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revision 726, Thu May 12 14:59:04 2005 UTC revision 1629, Fri Oct 13 12:51:11 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
4            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
5    
6    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
9    
10    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * DESCRIPTION (Version): 0.9975-3
13    
14            * R/diagMatrix.R (bdiag): new function constructing block diagonal
15            (sparse) matrices.
16            * man/bdiag.Rd: docu + examples
17    
18            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
19    
20            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
21            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
22    
23            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
24            that result is sparse or diagonal (and not dense).
25    
26            * man/Subassign-methods.Rd: fix examples
27    
28            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
29            should always return a sparse (and not sometimes a diagonal) matrix.
30    
31    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
34    
35    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * DESCRIPTION (Version): 0.9975-2
38    
39            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
40    
41    2006-10-02  Douglas Bates  <bates@R-project.org>
42    
43            * tests/dg_Matrix.R: Simplify test taking into account new code.
44    
45    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
48    
49            * R/lsTMatrix.R: new files w/ missing methods
50            * R/nsTMatrix.R:  "  'for completeness'
51    
52            * tests/Class+Meth.R: a bit less 'not.ok.classes'
53    
54            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
55    
56    
57    2006-09-28  Douglas Bates  <bates@R-project.org>
58    
59            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
60            included.
61    
62            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
63            Export C-callable functions used in Zt_create in lme4.
64    
65    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * DESCRIPTION (Version): 0.9975-1
68    
69            * tests/simple.R: less checks fail; using NA, found that our
70                    kronecker() is not base-compatible with NA's.
71    
72            * R/dMatrix.R: "Compare" method now implemented for all cases
73    
74            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
75    
76            * man/dtpMatrix-class.Rd: mention length of 'x' slot
77    
78            * src/dtpMatrix.c (dtpMatrix_validate): fix check
79            * src/dspMatrix.c (dspMatrix_validate): ditto
80    
81            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
82              including coercion to [nl]tTMatrix.
83    
84            * R/diagMatrix.R (show): print a header line as for other classes.
85    
86    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * src/Makefile.win (SUBDIRS): fix typo
89    
90    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
93    
94    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
97            symmetric and y missing in R code using %*% (cholmod_aat doesn't
98            accept a symmetric matrix).
99            * tests/group-methods.R: Uncomment test of crossprod applied to
100            lsCMatrix objects.
101    
102    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/AllClass.R (symmetricMatrix): add validity method (available
105            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
106    
107            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
108    
109            * tests/indexing.Rout.save:
110            * tests/indexing.R: additions, mainly for 'lsparse'
111    
112            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
113            case.
114    
115            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
116    
117    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
120                    as 'N' (1-letter - Ok?)
121    
122            * tests/group-methods.R: add test for logical + NAs
123    
124            * R/dMatrix.R ("Compare"): fix to work with NA's
125    
126            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
127    
128            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
129                    which is implemented.
130    
131    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * src/chm_common.c: coerce logical <-> double instead of
134            typecasting;  needed for "l" matrix handling in cholmod.
135    
136            * tests/other-pkgs.R (graph): small extension in "graph" checks.
137    
138            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
139            (Tsp2grNEL): other fixes needed
140    
141    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
144                    Matrices, since "lMatrix", also "lsparseM" can have NA
145            * R/ndenseMatrix.R, etc: new source files
146            * man/nsparseMatrix-classes.Rd, etc: new help files
147            * tests/: adaptions
148            * src/chm_common.c (chm_dense_to_SEXP): and others:
149                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
150            * src/Csparse.c, etc: ditto
151    
152    2006-09-11  Douglas Bates  <bates@R-project.org>
153    
154            * src/Mutils.[ch],init.c inst/include/*.h: Move the
155            alloc_d**Matrix functions to the lme4 package.
156    
157    2006-09-09  Douglas Bates  <bates@R-project.org>
158    
159            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
160            fixed
161    
162    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/lMatrix.R: new
165    
166            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
167    
168            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
169            * man/tcrossprod.Rd: ditto
170    
171    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
174            for exported functions
175            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
176            Remove partitioning algorithms for sparse matrix reordering.  The
177            copyright on the Metis code was problematic and the methods were
178            rarely used.
179            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
180            operations are now done entirely in CHOLMOD code.
181    
182    2006-09-06  Douglas Bates  <bates@R-project.org>
183    
184            * src/Mutils.h: Remove functions that are no longer used.
185    
186    2006-09-04  Douglas Bates  <bates@R-project.org>
187    
188            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
189            * src/DEPS.mkf: update
190    
191    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * created branches/Matrix-for-R-2.3.x;  on trunk: do
194            * DESCRIPTION (Version): 0.9975-0
195            (Depends): R (>= 2.4.0)
196    
197    2006-09-01  Douglas Bates  <bates@R-project.org>
198    
199            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
200    
201    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
204            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
205    
206            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
207    
208    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
211            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
212            * R/dsparseMatrix.R: ditto
213            * R/Csparse.R: ditto
214    
215    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/dMatrix.R (Compare): improve availability of "<", etc
218            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
219    
220    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
223            of a 0-index which was used as 1-index (..hmm)
224    
225            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
226    
227            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
228            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
229            (.is.diagonal): ditto
230    
231            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
232    
233            * R/Matrix.R (Matrix): also work for NA data
234    
235    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
238            in all cases.
239    
240    2006-08-27  Douglas Bates  <bates@R-project.org>
241    
242            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
243            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
244    
245    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
248            subclasses of "ddenseMatrix"
249            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
250            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
251            instead of half dozen specialized ones.
252    
253    2006-08-25  Douglas Bates  <bates@R-project.org>
254    
255            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
256            <tillard@cirad.fr> - ordering standard errors to match effects.
257    
258    2006-08-24  Douglas Bates  <bates@R-project.org>
259    
260            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
261            on R_ldl.
262            * R/lCholCMatrix.R,
263            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
264            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
265            * many files in ./R and ./src: Use more general version of
266            dup_mMatrix_as_dgeMatrix to simplify method definitions.
267            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
268            dtpMatrix, dspMatrix and dppMatrix conversions.
269    
270    
271    2006-08-23  Douglas Bates  <bates@R-project.org>
272    
273            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
274            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
275            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
276            dgeMatrix_crossprod (may need to do this in other places).
277            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
278            generic and method for dsCMatrix.  Use CHOLMOD for chol().
279    
280    2006-08-22  Douglas Bates  <bates@R-project.org>
281    
282            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
283            types of classed Matrices, matrices or numeric or logical vectors.
284            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
285            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
286            to Mutils.h (as an inline) and change name to Matrix_check_class;
287            fixes in as_cholmod_factor and chm_factor_to_SEXP.
288            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
289            dsCMatrix_matrix_solve.  Comment out vestigial functions.
290            * src/Csparse.c: use diag_P and uplo_P macros.
291    
292    2006-08-21  Douglas Bates  <bates@R-project.org>
293    
294            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
295            valgrind.
296            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
297            inverses.
298            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
299            -Wall warnings.
300            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
301            Use dup_mMatrix_as_dgeMatrix.
302    
303    2006-08-20  Douglas Bates  <bates@R-project.org>
304    
305            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
306            * tests/sparseQR.R: Added
307            * man/sparseQR-class.Rd: Document methods for qr.* generics
308            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
309    
310    2006-08-19  Douglas Bates  <bates@R-project.org>
311    
312            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
313            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
314            and qr.fitted.
315            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
316            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
317    
318    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
321            the base version has no "..." argument.
322    
323            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
324    
325            * R/Matrix.R: define and
326            * NAMESPACE: export as.numeric() and as.logical() methods.
327                    Let's hope these do not badly slow down something...
328            Finally export the zapsmall() method.
329    
330    2006-08-17  Douglas Bates  <bates@R-project.org>
331    
332            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
333            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
334            * src/dtCMatrix.c :Remove code that is no longer used
335            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
336    
337    2006-08-14  Douglas Bates  <bates@R-project.org>
338    
339            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
340            Csparse_to_logical and Csparse_symmetric_to_general.
341            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
342            coercion methods between CsparseMatrix and TsparseMatrix.
343    
344    2006-08-14  Douglas Bates  <bates@R-project.org>
345    
346            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
347            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
348            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
349            possible.
350    
351    2006-08-12  Douglas Bates  <bates@R-project.org>
352    
353            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
354              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
355              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
356              generalize conversions between TsparseMatrix, CsparseMatrix,
357              denseMatrix and matrix.  Preserve triangularity property and
358              propagate Dimnames in the easy cases.
359    
360    2006-08-10  Douglas Bates  <bates@R-project.org>
361    
362            * src/lmer.c: adjust checks in glmer_init for S4SXP
363            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
364            before S4SXP but for the wrong reasons.
365    
366    2006-08-08  Douglas Bates  <bates@R-project.org>
367    
368            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
369            Later modified to return the upper triangle only.
370            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
371    
372    2006-08-07  Douglas Bates  <bates@R-project.org>
373    
374            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
375            R-level conversion to a sparse symmetric class.
376            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
377            Remove conversion to sparse symmetric classes (now done in C code).
378    
379    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
382            * man/band.Rd:  adapt the \dontshow{} unit test.
383    
384    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * DESCRIPTION (Version): 0.995-14  for CRAN
387    
388            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
389    
390            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
391            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
392    
393            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
394            * R/Tsparse.R (tril, triu, band): methods
395            * R/dgRMatrix.R (tril, ...):    ditto
396            * man/band.Rd:                  ditto
397    
398    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R (head, tail): directly use utils:::head.matrix
401                    to be up-to-date automatically.
402    
403    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
406    
407            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
408            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
409            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
410            such that the S4 objects are always created by the current version
411            of R and 'Matrix' class definitions.
412    
413    2006-08-01  Douglas Bates  <bates@R-project.org>
414    
415            * R/lmer.R (LMEoptimize method), tests/lmer.R,
416            inst/external/test3comp.rda: Added warnings for convergence on
417            boundary and test cases.
418    
419            * src/lmer.c (mer_postVar): Modified to return the variances that
420            are marginal to the fixed effects, not conditional on them (which
421            is what the bVar slot contents represent).
422    
423    2006-07-31  Douglas Bates  <bates@R-project.org>
424    
425            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
426            function which calls the C function mer_hat_trace2.
427    
428            * man/ranef.Rd: Include description of "postVar" argument and
429            producing a caterpillar plot.
430    
431    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * NAMESPACE:    change  "correlation" to "corMatrix"
434            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
435            * R/dpoMatrix.R: ditto
436            * R/lmer.R:      ditto
437    
438    2006-07-28  Douglas Bates  <bates@R-project.org>
439    
440            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
441            RZXinv slot's contents into a separate internal function that can
442            be used in mer_hat_trace.
443    
444    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
447            via new smart
448            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
449            utility functions.
450    
451    
452    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Csparse.R (tril, triu, band): do return *triangular* classed
455            matrices when appropriate; band() even symmetric ones.
456            (replCmat): extend to potentially all "CsparseMatrix"
457            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
458            allow subassignment for special sparse matrices.
459    
460            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
461    
462            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
463            argument; in glmer_*(): print only if(verbose).
464    
465            speed-optimize a few places by moving REAL(.) out of loops.
466    
467            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
468    
469    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
472                    since that wrongly triggers also for M[ logi , ]
473    
474            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
475            a symmetric matrix that results in a non-symmetric one.
476            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
477    
478            * R/dMatrix.R: make round(M) work as round(M, 0)
479    
480            * R/dgTMatrix.R (image): coordinate system and axis now use
481            1-based indices, not 0-based ones.
482    
483            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
484            * tests/indexing.R: test it.
485    
486            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
487            * man/isSymmetric-methods.Rd: and document it.
488    
489            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
490            * man/SparseM-conv.Rd: docu them
491    
492            * tests/other-pkgs.R: renamed from tests/graph.R and add example
493                    for 'SparseM' conversions
494    
495    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
496    
497            * R/Matrix.R (head): added head() and tail() methods.
498    
499    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * DESCRIPTION (Version): 0.995-12 released to CRAN
502    
503    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * tests/simple.R: add check for correct dsT -> dgT coercion;
506                    add check for correct printing of symmetric sparse matrices.
507    
508            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
509            for sparse symmetric matrices.
510    
511            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
512            diagonal twice.
513    
514    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
515    
516            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
517            being applied to the x slot (detected by Brian Ripley).
518    
519    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
522    
523            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
524    
525    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * src/lgCMatrix.c (lgCMatrix_diag): new function
528            * R/lgCMatrix.R (diag): for new method
529    
530            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
531                 ==> construction of illegal "*gTMatrix" via new() should
532                 now be much less easy:
533            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
534    
535            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
536                    directly.
537            * man/Matrix.Rd: documents it.
538    
539    2006-07-06  Douglas Bates  <bates@R-project.org>
540    
541            * src/pedigree.c (pedigree_inbreeding): Correction in
542            initialization.  This function is not currently being used and is
543            not fully tested.
544    
545            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
546            Introduced the glmer class.  Added code for mcmcmsamp on glmer
547            objects.  Modified validity check on pedigree objects to account
548            for nonparallel patterns of missingness of parents.
549    
550            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
551            class.
552    
553    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/pMatrix.R: coercion pMatrix -> Tsparse
556    
557    2006-06-12  Douglas Bates  <bates@R-project.org>
558    
559            * DESCRIPTION (Version): 0.995-11 released to CRAN
560    
561            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
562            the output from mcmcsamp.
563    
564    2006-06-10  Douglas Bates  <bates@R-project.org>
565    
566            * R/lmer.R (simulestimate): added C code for calculating the trace
567            of the hat matrix.
568    
569    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
572            classes.
573            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
574    
575    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/dgTMatrix.R (colSums): etc. All four of
578            colSums(), rowSums(), colMeans(), rowMeans() now should work for
579            all "Matrices".
580    
581    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
582    
583            * R/lmer.R (panel.ci): Add a reference line at zero and a
584            background grid to the qqmath plot of ranef.lmer.
585    
586    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
587    
588            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
589            grouping factors to be specified in the formula as (1|foo/bar).
590    
591    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
592    
593            * R/lmer.R (findbars and others): Change check of is.numeric to
594            !is.language to resolve the bug reported by Jacob Wegelin.
595    
596            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
597            code to evaluate inbreeding coefficients without calculating T,
598            based on code in Sargolzaei and Iwaisaki's paper.
599    
600    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
603            generic and mer methods for isNested and denomDF. This denomDF was
604            an attempt to emulate that in lme but I don't think that makes
605            sense.  Use the trace of the hat matrix instead.
606    
607    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
610            the C code depending on a slot structure that's no longer valid.
611            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
612    
613    
614    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
615    
616            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
617            of lowerTriMatrix generic and methods to tril (also upper to triu)
618            and added a general band extractor.
619    
620    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * R/pedigree.R (pedigree): Replace sire and dam values outside the
623            allowable range with NAs. Added a corresponding check in the
624            validity check for the pedigree class.
625    
626            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
627            crossprod methods now inherits from symmetricMatrix.
628    
629    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
630    
631            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
632            generics lowerTriMatrix and upperTriMatrix along with methods for
633            the Csparse virtual class.  Also added a C function Csparse_band
634            that implements these methods by calling cholmod_band.
635    
636    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
639            erased when it was NULL.  This led to invalid subselections!
640    
641    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
642    
643            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
644            in method for "t" so as not to lose the unit diagonal property.
645    
646    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
649            and methods.  This is now an option to the ranef method for the
650            mer class.
651    
652            * src/cs_utils.c: Ensure that the nz component is -1 for a
653            compressed column-oriented matrix.  Minor formatting cleanup.
654    
655            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
656            objects.
657    
658    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
661            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
662    
663    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
664    
665            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
666            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
667    
668            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
669            for the dtCMatrix class.
670    
671    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
674            and methods for it.
675    
676    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
679            arguments, such that M %*% 1:6 now works
680            * Tests/matprod.R: test the above
681    
682    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
683    
684            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
685            the ranef.lmer class.
686    
687            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
688            methods to extract the posterior variances from the bVar slot.
689    
690    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
693            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
694    
695            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
696            * tests/simple: (extended)
697    
698            * R/sparseMatrix.R (isTriangular): now using much improved
699            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
700    
701    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
702    
703            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
704            (problem report from Franklin Parlamis).  This should be done
705            generally.
706    
707    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
708    
709            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
710            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
711            update the plot methods.
712    
713    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
714    
715            * R/lmer.R (resid and ranef methods):  Added methods for the
716            "residuals" and "resid" generic but only for linear mixed model
717            fits.  Changed the ranef method to return a list of data frames so
718            that the plot methods now work.
719    
720    2006-03-16  Douglas Bates  <bates@bates2>
721    
722            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
723            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
724    
725            * DESCRIPTION (Date): New release
726    
727    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
730    
731            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
732            * man/KNex.Rd: and other help files
733            * tests/*.R: several ones needed adaption
734            * inst/doc/Comparisons.Rnw: ditto
735    
736    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
739    
740            * tests/indexing.R: tests for new [<- methods for sparse matrices.
741    
742    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
745    
746            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
747    
748    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/dMatrix.R: enable things like  M [ M < 10 ]
751            * R/dgeMatrix.R: implement it
752    
753    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/AllClass.R: define "summary.mer" and "*.lmer"
756            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
757            * R/lmer.R (show): now works with summary()
758    
759    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
760    
761            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
762            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
763                    support the above
764    
765    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
766    
767            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
768            Use glmFit$prior.weights for weights in a glmm.
769            Allow an option usePQL = FALSE to skip the PQL steps for the
770            Laplace method (and, in time, the AGQ method).
771    
772            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
773            into a separate function internal_mer_Xfactor to be able to call
774            it from internal_bhat.
775    
776    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * tests/Class+Meth.R (tstMatrixClass): function for much better
779            testing; now again of all actual classes.
780    
781            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
782                    use macros and define make_d_matrix_* and make_i_matrix_*
783                    where _i_ is for the ldense routines:
784    
785            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
786            * src/ldense.c (lsyMatrix_as_lgeMatrix):
787    
788            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
789    
790    
791    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
794                    many different kinds of matrices.
795            * R/*.R: quite a few new methods were needed for R CMD check with
796                    new Matrix().  Very good for users playing around.
797    
798    
799    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * src/dgeMatrix.c (dMatrix_validate): new
802            * src/Mutils.c (dense_nonpacked_validate): new
803    
804            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
805    
806    
807    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
808    
809            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
810    
811    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
812    
813            * DESCRIPTION (Version): 0.99-6 released to CRAN
814    
815            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
816            segfault in cases with multiple non-nested grouping factors.
817    
818    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
821                    (Depends): also on 'utils'
822    
823            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
824            * R/diagMatrix.R (Diagonal): constructor and methods for
825            diagonal matrices
826    
827            * R/ltTMatrix.R: new "minimal methods"
828    
829    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
832            all methods (and help files).
833    
834    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
837                    for case (dimn.  op  no_dimn.)
838    
839    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
840    
841            * DESCRIPTION (Version): 0.99-2  released to CRAN
842    
843    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
844    
845            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
846            by Julian Faraway.
847    
848    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/Auxiliaries.R (try_as): new utility
851            * R/sparseMatrix.R: use try_as() in coercion to original class
852    
853    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
856    
857    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/Auxiliaries.R (dimNamesCheck): added
860    
861            * R/Matrix.R (as.array), (as.vector): new
862    
863    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
866                    default.
867            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
868                    "pMatrix" now contains "sparseMatrix"
869    
870    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * tests/Class+Meth.R: new tests; t(t(m)) == m
873    
874            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
875    
876            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
877            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
878    
879            * R/dspMatrix.R: typo in "t" method
880    
881    2005-09-18  Douglas Bates  <bates@wisc.edu>
882    
883            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
884            * R/Tsparse.R: instead of R/gTMatrix.R
885            * R/Csparse.R: new
886            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
887            * src/Tsparse.c: new; many trivial methods calling cholmod_()
888            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
889                            via cholmod
890    
891    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/Auxiliaries.R (non0ind): new function using new C code
894            * src/dgCMatrix.c (compressed_non_0_ij): new utility
895    
896    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
897    
898            * src/chm_common.h: header file required by all C sources that
899            call CHOLMOD functions.  It defines a cholmod_common structure
900            called 'c' whose address is passed as the last argument to
901            (virtually) every CHOLMOD function.
902    
903            * src/Pattern.c: Simple example of the use of CHOLMOD.
904    
905            * src/init.c: initialize and finalize the cholmod_common structure.
906    
907            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
908            LDL and CCOLAMD from the U. of Florida sparse matrix library.
909    
910    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * inst/test-tools.R: new file collecting the utility functions used
913                    in ./tests/*.R
914    
915            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
916            * R/Matrix.R (cbind2): methods for NULL and missing
917    
918    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * R/AllClass.R: new "index" class for "[" and "[<-":
921                    First cut at "symmetricMatrix" and "triangularMatrix"
922            * R/gTMatrix.R (.ind.prep): new function;
923                    Logical and character indexing now work too.
924            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
925            * tests/indexing.R: new, including *.Rout.save
926            * tests/dgTMatrix.R: new
927    
928    2005-08-29  Douglas Bates  <bates@wisc.edu>
929    
930            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
931            indicator pos not being updated.  Also enforced upper triangular
932            for symmetric case.  Need to coerce edges component of elements of
933            edge list - grr! (Why don't they define their classes cleanly?)
934    
935    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
936    
937            * R/Matrix.R:  added first "[<-" methods; not yet functional
938            * R/denseMatrix.R: ditto
939            * man/Subassign-methods.Rd: new help file for these
940    
941    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * DESCRIPTION (Version): 0.98-6
944    
945            * R/denseMatrix.R: new file for "[" fallback methods for all dense
946            matrices.
947    
948    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
951                    as( <logical>, "matrix")
952    
953            * R/pMatrix.R: coercion to "lgTMatrix"
954    
955            * R/gTMatrix.R: new virtual class to define "[" methods for.
956            * man/gTMatrix-class.Rd:
957            * General slight re-organization of where "[" methods are defined.
958              more to come.
959    
960    2005-08-18  Douglas Bates  <bates@wisc.edu>
961    
962            * DESCRIPTION (Version): 0.98-5  released to CRAN
963    
964            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
965            * .....
966    
967    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
968    
969            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
970            or glmer objects.
971    
972    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
973    
974            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
975    
976    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
977    
978            * R/HBMM.R: finish re-writing R-only code.
979    
980    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
981    
982            * man/externalFormats.Rd: move documentation for writeHB and
983            writeMM here.
984    
985            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
986            (suggested by Paul Roecker).
987    
988            * tests/validObj.R (assertError): Comment out test that is failing
989            after recent changes in r-devel.
990    
991    
992    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/AllClass.R: intermediate virtual class "denseMatrix"
995            * man/denseMatrix-class.Rd
996            * NAMESPACE: export it, and also export
997            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
998    
999    2005-08-10  Douglas Bates  <bates@wisc.edu>
1000    
1001            * DESCRIPTION (Version): 0.98-3 to CRAN
1002    
1003            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1004            matrix_solve code (which was really, really wrong).
1005    
1006    2005-08-07  Douglas Bates  <bates@wisc.edu>
1007    
1008            * DESCRIPTION (Version): 0.98-2
1009    
1010            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1011    
1012            * R/lmer.R (abbrvNms): new
1013            * R/lmer.R (mcmcsamp): allow transformed parameters
1014            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1015            for the Harwell-Boeing and the MatrixMarket formats.
1016    
1017    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * man/dtrMatrix-class.Rd: add examples
1020            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1021    
1022            * TODO: note the dtpMatrix (docu) bug
1023    
1024            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1025            in order to ensure that new as.matrix() is used by old functions,
1026            e.g., svd(), qr(), eigen(), dist(),..;
1027                  apply(), also matplot() or pairs().
1028    
1029    
1030    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1033              add comments about 'control' / lmerControl() arguments
1034    
1035    2005-07-27  Douglas Bates  <bates@wisc.edu>
1036    
1037            * man/sleepstudy.Rd: Added the sleep data set.
1038            * DESCRIPTION (Version): 0.98-1  released to CRAN
1039    
1040    2005-07-12  Douglas Bates  <bates@wisc.edu>
1041            * man/sleepstudy.Rd: Added the sleep data set.
1042    
1043            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1044            .Call calls that were producing spurious output.
1045    
1046    2005-07-05  Douglas Bates  <bates@wisc.edu>
1047    
1048            * R/lmer.R (lmer): stored updated variance component estimates in
1049            mer object for the generalized model.  (Bug reported by Renaud
1050            Lancelot).
1051    
1052    2005-07-03  Douglas Bates  <bates@wisc.edu>
1053    
1054            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1055            unidimensional case.
1056    
1057    2005-06-08  Douglas Bates  <bates@wisc.edu>
1058    
1059            * DESCRIPTION (Version): 0.96-1
1060    
1061            * moved  lmer-class' R and C code moved from lme4 to here
1062    
1063    2005-06-04  Douglas Bates  <bates@wisc.edu>
1064    
1065            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1066            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1067    
1068    2005-06-02  Douglas Bates  <bates@wisc.edu>
1069    
1070            * src/Makefile.win: Forgot to update this when Makefile changed.
1071    
1072    2005-05-11  Douglas Bates  <bates@wisc.edu>
1073    
1074          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1075          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1076    
1077  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1078    
1079          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1080          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 1083 
1083          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1084          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
1085    
1086  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1087    
1088          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1089          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1090    
1091  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1092    
1093          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1094          multiplication operation.          multiplication operation.
# Line 30  Line 1101 
1101    
1102          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1103    
1104  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1105    
1106          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1107    
1108          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1109    
1110    
1111  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1112    
1113          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1114    
# Line 46  Line 1117 
1117          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1118          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1119    
1120  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1121    
1122          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1123    
# Line 72  Line 1143 
1143          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1144            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1145    
1146  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1147    
1148          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1149          * ....          * ....
1150    
1151  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1152    
1153          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1154    
# Line 92  Line 1163 
1163            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1164          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1165    
1166  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1167    
1168          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1169    
1170  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1171    
1172          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1173    
1174  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1175    
1176          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1177          the package.          the package.
# Line 148  Line 1219 
1219    
1220          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1221    
1222  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1223    
1224          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1225          for the geMatrix class.          for the geMatrix class.
1226    
1227  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1228    
1229          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1230    
1231          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1232    
1233  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1234    
1235          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1236          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1237    
1238  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1239    
1240          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1241    
1242  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1243    
1244          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1245          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1246    
1247  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1248    
1249          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1250    
1251          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1252          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1253    
1254  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1255    
1256          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1257          no longer used.          no longer used.
# Line 192  Line 1263 
1263          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1264          Fixes part but not all of #15.          Fixes part but not all of #15.
1265    
1266  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1267    
1268          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1269          scalar grouping factors corrected.          scalar grouping factors corrected.
1270    
1271  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1272    
1273          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1274    
1275  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1276    
1277          * 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
1278          .h file can be included.          .h file can be included.
1279    
1280  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1281    
1282          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1283          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1284    
1285          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1286    
1287  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1288    
1289          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1290    
1291  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1292    
1293          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1294    
1295  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1296    
1297          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1298    
1299  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1300    
1301          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1302    
1303  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1304    
1305          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1306          routines.          routines.
1307    
1308  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1309    
1310          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1311    
1312  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1313    
1314          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1315    

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