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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1647, Mon Oct 23 12:36:27 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-5 ready for release
4    
5    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
8    
9    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R (corMatrix): add 'validity' check;
12                    comment out unused "LDL" class definition
13            * NAMESPACE: mention, but do not export "LDL" class
14            * R/corMatrix.R: new (simple), needed for R-devel with
15            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
16              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
17    
18    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
21            use Rprintf and R's error handling.
22    
23    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
26            * tests/matprod.R: add tests for the bug fixed.
27    
28    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
31            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
32    
33    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
36    
37    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * DESCRIPTION (Version): 0.9975-3
40    
41            * R/diagMatrix.R (bdiag): new function constructing block diagonal
42            (sparse) matrices.
43            * man/bdiag.Rd: docu + examples
44    
45            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
46    
47            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
48            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
49    
50            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
51            that result is sparse or diagonal (and not dense).
52    
53            * man/Subassign-methods.Rd: fix examples
54    
55            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
56            should always return a sparse (and not sometimes a diagonal) matrix.
57    
58    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
61    
62    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
63    
64            * DESCRIPTION (Version): 0.9975-2
65    
66            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
67    
68    2006-10-02  Douglas Bates  <bates@R-project.org>
69    
70            * tests/dg_Matrix.R: Simplify test taking into account new code.
71    
72    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
75    
76            * R/lsTMatrix.R: new files w/ missing methods
77            * R/nsTMatrix.R:  "  'for completeness'
78    
79            * tests/Class+Meth.R: a bit less 'not.ok.classes'
80    
81            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
82    
83    
84    2006-09-28  Douglas Bates  <bates@R-project.org>
85    
86            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
87            included.
88    
89            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
90            Export C-callable functions used in Zt_create in lme4.
91    
92    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION (Version): 0.9975-1
95    
96            * tests/simple.R: less checks fail; using NA, found that our
97                    kronecker() is not base-compatible with NA's.
98    
99            * R/dMatrix.R: "Compare" method now implemented for all cases
100    
101            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
102    
103            * man/dtpMatrix-class.Rd: mention length of 'x' slot
104    
105            * src/dtpMatrix.c (dtpMatrix_validate): fix check
106            * src/dspMatrix.c (dspMatrix_validate): ditto
107    
108            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
109              including coercion to [nl]tTMatrix.
110    
111            * R/diagMatrix.R (show): print a header line as for other classes.
112    
113    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * src/Makefile.win (SUBDIRS): fix typo
116    
117    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
120    
121    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
124            symmetric and y missing in R code using %*% (cholmod_aat doesn't
125            accept a symmetric matrix).
126            * tests/group-methods.R: Uncomment test of crossprod applied to
127            lsCMatrix objects.
128    
129    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/AllClass.R (symmetricMatrix): add validity method (available
132            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
133    
134            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
135    
136            * tests/indexing.Rout.save:
137            * tests/indexing.R: additions, mainly for 'lsparse'
138    
139            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
140            case.
141    
142            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
143    
144    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
147                    as 'N' (1-letter - Ok?)
148    
149            * tests/group-methods.R: add test for logical + NAs
150    
151            * R/dMatrix.R ("Compare"): fix to work with NA's
152    
153            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
154    
155            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
156                    which is implemented.
157    
158    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * src/chm_common.c: coerce logical <-> double instead of
161            typecasting;  needed for "l" matrix handling in cholmod.
162    
163            * tests/other-pkgs.R (graph): small extension in "graph" checks.
164    
165            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
166            (Tsp2grNEL): other fixes needed
167    
168    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
171                    Matrices, since "lMatrix", also "lsparseM" can have NA
172            * R/ndenseMatrix.R, etc: new source files
173            * man/nsparseMatrix-classes.Rd, etc: new help files
174            * tests/: adaptions
175            * src/chm_common.c (chm_dense_to_SEXP): and others:
176                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
177            * src/Csparse.c, etc: ditto
178    
179    2006-09-11  Douglas Bates  <bates@R-project.org>
180    
181            * src/Mutils.[ch],init.c inst/include/*.h: Move the
182            alloc_d**Matrix functions to the lme4 package.
183    
184    2006-09-09  Douglas Bates  <bates@R-project.org>
185    
186            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
187            fixed
188    
189    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/lMatrix.R: new
192    
193            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
194    
195            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
196            * man/tcrossprod.Rd: ditto
197    
198    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
201            for exported functions
202            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
203            Remove partitioning algorithms for sparse matrix reordering.  The
204            copyright on the Metis code was problematic and the methods were
205            rarely used.
206            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
207            operations are now done entirely in CHOLMOD code.
208    
209    2006-09-06  Douglas Bates  <bates@R-project.org>
210    
211            * src/Mutils.h: Remove functions that are no longer used.
212    
213    2006-09-04  Douglas Bates  <bates@R-project.org>
214    
215            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
216            * src/DEPS.mkf: update
217    
218    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * created branches/Matrix-for-R-2.3.x;  on trunk: do
221            * DESCRIPTION (Version): 0.9975-0
222            (Depends): R (>= 2.4.0)
223    
224    2006-09-01  Douglas Bates  <bates@R-project.org>
225    
226            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
227    
228    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
231            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
232    
233            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
234    
235    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
238            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
239            * R/dsparseMatrix.R: ditto
240            * R/Csparse.R: ditto
241    
242    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/dMatrix.R (Compare): improve availability of "<", etc
245            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
246    
247    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
250            of a 0-index which was used as 1-index (..hmm)
251    
252            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
253    
254            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
255            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
256            (.is.diagonal): ditto
257    
258            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
259    
260            * R/Matrix.R (Matrix): also work for NA data
261    
262    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
265            in all cases.
266    
267    2006-08-27  Douglas Bates  <bates@R-project.org>
268    
269            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
270            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
271    
272    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
275            subclasses of "ddenseMatrix"
276            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
277            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
278            instead of half dozen specialized ones.
279    
280    2006-08-25  Douglas Bates  <bates@R-project.org>
281    
282            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
283            <tillard@cirad.fr> - ordering standard errors to match effects.
284    
285    2006-08-24  Douglas Bates  <bates@R-project.org>
286    
287            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
288            on R_ldl.
289            * R/lCholCMatrix.R,
290            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
291            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
292            * many files in ./R and ./src: Use more general version of
293            dup_mMatrix_as_dgeMatrix to simplify method definitions.
294            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
295            dtpMatrix, dspMatrix and dppMatrix conversions.
296    
297    
298    2006-08-23  Douglas Bates  <bates@R-project.org>
299    
300            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
301            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
302            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
303            dgeMatrix_crossprod (may need to do this in other places).
304            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
305            generic and method for dsCMatrix.  Use CHOLMOD for chol().
306    
307    2006-08-22  Douglas Bates  <bates@R-project.org>
308    
309            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
310            types of classed Matrices, matrices or numeric or logical vectors.
311            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
312            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
313            to Mutils.h (as an inline) and change name to Matrix_check_class;
314            fixes in as_cholmod_factor and chm_factor_to_SEXP.
315            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
316            dsCMatrix_matrix_solve.  Comment out vestigial functions.
317            * src/Csparse.c: use diag_P and uplo_P macros.
318    
319    2006-08-21  Douglas Bates  <bates@R-project.org>
320    
321            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
322            valgrind.
323            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
324            inverses.
325            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
326            -Wall warnings.
327            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
328            Use dup_mMatrix_as_dgeMatrix.
329    
330    2006-08-20  Douglas Bates  <bates@R-project.org>
331    
332            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
333            * tests/sparseQR.R: Added
334            * man/sparseQR-class.Rd: Document methods for qr.* generics
335            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
336    
337    2006-08-19  Douglas Bates  <bates@R-project.org>
338    
339            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
340            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
341            and qr.fitted.
342            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
343            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
344    
345    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
348            the base version has no "..." argument.
349    
350            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
351    
352            * R/Matrix.R: define and
353            * NAMESPACE: export as.numeric() and as.logical() methods.
354                    Let's hope these do not badly slow down something...
355            Finally export the zapsmall() method.
356    
357    2006-08-17  Douglas Bates  <bates@R-project.org>
358    
359            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
360            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
361            * src/dtCMatrix.c :Remove code that is no longer used
362            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
363    
364    2006-08-14  Douglas Bates  <bates@R-project.org>
365    
366            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
367            Csparse_to_logical and Csparse_symmetric_to_general.
368            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
369            coercion methods between CsparseMatrix and TsparseMatrix.
370    
371    2006-08-14  Douglas Bates  <bates@R-project.org>
372    
373            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
374            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
375            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
376            possible.
377    
378    2006-08-12  Douglas Bates  <bates@R-project.org>
379    
380            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
381              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
382              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
383              generalize conversions between TsparseMatrix, CsparseMatrix,
384              denseMatrix and matrix.  Preserve triangularity property and
385              propagate Dimnames in the easy cases.
386    
387    2006-08-10  Douglas Bates  <bates@R-project.org>
388    
389            * src/lmer.c: adjust checks in glmer_init for S4SXP
390            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
391            before S4SXP but for the wrong reasons.
392    
393    2006-08-08  Douglas Bates  <bates@R-project.org>
394    
395            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
396            Later modified to return the upper triangle only.
397            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
398    
399    2006-08-07  Douglas Bates  <bates@R-project.org>
400    
401            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
402            R-level conversion to a sparse symmetric class.
403            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
404            Remove conversion to sparse symmetric classes (now done in C code).
405    
406    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
409            * man/band.Rd:  adapt the \dontshow{} unit test.
410    
411    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * DESCRIPTION (Version): 0.995-14  for CRAN
414    
415            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
416    
417            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
418            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
419    
420            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
421            * R/Tsparse.R (tril, triu, band): methods
422            * R/dgRMatrix.R (tril, ...):    ditto
423            * man/band.Rd:                  ditto
424    
425    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Matrix.R (head, tail): directly use utils:::head.matrix
428                    to be up-to-date automatically.
429    
430    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
433    
434            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
435            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
436            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
437            such that the S4 objects are always created by the current version
438            of R and 'Matrix' class definitions.
439    
440    2006-08-01  Douglas Bates  <bates@R-project.org>
441    
442            * R/lmer.R (LMEoptimize method), tests/lmer.R,
443            inst/external/test3comp.rda: Added warnings for convergence on
444            boundary and test cases.
445    
446            * src/lmer.c (mer_postVar): Modified to return the variances that
447            are marginal to the fixed effects, not conditional on them (which
448            is what the bVar slot contents represent).
449    
450    2006-07-31  Douglas Bates  <bates@R-project.org>
451    
452            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
453            function which calls the C function mer_hat_trace2.
454    
455            * man/ranef.Rd: Include description of "postVar" argument and
456            producing a caterpillar plot.
457    
458    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * NAMESPACE:    change  "correlation" to "corMatrix"
461            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
462            * R/dpoMatrix.R: ditto
463            * R/lmer.R:      ditto
464    
465    2006-07-28  Douglas Bates  <bates@R-project.org>
466    
467            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
468            RZXinv slot's contents into a separate internal function that can
469            be used in mer_hat_trace.
470    
471    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
474            via new smart
475            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
476            utility functions.
477    
478    
479    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/Csparse.R (tril, triu, band): do return *triangular* classed
482            matrices when appropriate; band() even symmetric ones.
483            (replCmat): extend to potentially all "CsparseMatrix"
484            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
485            allow subassignment for special sparse matrices.
486    
487            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
488    
489            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
490            argument; in glmer_*(): print only if(verbose).
491    
492            speed-optimize a few places by moving REAL(.) out of loops.
493    
494            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
495    
496    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
499                    since that wrongly triggers also for M[ logi , ]
500    
501            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
502            a symmetric matrix that results in a non-symmetric one.
503            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
504    
505            * R/dMatrix.R: make round(M) work as round(M, 0)
506    
507            * R/dgTMatrix.R (image): coordinate system and axis now use
508            1-based indices, not 0-based ones.
509    
510            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
511            * tests/indexing.R: test it.
512    
513            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
514            * man/isSymmetric-methods.Rd: and document it.
515    
516            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
517            * man/SparseM-conv.Rd: docu them
518    
519            * tests/other-pkgs.R: renamed from tests/graph.R and add example
520                    for 'SparseM' conversions
521    
522    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
523    
524            * R/Matrix.R (head): added head() and tail() methods.
525    
526    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * DESCRIPTION (Version): 0.995-12 released to CRAN
529    
530    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * tests/simple.R: add check for correct dsT -> dgT coercion;
533                    add check for correct printing of symmetric sparse matrices.
534    
535            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
536            for sparse symmetric matrices.
537    
538            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
539            diagonal twice.
540    
541    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
542    
543            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
544            being applied to the x slot (detected by Brian Ripley).
545    
546    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
549    
550            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
551    
552    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * src/lgCMatrix.c (lgCMatrix_diag): new function
555            * R/lgCMatrix.R (diag): for new method
556    
557            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
558                 ==> construction of illegal "*gTMatrix" via new() should
559                 now be much less easy:
560            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
561    
562            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
563                    directly.
564            * man/Matrix.Rd: documents it.
565    
566    2006-07-06  Douglas Bates  <bates@R-project.org>
567    
568            * src/pedigree.c (pedigree_inbreeding): Correction in
569            initialization.  This function is not currently being used and is
570            not fully tested.
571    
572            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
573            Introduced the glmer class.  Added code for mcmcmsamp on glmer
574            objects.  Modified validity check on pedigree objects to account
575            for nonparallel patterns of missingness of parents.
576    
577            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
578            class.
579    
580    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/pMatrix.R: coercion pMatrix -> Tsparse
583    
584    2006-06-12  Douglas Bates  <bates@R-project.org>
585    
586            * DESCRIPTION (Version): 0.995-11 released to CRAN
587    
588            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
589            the output from mcmcsamp.
590    
591    2006-06-10  Douglas Bates  <bates@R-project.org>
592    
593            * R/lmer.R (simulestimate): added C code for calculating the trace
594            of the hat matrix.
595    
596    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
599            classes.
600            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
601    
602    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/dgTMatrix.R (colSums): etc. All four of
605            colSums(), rowSums(), colMeans(), rowMeans() now should work for
606            all "Matrices".
607    
608    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
609    
610            * R/lmer.R (panel.ci): Add a reference line at zero and a
611            background grid to the qqmath plot of ranef.lmer.
612    
613    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
614    
615            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
616            grouping factors to be specified in the formula as (1|foo/bar).
617    
618    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
619    
620            * R/lmer.R (findbars and others): Change check of is.numeric to
621            !is.language to resolve the bug reported by Jacob Wegelin.
622    
623            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
624            code to evaluate inbreeding coefficients without calculating T,
625            based on code in Sargolzaei and Iwaisaki's paper.
626    
627    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
628    
629            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
630            generic and mer methods for isNested and denomDF. This denomDF was
631            an attempt to emulate that in lme but I don't think that makes
632            sense.  Use the trace of the hat matrix instead.
633    
634    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
637            the C code depending on a slot structure that's no longer valid.
638            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
639    
640    
641    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
642    
643            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
644            of lowerTriMatrix generic and methods to tril (also upper to triu)
645            and added a general band extractor.
646    
647    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
648    
649            * R/pedigree.R (pedigree): Replace sire and dam values outside the
650            allowable range with NAs. Added a corresponding check in the
651            validity check for the pedigree class.
652    
653            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
654            crossprod methods now inherits from symmetricMatrix.
655    
656    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
657    
658            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
659            generics lowerTriMatrix and upperTriMatrix along with methods for
660            the Csparse virtual class.  Also added a C function Csparse_band
661            that implements these methods by calling cholmod_band.
662    
663    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
666            erased when it was NULL.  This led to invalid subselections!
667    
668    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
669    
670            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
671            in method for "t" so as not to lose the unit diagonal property.
672    
673    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
674    
675            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
676            and methods.  This is now an option to the ranef method for the
677            mer class.
678    
679            * src/cs_utils.c: Ensure that the nz component is -1 for a
680            compressed column-oriented matrix.  Minor formatting cleanup.
681    
682            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
683            objects.
684    
685    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
688            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
689    
690    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
691    
692            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
693            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
694    
695            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
696            for the dtCMatrix class.
697    
698    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
699    
700            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
701            and methods for it.
702    
703    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
706            arguments, such that M %*% 1:6 now works
707            * Tests/matprod.R: test the above
708    
709    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
710    
711            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
712            the ranef.lmer class.
713    
714            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
715            methods to extract the posterior variances from the bVar slot.
716    
717    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
720            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
721    
722            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
723            * tests/simple: (extended)
724    
725            * R/sparseMatrix.R (isTriangular): now using much improved
726            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
727    
728    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
729    
730            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
731            (problem report from Franklin Parlamis).  This should be done
732            generally.
733    
734    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
735    
736            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
737            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
738            update the plot methods.
739    
740    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
741    
742            * R/lmer.R (resid and ranef methods):  Added methods for the
743            "residuals" and "resid" generic but only for linear mixed model
744            fits.  Changed the ranef method to return a list of data frames so
745            that the plot methods now work.
746    
747    2006-03-16  Douglas Bates  <bates@bates2>
748    
749            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
750            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
751    
752            * DESCRIPTION (Date): New release
753    
754    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
757    
758            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
759            * man/KNex.Rd: and other help files
760            * tests/*.R: several ones needed adaption
761            * inst/doc/Comparisons.Rnw: ditto
762    
763    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
766    
767            * tests/indexing.R: tests for new [<- methods for sparse matrices.
768    
769    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
772    
773            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
774    
775    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/dMatrix.R: enable things like  M [ M < 10 ]
778            * R/dgeMatrix.R: implement it
779    
780    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * R/AllClass.R: define "summary.mer" and "*.lmer"
783            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
784            * R/lmer.R (show): now works with summary()
785    
786    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
789            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
790                    support the above
791    
792    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
793    
794            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
795            Use glmFit$prior.weights for weights in a glmm.
796            Allow an option usePQL = FALSE to skip the PQL steps for the
797            Laplace method (and, in time, the AGQ method).
798    
799            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
800            into a separate function internal_mer_Xfactor to be able to call
801            it from internal_bhat.
802    
803    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * tests/Class+Meth.R (tstMatrixClass): function for much better
806            testing; now again of all actual classes.
807    
808            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
809                    use macros and define make_d_matrix_* and make_i_matrix_*
810                    where _i_ is for the ldense routines:
811    
812            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
813            * src/ldense.c (lsyMatrix_as_lgeMatrix):
814    
815            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
816    
817    
818    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
821                    many different kinds of matrices.
822            * R/*.R: quite a few new methods were needed for R CMD check with
823                    new Matrix().  Very good for users playing around.
824    
825    
826    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * src/dgeMatrix.c (dMatrix_validate): new
829            * src/Mutils.c (dense_nonpacked_validate): new
830    
831            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
832    
833    
834    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
835    
836            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
837    
838    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
839    
840            * DESCRIPTION (Version): 0.99-6 released to CRAN
841    
842            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
843            segfault in cases with multiple non-nested grouping factors.
844    
845    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
848                    (Depends): also on 'utils'
849    
850            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
851            * R/diagMatrix.R (Diagonal): constructor and methods for
852            diagonal matrices
853    
854            * R/ltTMatrix.R: new "minimal methods"
855    
856    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
859            all methods (and help files).
860    
861    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
864                    for case (dimn.  op  no_dimn.)
865    
866    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
867    
868            * DESCRIPTION (Version): 0.99-2  released to CRAN
869    
870    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
871    
872            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
873            by Julian Faraway.
874    
875    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * R/Auxiliaries.R (try_as): new utility
878            * R/sparseMatrix.R: use try_as() in coercion to original class
879    
880    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
883    
884    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * R/Auxiliaries.R (dimNamesCheck): added
887    
888            * R/Matrix.R (as.array), (as.vector): new
889    
890    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
893                    default.
894            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
895                    "pMatrix" now contains "sparseMatrix"
896    
897    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * tests/Class+Meth.R: new tests; t(t(m)) == m
900    
901            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
902    
903            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
904            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
905    
906            * R/dspMatrix.R: typo in "t" method
907    
908    2005-09-18  Douglas Bates  <bates@wisc.edu>
909    
910            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
911            * R/Tsparse.R: instead of R/gTMatrix.R
912            * R/Csparse.R: new
913            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
914            * src/Tsparse.c: new; many trivial methods calling cholmod_()
915            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
916                            via cholmod
917    
918    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * R/Auxiliaries.R (non0ind): new function using new C code
921            * src/dgCMatrix.c (compressed_non_0_ij): new utility
922    
923    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
924    
925            * src/chm_common.h: header file required by all C sources that
926            call CHOLMOD functions.  It defines a cholmod_common structure
927            called 'c' whose address is passed as the last argument to
928            (virtually) every CHOLMOD function.
929    
930            * src/Pattern.c: Simple example of the use of CHOLMOD.
931    
932            * src/init.c: initialize and finalize the cholmod_common structure.
933    
934            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
935            LDL and CCOLAMD from the U. of Florida sparse matrix library.
936    
937    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * inst/test-tools.R: new file collecting the utility functions used
940                    in ./tests/*.R
941    
942            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
943            * R/Matrix.R (cbind2): methods for NULL and missing
944    
945    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * R/AllClass.R: new "index" class for "[" and "[<-":
948                    First cut at "symmetricMatrix" and "triangularMatrix"
949            * R/gTMatrix.R (.ind.prep): new function;
950                    Logical and character indexing now work too.
951            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
952            * tests/indexing.R: new, including *.Rout.save
953            * tests/dgTMatrix.R: new
954    
955    2005-08-29  Douglas Bates  <bates@wisc.edu>
956    
957            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
958            indicator pos not being updated.  Also enforced upper triangular
959            for symmetric case.  Need to coerce edges component of elements of
960            edge list - grr! (Why don't they define their classes cleanly?)
961    
962    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * R/Matrix.R:  added first "[<-" methods; not yet functional
965            * R/denseMatrix.R: ditto
966            * man/Subassign-methods.Rd: new help file for these
967    
968    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * DESCRIPTION (Version): 0.98-6
971    
972            * R/denseMatrix.R: new file for "[" fallback methods for all dense
973            matrices.
974    
975    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
978                    as( <logical>, "matrix")
979    
980            * R/pMatrix.R: coercion to "lgTMatrix"
981    
982            * R/gTMatrix.R: new virtual class to define "[" methods for.
983            * man/gTMatrix-class.Rd:
984            * General slight re-organization of where "[" methods are defined.
985              more to come.
986    
987    2005-08-18  Douglas Bates  <bates@wisc.edu>
988    
989            * DESCRIPTION (Version): 0.98-5  released to CRAN
990    
991            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
992            * .....
993    
994    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
995    
996            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
997            or glmer objects.
998    
999    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1002    
1003    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1004    
1005            * R/HBMM.R: finish re-writing R-only code.
1006    
1007    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1008    
1009            * man/externalFormats.Rd: move documentation for writeHB and
1010            writeMM here.
1011    
1012            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1013            (suggested by Paul Roecker).
1014    
1015            * tests/validObj.R (assertError): Comment out test that is failing
1016            after recent changes in r-devel.
1017    
1018    
1019    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/AllClass.R: intermediate virtual class "denseMatrix"
1022            * man/denseMatrix-class.Rd
1023            * NAMESPACE: export it, and also export
1024            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1025    
1026    2005-08-10  Douglas Bates  <bates@wisc.edu>
1027    
1028            * DESCRIPTION (Version): 0.98-3 to CRAN
1029    
1030            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1031            matrix_solve code (which was really, really wrong).
1032    
1033    2005-08-07  Douglas Bates  <bates@wisc.edu>
1034    
1035            * DESCRIPTION (Version): 0.98-2
1036    
1037            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1038    
1039            * R/lmer.R (abbrvNms): new
1040            * R/lmer.R (mcmcsamp): allow transformed parameters
1041            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1042            for the Harwell-Boeing and the MatrixMarket formats.
1043    
1044    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1045    
1046            * man/dtrMatrix-class.Rd: add examples
1047            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1048    
1049            * TODO: note the dtpMatrix (docu) bug
1050    
1051            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1052            in order to ensure that new as.matrix() is used by old functions,
1053            e.g., svd(), qr(), eigen(), dist(),..;
1054                  apply(), also matplot() or pairs().
1055    
1056    
1057    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1058    
1059            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1060              add comments about 'control' / lmerControl() arguments
1061    
1062    2005-07-27  Douglas Bates  <bates@wisc.edu>
1063    
1064            * man/sleepstudy.Rd: Added the sleep data set.
1065            * DESCRIPTION (Version): 0.98-1  released to CRAN
1066    
1067    2005-07-12  Douglas Bates  <bates@wisc.edu>
1068            * man/sleepstudy.Rd: Added the sleep data set.
1069    
1070            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1071            .Call calls that were producing spurious output.
1072    
1073    2005-07-05  Douglas Bates  <bates@wisc.edu>
1074    
1075            * R/lmer.R (lmer): stored updated variance component estimates in
1076            mer object for the generalized model.  (Bug reported by Renaud
1077            Lancelot).
1078    
1079    2005-07-03  Douglas Bates  <bates@wisc.edu>
1080    
1081            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1082            unidimensional case.
1083    
1084    2005-06-08  Douglas Bates  <bates@wisc.edu>
1085    
1086            * DESCRIPTION (Version): 0.96-1
1087    
1088            * moved  lmer-class' R and C code moved from lme4 to here
1089    
1090    2005-06-04  Douglas Bates  <bates@wisc.edu>
1091    
1092            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1093            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1094    
1095    2005-06-02  Douglas Bates  <bates@wisc.edu>
1096    
1097            * src/Makefile.win: Forgot to update this when Makefile changed.
1098    
1099    2005-05-11  Douglas Bates  <bates@wisc.edu>
1100    
1101            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1102            bug reported by Kurt Hornik and Michael Hahsler.
1103    
1104    2005-05-10  Douglas Bates  <bates@wisc.edu>
1105    
1106            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1107            logical sparse matrices.  These will also be used in the symbolic
1108            analysis for lmer objects.
1109    
1110            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1111            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1112    
1113    2005-05-06  Douglas Bates  <bates@wisc.edu>
1114    
1115            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1116            colMeans, colSums, rowMeans and rowSums.
1117    
1118    2005-04-18  Douglas Bates  <bates@wisc.edu>
1119    
1120            * src/lgCMatrix.[ch]: code for _validate method and stub for
1121            multiplication operation.
1122    
1123            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1124            to dgetrs.
1125    
1126            * src/init.c: Fix cut-and-paste error in definition of
1127            dgeMatrix_matrix_solve
1128    
1129            * src/{many files}: Tighten code by using ALLOC_SLOT.
1130    
1131    2005-04-15  Douglas Bates  <bates@wisc.edu>
1132    
1133            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1134    
1135            * DESCRIPTION: Eliminate import of stats.
1136    
1137    
1138    2005-04-06  Douglas Bates  <bates@wisc.edu>
1139    
1140            * R/AllClass.R : add logical sparse matrix classes
1141    
1142    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1143    
1144            * R/dgTMatrix.R: add "[" method for triplet matrices
1145            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1146    
1147    2005-03-31  Douglas Bates  <bates@wisc.edu>
1148    
1149            * DESCRIPTION (Version): release 0.95-5 to CRAN
1150    
1151            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1152            * R/sparseMatrix.R: %*%, crossprod()
1153            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1154            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1155            * src/lmer.c (lmer_fitted): fix thinko
1156    
1157    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1158    
1159            * R/AllClass.R: add two virtual sparse classes ``on top''
1160    
1161    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1164                    correspondingly fix examples and tests/ since new()
1165                    doesn't work for virtual classes.
1166    
1167    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1168    
1169            * R/Matrix.R (as.matrix): method and one for unname()
1170            * tests/dpoMatrix.R: tests should now be less platform dependent;
1171              also run for R 2.1.0; using as.matrix()
1172    
1173    2005-03-15  Douglas Bates  <bates@wisc.edu>
1174    
1175            * R/pMatrix.R: "pMatrix" class added
1176            * ....
1177    
1178    2005-03-14  Douglas Bates  <bates@wisc.edu>
1179    
1180            * R/dtpMatrix.R: Add unpack method and an example.
1181    
1182            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1183            of general symmetric matrices and associated S4 methods.
1184    
1185    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1186            +
1187    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1188    
1189            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1190              crossprod() and "%*%" methods added; tests, too.
1191            * tests/matprod.R: new, for testing these
1192    
1193    2005-03-03  Douglas Bates  <bates@wisc.edu>
1194    
1195            * src/lmer.c (lmer_fitted): Added.
1196    
1197    2005-03-02  Douglas Bates  <bates@wisc.edu>
1198    
1199            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1200    
1201    2005-02-28  Douglas Bates  <bates@wisc.edu>
1202    
1203            * src/*.c,po/,inst/po: Internationalization and localization of
1204            the package.
1205    
1206            * src/ldl.[ch]: Removed these as their contents are referenced in the
1207            R_ldl.c file.
1208    
1209            * src/flame.[ch]: Removed these source files.
1210    
1211            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1212    
1213            * src/LU.[ch],src/init.c: absorb in factorizations
1214    
1215            * src/Mutils.h: prepare for internationalization
1216    
1217            * src/cblas.h: move the enum definitions to Mutils.h and remove
1218            this file
1219    
1220    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1221    
1222            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1223    
1224            * R/dtrMatrix.R: fix t() method
1225    
1226            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1227            * NAMESPACE: export them (and import generics from "methods")
1228            * tests/group-methods.R : and test them.
1229    
1230            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1231            border case
1232    
1233    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1234    
1235            * DESCRIPTION (Version): 0.95-2  released to CRAN
1236    
1237            * src/dgBCMatrix.c:
1238            * src/lmer.c: many changes
1239            * ...
1240    
1241    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1242    
1243            * R/Matrix.R: add more sophisticated show() method.
1244    
1245    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1246    
1247            * */* : almost complete reorganization of classes.
1248    
1249    2005-01-26  Douglas Bates  <bates@wisc.edu>
1250    
1251            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1252            for the geMatrix class.
1253    
1254    2005-01-24  Douglas Bates  <bates@wisc.edu>
1255    
1256            * src/Makefile (clean): Remove *.a and *.so
1257    
1258            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1259    
1260    2005-01-23  Douglas Bates  <bates@wisc.edu>
1261    
1262            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1263            had an effect in cases with more than 2 grouping factors.
1264    
1265    2005-01-03  Douglas Bates  <bates@wisc.edu>
1266    
1267            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1268    
1269    2004-12-23  Douglas Bates  <bates@wisc.edu>
1270    
1271            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1272            and R_useDynamicSymbols (suggested by B.D.Ripley).
1273    
1274    2004-12-14  Douglas Bates  <bates@wisc.edu>
1275    
1276            * R/sscMatrix.R: Add determinant methods
1277    
1278            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1279            for tripletMatrix to matrix.
1280    
1281    2004-12-13  Douglas Bates  <bates@wisc.edu>
1282    
1283            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1284            no longer used.
1285    
1286          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1287          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1290 
1290          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1291          Fixes part but not all of #15.          Fixes part but not all of #15.
1292    
1293  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1294    
1295          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1296          scalar grouping factors corrected.          scalar grouping factors corrected.
1297    
1298  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1299    
1300          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1301    
1302  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1303    
1304          * 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
1305          .h file can be included.          .h file can be included.
1306    
1307  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1308    
1309          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1310          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1311    
1312          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1313    
1314  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1315    
1316          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1317    
1318  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1319    
1320          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1321    
1322  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1323    
1324          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1325    
1326  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1327    
1328          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1329    
1330  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1331    
1332          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1333          routines.          routines.
1334    
1335  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1336    
1337          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1338    
1339  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1340    
1341          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1342    

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