    
913            * R/sparseMatrix.R (isTriangular): now using much improved
914            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
915    
916    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
917    
918            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
919            (problem report from Franklin Parlamis).  This should be done
920            generally.
921    
922    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
923    
924            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
925            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
926            update the plot methods.
927    
928    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
929    
930            * R/lmer.R (resid and ranef methods):  Added methods for the
931            "residuals" and "resid" generic but only for linear mixed model
932            fits.  Changed the ranef method to return a list of data frames so
933            that the plot methods now work.
934    
935    2006-03-16  Douglas Bates  <bates@bates2>
936    
937            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
938            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
939    
940            * DESCRIPTION (Date): New release
941    
942    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
945    
946            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
947            * man/KNex.Rd: and other help files
948            * tests/*.R: several ones needed adaption
949            * inst/doc/Comparisons.Rnw: ditto
950    
951    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
954    
955            * tests/indexing.R: tests for new [<- methods for sparse matrices.
956    
957    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
958    
959            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
960    
961            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
962    
963    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/dMatrix.R: enable things like  M [ M < 10 ]
966            * R/dgeMatrix.R: implement it
967    
968    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * R/AllClass.R: define "summary.mer" and "*.lmer"
971            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
972            * R/lmer.R (show): now works with summary()
973    
974    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
977            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
978                    support the above
979    
980    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
981    
982            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
983            Use glmFit$prior.weights for weights in a glmm.
984            Allow an option usePQL = FALSE to skip the PQL steps for the
985            Laplace method (and, in time, the AGQ method).
986    
987            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
988            into a separate function internal_mer_Xfactor to be able to call
989            it from internal_bhat.
990    
991    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * tests/Class+Meth.R (tstMatrixClass): function for much better
994            testing; now again of all actual classes.
995    
996            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
997                    use macros and define make_d_matrix_* and make_i_matrix_*
998                    where _i_ is for the ldense routines:
999    
1000            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1001            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1002    
1003            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1004    
1005    
1006    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1009                    many different kinds of matrices.
1010            * R/*.R: quite a few new methods were needed for R CMD check with
1011                    new Matrix().  Very good for users playing around.
1012    
1013    
1014    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * src/dgeMatrix.c (dMatrix_validate): new
1017            * src/Mutils.c (dense_nonpacked_validate): new
1018    
1019            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1020    
1021    
1022    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1023    
1024            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1025    
1026    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1027    
1028            * DESCRIPTION (Version): 0.99-6 released to CRAN
1029    
1030            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1031            segfault in cases with multiple non-nested grouping factors.
1032    
1033    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1034    
1035            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1036                    (Depends): also on 'utils'
1037    
1038            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1039            * R/diagMatrix.R (Diagonal): constructor and methods for
1040            diagonal matrices
1041    
1042            * R/ltTMatrix.R: new "minimal methods"
1043    
1044    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1045    
1046            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1047            all methods (and help files).
1048    
1049    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1052                    for case (dimn.  op  no_dimn.)
1053    
1054    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1055    
1056            * DESCRIPTION (Version): 0.99-2  released to CRAN
1057    
1058    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1059    
1060            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1061            by Julian Faraway.
1062    
1063    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * R/Auxiliaries.R (try_as): new utility
1066            * R/sparseMatrix.R: use try_as() in coercion to original class
1067    
1068    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1071    
1072    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * R/Auxiliaries.R (dimNamesCheck): added
1075    
1076            * R/Matrix.R (as.array), (as.vector): new
1077    
1078    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1081                    default.
1082            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1083                    "pMatrix" now contains "sparseMatrix"
1084    
1085    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * tests/Class+Meth.R: new tests; t(t(m)) == m
1088    
1089            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1090    
1091            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1092            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1093    
1094            * R/dspMatrix.R: typo in "t" method
1095    
1096    2005-09-18  Douglas Bates  <bates@wisc.edu>
1097    
1098            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1099            * R/Tsparse.R: instead of R/gTMatrix.R
1100            * R/Csparse.R: new
1101            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1102            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1103            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1104                            via cholmod
1105    
1106    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1107    
1108            * R/Auxiliaries.R (non0ind): new function using new C code
1109            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1110    
1111    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1112    
1113            * src/chm_common.h: header file required by all C sources that
1114            call CHOLMOD functions.  It defines a cholmod_common structure
1115            called 'c' whose address is passed as the last argument to
1116            (virtually) every CHOLMOD function.
1117    
1118            * src/Pattern.c: Simple example of the use of CHOLMOD.
1119    
1120            * src/init.c: initialize and finalize the cholmod_common structure.
1121    
1122            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1123            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1124    
1125    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1126    
1127            * inst/test-tools.R: new file collecting the utility functions used
1128                    in ./tests/*.R
1129    
1130            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1131            * R/Matrix.R (cbind2): methods for NULL and missing
1132    
1133    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1134    
1135            * R/AllClass.R: new "index" class for "[" and "[<-":
1136                    First cut at "symmetricMatrix" and "triangularMatrix"
1137            * R/gTMatrix.R (.ind.prep): new function;
1138                    Logical and character indexing now work too.
1139            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1140            * tests/indexing.R: new, including *.Rout.save
1141            * tests/dgTMatrix.R: new
1142    
1143    2005-08-29  Douglas Bates  <bates@wisc.edu>
1144    
1145            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1146            indicator pos not being updated.  Also enforced upper triangular
1147            for symmetric case.  Need to coerce edges component of elements of
1148            edge list - grr! (Why don't they define their classes cleanly?)
1149    
1150    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1151    
1152            * R/Matrix.R:  added first "[<-" methods; not yet functional
1153            * R/denseMatrix.R: ditto
1154            * man/Subassign-methods.Rd: new help file for these
1155    
1156    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1157    
1158            * DESCRIPTION (Version): 0.98-6
1159    
1160            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1161            matrices.
1162    
1163    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1164    
1165            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1166                    as( <logical>, "matrix")
1167    
1168            * R/pMatrix.R: coercion to "lgTMatrix"
1169    
1170            * R/gTMatrix.R: new virtual class to define "[" methods for.
1171            * man/gTMatrix-class.Rd:
1172            * General slight re-organization of where "[" methods are defined.
1173              more to come.
1174    
1175    2005-08-18  Douglas Bates  <bates@wisc.edu>
1176    
1177            * DESCRIPTION (Version): 0.98-5  released to CRAN
1178    
1179            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1180            * .....
1181    
1182    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1183    
1184            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1185            or glmer objects.
1186    
1187    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1188    
1189            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1190    
1191    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1192    
1193            * R/HBMM.R: finish re-writing R-only code.
1194    
1195    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1196    
1197            * man/externalFormats.Rd: move documentation for writeHB and
1198            writeMM here.
1199    
1200            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1201            (suggested by Paul Roecker).
1202    
1203            * tests/validObj.R (assertError): Comment out test that is failing
1204            after recent changes in r-devel.
1205    
1206    
1207    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1208    
1209            * R/AllClass.R: intermediate virtual class "denseMatrix"
1210            * man/denseMatrix-class.Rd
1211            * NAMESPACE: export it, and also export
1212            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1213    
1214    2005-08-10  Douglas Bates  <bates@wisc.edu>
1215    
1216            * DESCRIPTION (Version): 0.98-3 to CRAN
1217    
1218            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1219            matrix_solve code (which was really, really wrong).
1220    
1221    2005-08-07  Douglas Bates  <bates@wisc.edu>
1222    
1223            * DESCRIPTION (Version): 0.98-2
1224    
1225            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1226    
1227            * R/lmer.R (abbrvNms): new
1228            * R/lmer.R (mcmcsamp): allow transformed parameters
1229            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1230            for the Harwell-Boeing and the MatrixMarket formats.
1231    
1232    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * man/dtrMatrix-class.Rd: add examples
1235            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1236    
1237            * TODO: note the dtpMatrix (docu) bug
1238    
1239            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1240            in order to ensure that new as.matrix() is used by old functions,
1241            e.g., svd(), qr(), eigen(), dist(),..;
1242                  apply(), also matplot() or pairs().
1243    
1244    
1245    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1248              add comments about 'control' / lmerControl() arguments
1249    
1250    2005-07-27  Douglas Bates  <bates@wisc.edu>
1251    
1252            * man/sleepstudy.Rd: Added the sleep data set.
1253            * DESCRIPTION (Version): 0.98-1  released to CRAN
1254    
1255    2005-07-12  Douglas Bates  <bates@wisc.edu>
1256            * man/sleepstudy.Rd: Added the sleep data set.
1257    
1258            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1259            .Call calls that were producing spurious output.
1260    
1261    2005-07-05  Douglas Bates  <bates@wisc.edu>
1262    
1263            * R/lmer.R (lmer): stored updated variance component estimates in
1264            mer object for the generalized model.  (Bug reported by Renaud
1265            Lancelot).
1266    
1267    2005-07-03  Douglas Bates  <bates@wisc.edu>
1268    
1269            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1270            unidimensional case.
1271    
1272    2005-06-08  Douglas Bates  <bates@wisc.edu>
1273    
1274            * DESCRIPTION (Version): 0.96-1
1275    
1276            * moved  lmer-class' R and C code moved from lme4 to here
1277    
1278    2005-06-04  Douglas Bates  <bates@wisc.edu>
1279    
1280            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1281            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1282    
1283    2005-06-02  Douglas Bates  <bates@wisc.edu>
1284    
1285            * src/Makefile.win: Forgot to update this when Makefile changed.
1286    
1287    2005-05-11  Douglas Bates  <bates@wisc.edu>
1288    
1289            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1290            bug reported by Kurt Hornik and Michael Hahsler.
1291    
1292    2005-05-10  Douglas Bates  <bates@wisc.edu>
1293    
1294            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1295            logical sparse matrices.  These will also be used in the symbolic
1296            analysis for lmer objects.
1297    
1298            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1299            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1300    
1301    2005-05-06  Douglas Bates  <bates@wisc.edu>
1302    
1303            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1304            colMeans, colSums, rowMeans and rowSums.
1305    
1306    2005-04-18  Douglas Bates  <bates@wisc.edu>
1307    
1308            * src/lgCMatrix.[ch]: code for _validate method and stub for
1309            multiplication operation.
1310    
1311            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1312            to dgetrs.
1313    
1314            * src/init.c: Fix cut-and-paste error in definition of
1315            dgeMatrix_matrix_solve
1316    
1317            * src/{many files}: Tighten code by using ALLOC_SLOT.
1318    
1319    2005-04-15  Douglas Bates  <bates@wisc.edu>
1320    
1321            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1322    
1323            * DESCRIPTION: Eliminate import of stats.
1324    
1325    
1326    2005-04-06  Douglas Bates  <bates@wisc.edu>
1327    
1328            * R/AllClass.R : add logical sparse matrix classes
1329    
1330  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1331    
1332          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1333          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1334    
1335  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1336    
1337          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1338    
# Line 29  Line 1358 
1358          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1359            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1360    
1361  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1362    
1363          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1364          * ....          * ....
1365    
1366  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1367    
1368          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1369    
# Line 49  Line 1378 
1378            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1379          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1380    
1381  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1382    
1383          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1384    
1385  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1386    
1387          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1388    
1389  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1390    
1391          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1392          the package.          the package.
# Line 105  Line 1434 
1434    
1435          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1436    
1437  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1438    
1439          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1440          for the geMatrix class.          for the geMatrix class.
1441    
1442  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1443    
1444          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1445    
1446          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1447    
1448  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1449    
1450          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1451          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1452    
1453  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1454    
1455          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1456    
1457  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1458    
1459          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1460          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1461    
1462  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1463    
1464          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1465    
1466          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1467          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1468    
1469  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1470    
1471          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1472          no longer used.          no longer used.
# Line 149  Line 1478 
1478          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1479          Fixes part but not all of #15.          Fixes part but not all of #15.
1480    
1481  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1482    
1483          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1484          scalar grouping factors corrected.          scalar grouping factors corrected.
1485    
1486  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1487    
1488          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1489    
1490  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1491    
1492          * 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
1493          .h file can be included.          .h file can be included.
1494    
1495  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1496    
1497          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1498          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1499    
1500          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1501    
1502  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1503    
1504          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1505    
1506  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1507    
1508          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1509    
1510  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1511    
1512          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1513    
1514  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1515    
1516          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1517    
1518  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1519    
1520          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1521          routines.          routines.
1522    
1523  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1524    
1525          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1526    
1527  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1528    
1529          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1530    

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