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revision 1264, Mon May 15 21:05:20 2006 UTC revision 1624, Wed Oct 11 15:00:11 2006 UTC
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1    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/dgCMatrix.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>  2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638          * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got          * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
# Line 96  Line 731 
731          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
732          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
733          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
734          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
735    
736  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
# Line 300  Line 935 
935  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
936    
937          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
938          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
939          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
940    
941  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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