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revision 726, Thu May 12 14:59:04 2005 UTC revision 1618, Fri Oct 6 15:44:01 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-3
4    
5            * R/diagMatrix.R (bdiag): new function constructing block diagonal
6            (sparse) matrices.
7            * man/bdiag.Rd: docu + examples
8    
9            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
10            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
11    
12            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
13            that result is sparse or diagonal (and not dense).
14    
15            * man/Subassign-methods.Rd: fix examples
16    
17            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
18            should always return a sparse (and not sometimes a diagonal) matrix.
19    
20    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
23    
24    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
25    
26            * DESCRIPTION (Version): 0.9975-2
27    
28            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
29    
30    2006-10-02  Douglas Bates  <bates@R-project.org>
31    
32            * tests/dg_Matrix.R: Simplify test taking into account new code.
33    
34    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
37    
38            * R/lsTMatrix.R: new files w/ missing methods
39            * R/nsTMatrix.R:  "  'for completeness'
40    
41            * tests/Class+Meth.R: a bit less 'not.ok.classes'
42    
43            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
44    
45    
46    2006-09-28  Douglas Bates  <bates@R-project.org>
47    
48            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
49            included.
50    
51            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
52            Export C-callable functions used in Zt_create in lme4.
53    
54    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Version): 0.9975-1
57    
58            * tests/simple.R: less checks fail; using NA, found that our
59                    kronecker() is not base-compatible with NA's.
60    
61            * R/dMatrix.R: "Compare" method now implemented for all cases
62    
63            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
64    
65            * man/dtpMatrix-class.Rd: mention length of 'x' slot
66    
67            * src/dtpMatrix.c (dtpMatrix_validate): fix check
68            * src/dspMatrix.c (dspMatrix_validate): ditto
69    
70            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
71              including coercion to [nl]tTMatrix.
72    
73            * R/diagMatrix.R (show): print a header line as for other classes.
74    
75    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/Makefile.win (SUBDIRS): fix typo
78    
79    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
82    
83    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
86            symmetric and y missing in R code using %*% (cholmod_aat doesn't
87            accept a symmetric matrix).
88            * tests/group-methods.R: Uncomment test of crossprod applied to
89            lsCMatrix objects.
90    
91    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/AllClass.R (symmetricMatrix): add validity method (available
94            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
95    
96            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
97    
98            * tests/indexing.Rout.save:
99            * tests/indexing.R: additions, mainly for 'lsparse'
100    
101            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
102            case.
103    
104            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
105    
106    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
109                    as 'N' (1-letter - Ok?)
110    
111            * tests/group-methods.R: add test for logical + NAs
112    
113            * R/dMatrix.R ("Compare"): fix to work with NA's
114    
115            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
116    
117            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
118                    which is implemented.
119    
120    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * src/chm_common.c: coerce logical <-> double instead of
123            typecasting;  needed for "l" matrix handling in cholmod.
124    
125            * tests/other-pkgs.R (graph): small extension in "graph" checks.
126    
127            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
128            (Tsp2grNEL): other fixes needed
129    
130    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
133                    Matrices, since "lMatrix", also "lsparseM" can have NA
134            * R/ndenseMatrix.R, etc: new source files
135            * man/nsparseMatrix-classes.Rd, etc: new help files
136            * tests/: adaptions
137            * src/chm_common.c (chm_dense_to_SEXP): and others:
138                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
139            * src/Csparse.c, etc: ditto
140    
141    2006-09-11  Douglas Bates  <bates@R-project.org>
142    
143            * src/Mutils.[ch],init.c inst/include/*.h: Move the
144            alloc_d**Matrix functions to the lme4 package.
145    
146    2006-09-09  Douglas Bates  <bates@R-project.org>
147    
148            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
149            fixed
150    
151    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/lMatrix.R: new
154    
155            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
156    
157            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
158            * man/tcrossprod.Rd: ditto
159    
160    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
161    
162            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
163            for exported functions
164            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
165            Remove partitioning algorithms for sparse matrix reordering.  The
166            copyright on the Metis code was problematic and the methods were
167            rarely used.
168            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
169            operations are now done entirely in CHOLMOD code.
170    
171    2006-09-06  Douglas Bates  <bates@R-project.org>
172    
173            * src/Mutils.h: Remove functions that are no longer used.
174    
175    2006-09-04  Douglas Bates  <bates@R-project.org>
176    
177            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
178            * src/DEPS.mkf: update
179    
180    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * created branches/Matrix-for-R-2.3.x;  on trunk: do
183            * DESCRIPTION (Version): 0.9975-0
184            (Depends): R (>= 2.4.0)
185    
186    2006-09-01  Douglas Bates  <bates@R-project.org>
187    
188            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
189    
190    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
193            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
194    
195            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
196    
197    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
200            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
201            * R/dsparseMatrix.R: ditto
202            * R/Csparse.R: ditto
203    
204    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dMatrix.R (Compare): improve availability of "<", etc
207            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
208    
209    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
212            of a 0-index which was used as 1-index (..hmm)
213    
214            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
215    
216            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
217            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
218            (.is.diagonal): ditto
219    
220            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
221    
222            * R/Matrix.R (Matrix): also work for NA data
223    
224    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
227            in all cases.
228    
229    2006-08-27  Douglas Bates  <bates@R-project.org>
230    
231            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
232            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
233    
234    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
237            subclasses of "ddenseMatrix"
238            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
239            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
240            instead of half dozen specialized ones.
241    
242    2006-08-25  Douglas Bates  <bates@R-project.org>
243    
244            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
245            <tillard@cirad.fr> - ordering standard errors to match effects.
246    
247    2006-08-24  Douglas Bates  <bates@R-project.org>
248    
249            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
250            on R_ldl.
251            * R/lCholCMatrix.R,
252            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
253            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
254            * many files in ./R and ./src: Use more general version of
255            dup_mMatrix_as_dgeMatrix to simplify method definitions.
256            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
257            dtpMatrix, dspMatrix and dppMatrix conversions.
258    
259    
260    2006-08-23  Douglas Bates  <bates@R-project.org>
261    
262            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
263            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
264            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
265            dgeMatrix_crossprod (may need to do this in other places).
266            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
267            generic and method for dsCMatrix.  Use CHOLMOD for chol().
268    
269    2006-08-22  Douglas Bates  <bates@R-project.org>
270    
271            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
272            types of classed Matrices, matrices or numeric or logical vectors.
273            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
274            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
275            to Mutils.h (as an inline) and change name to Matrix_check_class;
276            fixes in as_cholmod_factor and chm_factor_to_SEXP.
277            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
278            dsCMatrix_matrix_solve.  Comment out vestigial functions.
279            * src/Csparse.c: use diag_P and uplo_P macros.
280    
281    2006-08-21  Douglas Bates  <bates@R-project.org>
282    
283            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
284            valgrind.
285            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
286            inverses.
287            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
288            -Wall warnings.
289            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
290            Use dup_mMatrix_as_dgeMatrix.
291    
292    2006-08-20  Douglas Bates  <bates@R-project.org>
293    
294            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
295            * tests/sparseQR.R: Added
296            * man/sparseQR-class.Rd: Document methods for qr.* generics
297            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
298    
299    2006-08-19  Douglas Bates  <bates@R-project.org>
300    
301            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
302            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
303            and qr.fitted.
304            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
305            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
306    
307    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
310            the base version has no "..." argument.
311    
312            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
313    
314            * R/Matrix.R: define and
315            * NAMESPACE: export as.numeric() and as.logical() methods.
316                    Let's hope these do not badly slow down something...
317            Finally export the zapsmall() method.
318    
319    2006-08-17  Douglas Bates  <bates@R-project.org>
320    
321            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
322            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
323            * src/dtCMatrix.c :Remove code that is no longer used
324            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
325    
326    2006-08-14  Douglas Bates  <bates@R-project.org>
327    
328            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
329            Csparse_to_logical and Csparse_symmetric_to_general.
330            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
331            coercion methods between CsparseMatrix and TsparseMatrix.
332    
333    2006-08-14  Douglas Bates  <bates@R-project.org>
334    
335            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
336            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
337            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
338            possible.
339    
340    2006-08-12  Douglas Bates  <bates@R-project.org>
341    
342            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
343              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
344              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
345              generalize conversions between TsparseMatrix, CsparseMatrix,
346              denseMatrix and matrix.  Preserve triangularity property and
347              propagate Dimnames in the easy cases.
348    
349    2006-08-10  Douglas Bates  <bates@R-project.org>
350    
351            * src/lmer.c: adjust checks in glmer_init for S4SXP
352            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
353            before S4SXP but for the wrong reasons.
354    
355    2006-08-08  Douglas Bates  <bates@R-project.org>
356    
357            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
358            Later modified to return the upper triangle only.
359            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
360    
361    2006-08-07  Douglas Bates  <bates@R-project.org>
362    
363            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
364            R-level conversion to a sparse symmetric class.
365            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
366            Remove conversion to sparse symmetric classes (now done in C code).
367    
368    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
371            * man/band.Rd:  adapt the \dontshow{} unit test.
372    
373    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * DESCRIPTION (Version): 0.995-14  for CRAN
376    
377            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
378    
379            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
380            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
381    
382            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
383            * R/Tsparse.R (tril, triu, band): methods
384            * R/dgRMatrix.R (tril, ...):    ditto
385            * man/band.Rd:                  ditto
386    
387    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/Matrix.R (head, tail): directly use utils:::head.matrix
390                    to be up-to-date automatically.
391    
392    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
395    
396            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
397            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
398            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
399            such that the S4 objects are always created by the current version
400            of R and 'Matrix' class definitions.
401    
402    2006-08-01  Douglas Bates  <bates@R-project.org>
403    
404            * R/lmer.R (LMEoptimize method), tests/lmer.R,
405            inst/external/test3comp.rda: Added warnings for convergence on
406            boundary and test cases.
407    
408            * src/lmer.c (mer_postVar): Modified to return the variances that
409            are marginal to the fixed effects, not conditional on them (which
410            is what the bVar slot contents represent).
411    
412    2006-07-31  Douglas Bates  <bates@R-project.org>
413    
414            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
415            function which calls the C function mer_hat_trace2.
416    
417            * man/ranef.Rd: Include description of "postVar" argument and
418            producing a caterpillar plot.
419    
420    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * NAMESPACE:    change  "correlation" to "corMatrix"
423            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
424            * R/dpoMatrix.R: ditto
425            * R/lmer.R:      ditto
426    
427    2006-07-28  Douglas Bates  <bates@R-project.org>
428    
429            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
430            RZXinv slot's contents into a separate internal function that can
431            be used in mer_hat_trace.
432    
433    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
436            via new smart
437            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
438            utility functions.
439    
440    
441    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Csparse.R (tril, triu, band): do return *triangular* classed
444            matrices when appropriate; band() even symmetric ones.
445            (replCmat): extend to potentially all "CsparseMatrix"
446            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
447            allow subassignment for special sparse matrices.
448    
449            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
450    
451            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
452            argument; in glmer_*(): print only if(verbose).
453    
454            speed-optimize a few places by moving REAL(.) out of loops.
455    
456            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
457    
458    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
461                    since that wrongly triggers also for M[ logi , ]
462    
463            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
464            a symmetric matrix that results in a non-symmetric one.
465            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
466    
467            * R/dMatrix.R: make round(M) work as round(M, 0)
468    
469            * R/dgTMatrix.R (image): coordinate system and axis now use
470            1-based indices, not 0-based ones.
471    
472            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
473            * tests/indexing.R: test it.
474    
475            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
476            * man/isSymmetric-methods.Rd: and document it.
477    
478            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
479            * man/SparseM-conv.Rd: docu them
480    
481            * tests/other-pkgs.R: renamed from tests/graph.R and add example
482                    for 'SparseM' conversions
483    
484    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
485    
486            * R/Matrix.R (head): added head() and tail() methods.
487    
488    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * DESCRIPTION (Version): 0.995-12 released to CRAN
491    
492    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * tests/simple.R: add check for correct dsT -> dgT coercion;
495                    add check for correct printing of symmetric sparse matrices.
496    
497            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
498            for sparse symmetric matrices.
499    
500            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
501            diagonal twice.
502    
503    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
504    
505            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
506            being applied to the x slot (detected by Brian Ripley).
507    
508    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
511    
512            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
513    
514    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * src/lgCMatrix.c (lgCMatrix_diag): new function
517            * R/lgCMatrix.R (diag): for new method
518    
519            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
520                 ==> construction of illegal "*gTMatrix" via new() should
521                 now be much less easy:
522            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
523    
524            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
525                    directly.
526            * man/Matrix.Rd: documents it.
527    
528    2006-07-06  Douglas Bates  <bates@R-project.org>
529    
530            * src/pedigree.c (pedigree_inbreeding): Correction in
531            initialization.  This function is not currently being used and is
532            not fully tested.
533    
534            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
535            Introduced the glmer class.  Added code for mcmcmsamp on glmer
536            objects.  Modified validity check on pedigree objects to account
537            for nonparallel patterns of missingness of parents.
538    
539            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
540            class.
541    
542    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/pMatrix.R: coercion pMatrix -> Tsparse
545    
546    2006-06-12  Douglas Bates  <bates@R-project.org>
547    
548            * DESCRIPTION (Version): 0.995-11 released to CRAN
549    
550            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
551            the output from mcmcsamp.
552    
553    2006-06-10  Douglas Bates  <bates@R-project.org>
554    
555            * R/lmer.R (simulestimate): added C code for calculating the trace
556            of the hat matrix.
557    
558    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
561            classes.
562            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
563    
564    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/dgTMatrix.R (colSums): etc. All four of
567            colSums(), rowSums(), colMeans(), rowMeans() now should work for
568            all "Matrices".
569    
570    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
571    
572            * R/lmer.R (panel.ci): Add a reference line at zero and a
573            background grid to the qqmath plot of ranef.lmer.
574    
575    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
576    
577            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
578            grouping factors to be specified in the formula as (1|foo/bar).
579    
580    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
581    
582            * R/lmer.R (findbars and others): Change check of is.numeric to
583            !is.language to resolve the bug reported by Jacob Wegelin.
584    
585            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
586            code to evaluate inbreeding coefficients without calculating T,
587            based on code in Sargolzaei and Iwaisaki's paper.
588    
589    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
590    
591            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
592            generic and mer methods for isNested and denomDF. This denomDF was
593            an attempt to emulate that in lme but I don't think that makes
594            sense.  Use the trace of the hat matrix instead.
595    
596    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
599            the C code depending on a slot structure that's no longer valid.
600            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
601    
602    
603    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
604    
605            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
606            of lowerTriMatrix generic and methods to tril (also upper to triu)
607            and added a general band extractor.
608    
609    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
610    
611            * R/pedigree.R (pedigree): Replace sire and dam values outside the
612            allowable range with NAs. Added a corresponding check in the
613            validity check for the pedigree class.
614    
615            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
616            crossprod methods now inherits from symmetricMatrix.
617    
618    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
619    
620            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
621            generics lowerTriMatrix and upperTriMatrix along with methods for
622            the Csparse virtual class.  Also added a C function Csparse_band
623            that implements these methods by calling cholmod_band.
624    
625    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
628            erased when it was NULL.  This led to invalid subselections!
629    
630    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
631    
632            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
633            in method for "t" so as not to lose the unit diagonal property.
634    
635    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
636    
637            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
638            and methods.  This is now an option to the ranef method for the
639            mer class.
640    
641            * src/cs_utils.c: Ensure that the nz component is -1 for a
642            compressed column-oriented matrix.  Minor formatting cleanup.
643    
644            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
645            objects.
646    
647    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
650            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
651    
652    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
653    
654            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
655            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
656    
657            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
658            for the dtCMatrix class.
659    
660    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
661    
662            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
663            and methods for it.
664    
665    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
668            arguments, such that M %*% 1:6 now works
669            * Tests/matprod.R: test the above
670    
671    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
674            the ranef.lmer class.
675    
676            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
677            methods to extract the posterior variances from the bVar slot.
678    
679    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
682            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
683    
684            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
685            * tests/simple: (extended)
686    
687            * R/sparseMatrix.R (isTriangular): now using much improved
688            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
689    
690    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
691    
692            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
693            (problem report from Franklin Parlamis).  This should be done
694            generally.
695    
696    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
697    
698            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
699            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
700            update the plot methods.
701    
702    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
703    
704            * R/lmer.R (resid and ranef methods):  Added methods for the
705            "residuals" and "resid" generic but only for linear mixed model
706            fits.  Changed the ranef method to return a list of data frames so
707            that the plot methods now work.
708    
709    2006-03-16  Douglas Bates  <bates@bates2>
710    
711            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
712            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
713    
714            * DESCRIPTION (Date): New release
715    
716    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
719    
720            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
721            * man/KNex.Rd: and other help files
722            * tests/*.R: several ones needed adaption
723            * inst/doc/Comparisons.Rnw: ditto
724    
725    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
728    
729            * tests/indexing.R: tests for new [<- methods for sparse matrices.
730    
731    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
734    
735            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
736    
737    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/dMatrix.R: enable things like  M [ M < 10 ]
740            * R/dgeMatrix.R: implement it
741    
742    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/AllClass.R: define "summary.mer" and "*.lmer"
745            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
746            * R/lmer.R (show): now works with summary()
747    
748    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
751            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
752                    support the above
753    
754    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
757            Use glmFit$prior.weights for weights in a glmm.
758            Allow an option usePQL = FALSE to skip the PQL steps for the
759            Laplace method (and, in time, the AGQ method).
760    
761            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
762            into a separate function internal_mer_Xfactor to be able to call
763            it from internal_bhat.
764    
765    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * tests/Class+Meth.R (tstMatrixClass): function for much better
768            testing; now again of all actual classes.
769    
770            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
771                    use macros and define make_d_matrix_* and make_i_matrix_*
772                    where _i_ is for the ldense routines:
773    
774            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
775            * src/ldense.c (lsyMatrix_as_lgeMatrix):
776    
777            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
778    
779    
780    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
783                    many different kinds of matrices.
784            * R/*.R: quite a few new methods were needed for R CMD check with
785                    new Matrix().  Very good for users playing around.
786    
787    
788    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * src/dgeMatrix.c (dMatrix_validate): new
791            * src/Mutils.c (dense_nonpacked_validate): new
792    
793            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
794    
795    
796    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
797    
798            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
799    
800    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
801    
802            * DESCRIPTION (Version): 0.99-6 released to CRAN
803    
804            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
805            segfault in cases with multiple non-nested grouping factors.
806    
807    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
810                    (Depends): also on 'utils'
811    
812            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
813            * R/diagMatrix.R (Diagonal): constructor and methods for
814            diagonal matrices
815    
816            * R/ltTMatrix.R: new "minimal methods"
817    
818    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
821            all methods (and help files).
822    
823    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
826                    for case (dimn.  op  no_dimn.)
827    
828    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
829    
830            * DESCRIPTION (Version): 0.99-2  released to CRAN
831    
832    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
833    
834            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
835            by Julian Faraway.
836    
837    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
838    
839            * R/Auxiliaries.R (try_as): new utility
840            * R/sparseMatrix.R: use try_as() in coercion to original class
841    
842    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
845    
846    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Auxiliaries.R (dimNamesCheck): added
849    
850            * R/Matrix.R (as.array), (as.vector): new
851    
852    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
855                    default.
856            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
857                    "pMatrix" now contains "sparseMatrix"
858    
859    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * tests/Class+Meth.R: new tests; t(t(m)) == m
862    
863            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
864    
865            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
866            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
867    
868            * R/dspMatrix.R: typo in "t" method
869    
870    2005-09-18  Douglas Bates  <bates@wisc.edu>
871    
872            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
873            * R/Tsparse.R: instead of R/gTMatrix.R
874            * R/Csparse.R: new
875            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
876            * src/Tsparse.c: new; many trivial methods calling cholmod_()
877            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
878                            via cholmod
879    
880    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * R/Auxiliaries.R (non0ind): new function using new C code
883            * src/dgCMatrix.c (compressed_non_0_ij): new utility
884    
885    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
886    
887            * src/chm_common.h: header file required by all C sources that
888            call CHOLMOD functions.  It defines a cholmod_common structure
889            called 'c' whose address is passed as the last argument to
890            (virtually) every CHOLMOD function.
891    
892            * src/Pattern.c: Simple example of the use of CHOLMOD.
893    
894            * src/init.c: initialize and finalize the cholmod_common structure.
895    
896            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
897            LDL and CCOLAMD from the U. of Florida sparse matrix library.
898    
899    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * inst/test-tools.R: new file collecting the utility functions used
902                    in ./tests/*.R
903    
904            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
905            * R/Matrix.R (cbind2): methods for NULL and missing
906    
907    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
908    
909            * R/AllClass.R: new "index" class for "[" and "[<-":
910                    First cut at "symmetricMatrix" and "triangularMatrix"
911            * R/gTMatrix.R (.ind.prep): new function;
912                    Logical and character indexing now work too.
913            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
914            * tests/indexing.R: new, including *.Rout.save
915            * tests/dgTMatrix.R: new
916    
917    2005-08-29  Douglas Bates  <bates@wisc.edu>
918    
919            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
920            indicator pos not being updated.  Also enforced upper triangular
921            for symmetric case.  Need to coerce edges component of elements of
922            edge list - grr! (Why don't they define their classes cleanly?)
923    
924    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/Matrix.R:  added first "[<-" methods; not yet functional
927            * R/denseMatrix.R: ditto
928            * man/Subassign-methods.Rd: new help file for these
929    
930    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * DESCRIPTION (Version): 0.98-6
933    
934            * R/denseMatrix.R: new file for "[" fallback methods for all dense
935            matrices.
936    
937    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
940                    as( <logical>, "matrix")
941    
942            * R/pMatrix.R: coercion to "lgTMatrix"
943    
944            * R/gTMatrix.R: new virtual class to define "[" methods for.
945            * man/gTMatrix-class.Rd:
946            * General slight re-organization of where "[" methods are defined.
947              more to come.
948    
949    2005-08-18  Douglas Bates  <bates@wisc.edu>
950    
951            * DESCRIPTION (Version): 0.98-5  released to CRAN
952    
953            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
954            * .....
955    
956    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
957    
958            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
959            or glmer objects.
960    
961    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
964    
965    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
966    
967            * R/HBMM.R: finish re-writing R-only code.
968    
969    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
970    
971            * man/externalFormats.Rd: move documentation for writeHB and
972            writeMM here.
973    
974            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
975            (suggested by Paul Roecker).
976    
977            * tests/validObj.R (assertError): Comment out test that is failing
978            after recent changes in r-devel.
979    
980    
981    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
982    
983            * R/AllClass.R: intermediate virtual class "denseMatrix"
984            * man/denseMatrix-class.Rd
985            * NAMESPACE: export it, and also export
986            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
987    
988    2005-08-10  Douglas Bates  <bates@wisc.edu>
989    
990            * DESCRIPTION (Version): 0.98-3 to CRAN
991    
992            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
993            matrix_solve code (which was really, really wrong).
994    
995    2005-08-07  Douglas Bates  <bates@wisc.edu>
996    
997            * DESCRIPTION (Version): 0.98-2
998    
999            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1000    
1001            * R/lmer.R (abbrvNms): new
1002            * R/lmer.R (mcmcsamp): allow transformed parameters
1003            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1004            for the Harwell-Boeing and the MatrixMarket formats.
1005    
1006    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * man/dtrMatrix-class.Rd: add examples
1009            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1010    
1011            * TODO: note the dtpMatrix (docu) bug
1012    
1013            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1014            in order to ensure that new as.matrix() is used by old functions,
1015            e.g., svd(), qr(), eigen(), dist(),..;
1016                  apply(), also matplot() or pairs().
1017    
1018    
1019    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1022              add comments about 'control' / lmerControl() arguments
1023    
1024    2005-07-27  Douglas Bates  <bates@wisc.edu>
1025    
1026            * man/sleepstudy.Rd: Added the sleep data set.
1027            * DESCRIPTION (Version): 0.98-1  released to CRAN
1028    
1029    2005-07-12  Douglas Bates  <bates@wisc.edu>
1030            * man/sleepstudy.Rd: Added the sleep data set.
1031    
1032            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1033            .Call calls that were producing spurious output.
1034    
1035    2005-07-05  Douglas Bates  <bates@wisc.edu>
1036    
1037            * R/lmer.R (lmer): stored updated variance component estimates in
1038            mer object for the generalized model.  (Bug reported by Renaud
1039            Lancelot).
1040    
1041    2005-07-03  Douglas Bates  <bates@wisc.edu>
1042    
1043            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1044            unidimensional case.
1045    
1046    2005-06-08  Douglas Bates  <bates@wisc.edu>
1047    
1048            * DESCRIPTION (Version): 0.96-1
1049    
1050            * moved  lmer-class' R and C code moved from lme4 to here
1051    
1052    2005-06-04  Douglas Bates  <bates@wisc.edu>
1053    
1054            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1055            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1056    
1057    2005-06-02  Douglas Bates  <bates@wisc.edu>
1058    
1059            * src/Makefile.win: Forgot to update this when Makefile changed.
1060    
1061    2005-05-11  Douglas Bates  <bates@wisc.edu>
1062    
1063          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1064          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1065    
1066  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1067    
1068          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1069          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 1072 
1072          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1073          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1074    
1075  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1076    
1077          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1078          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1079    
1080  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1081    
1082          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1083          multiplication operation.          multiplication operation.
# Line 30  Line 1090 
1090    
1091          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1092    
1093  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1094    
1095          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1096    
1097          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1098    
1099    
1100  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1101    
1102          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1103    
# Line 46  Line 1106 
1106          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1107          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1108    
1109  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1110    
1111          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1112    
# Line 72  Line 1132 
1132          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1133            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1134    
1135  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1136    
1137          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1138          * ....          * ....
1139    
1140  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1141    
1142          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1143    
# Line 92  Line 1152 
1152            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1153          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1154    
1155  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1156    
1157          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1158    
1159  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1160    
1161          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1162    
1163  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1164    
1165          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1166          the package.          the package.
# Line 148  Line 1208 
1208    
1209          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1210    
1211  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1212    
1213          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1214          for the geMatrix class.          for the geMatrix class.
1215    
1216  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1217    
1218          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1219    
1220          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1221    
1222  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1223    
1224          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1225          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1226    
1227  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1228    
1229          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1230    
1231  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1232    
1233          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1234          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1235    
1236  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1237    
1238          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1239    
1240          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1241          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1242    
1243  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1244    
1245          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1246          no longer used.          no longer used.
# Line 192  Line 1252 
1252          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1253          Fixes part but not all of #15.          Fixes part but not all of #15.
1254    
1255  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1256    
1257          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1258          scalar grouping factors corrected.          scalar grouping factors corrected.
1259    
1260  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1261    
1262          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1263    
1264  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1265    
1266          * 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
1267          .h file can be included.          .h file can be included.
1268    
1269  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1270    
1271          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1272          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1273    
1274          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1275    
1276  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1277    
1278          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1279    
1280  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1281    
1282          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1283    
1284  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1285    
1286          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1287    
1288  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1289    
1290          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1291    
1292  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1293    
1294          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1295          routines.          routines.
1296    
1297  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1298    
1299          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1300    
1301  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1302    
1303          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1304    

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