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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1635, Tue Oct 17 21:21:44 2006 UTC
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1    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
4            * tests/matprod.R: add tests for the bug fixed.
5    
6    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
9            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
10    
11    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
14    
15    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Version): 0.9975-3
18    
19            * R/diagMatrix.R (bdiag): new function constructing block diagonal
20            (sparse) matrices.
21            * man/bdiag.Rd: docu + examples
22    
23            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
24    
25            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
26            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
27    
28            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
29            that result is sparse or diagonal (and not dense).
30    
31            * man/Subassign-methods.Rd: fix examples
32    
33            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
34            should always return a sparse (and not sometimes a diagonal) matrix.
35    
36    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
39    
40    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * DESCRIPTION (Version): 0.9975-2
43    
44            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
45    
46    2006-10-02  Douglas Bates  <bates@R-project.org>
47    
48            * tests/dg_Matrix.R: Simplify test taking into account new code.
49    
50    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
53    
54            * R/lsTMatrix.R: new files w/ missing methods
55            * R/nsTMatrix.R:  "  'for completeness'
56    
57            * tests/Class+Meth.R: a bit less 'not.ok.classes'
58    
59            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
60    
61    
62    2006-09-28  Douglas Bates  <bates@R-project.org>
63    
64            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
65            included.
66    
67            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
68            Export C-callable functions used in Zt_create in lme4.
69    
70    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Version): 0.9975-1
73    
74            * tests/simple.R: less checks fail; using NA, found that our
75                    kronecker() is not base-compatible with NA's.
76    
77            * R/dMatrix.R: "Compare" method now implemented for all cases
78    
79            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
80    
81            * man/dtpMatrix-class.Rd: mention length of 'x' slot
82    
83            * src/dtpMatrix.c (dtpMatrix_validate): fix check
84            * src/dspMatrix.c (dspMatrix_validate): ditto
85    
86            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
87              including coercion to [nl]tTMatrix.
88    
89            * R/diagMatrix.R (show): print a header line as for other classes.
90    
91    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * src/Makefile.win (SUBDIRS): fix typo
94    
95    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
98    
99    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
100    
101            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
102            symmetric and y missing in R code using %*% (cholmod_aat doesn't
103            accept a symmetric matrix).
104            * tests/group-methods.R: Uncomment test of crossprod applied to
105            lsCMatrix objects.
106    
107    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/AllClass.R (symmetricMatrix): add validity method (available
110            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
111    
112            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
113    
114            * tests/indexing.Rout.save:
115            * tests/indexing.R: additions, mainly for 'lsparse'
116    
117            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
118            case.
119    
120            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
121    
122    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
125                    as 'N' (1-letter - Ok?)
126    
127            * tests/group-methods.R: add test for logical + NAs
128    
129            * R/dMatrix.R ("Compare"): fix to work with NA's
130    
131            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
132    
133            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
134                    which is implemented.
135    
136    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/chm_common.c: coerce logical <-> double instead of
139            typecasting;  needed for "l" matrix handling in cholmod.
140    
141            * tests/other-pkgs.R (graph): small extension in "graph" checks.
142    
143            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
144            (Tsp2grNEL): other fixes needed
145    
146    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
149                    Matrices, since "lMatrix", also "lsparseM" can have NA
150            * R/ndenseMatrix.R, etc: new source files
151            * man/nsparseMatrix-classes.Rd, etc: new help files
152            * tests/: adaptions
153            * src/chm_common.c (chm_dense_to_SEXP): and others:
154                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
155            * src/Csparse.c, etc: ditto
156    
157    2006-09-11  Douglas Bates  <bates@R-project.org>
158    
159            * src/Mutils.[ch],init.c inst/include/*.h: Move the
160            alloc_d**Matrix functions to the lme4 package.
161    
162    2006-09-09  Douglas Bates  <bates@R-project.org>
163    
164            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
165            fixed
166    
167    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/lMatrix.R: new
170    
171            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
172    
173            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
174            * man/tcrossprod.Rd: ditto
175    
176    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
177    
178            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
179            for exported functions
180            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
181            Remove partitioning algorithms for sparse matrix reordering.  The
182            copyright on the Metis code was problematic and the methods were
183            rarely used.
184            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
185            operations are now done entirely in CHOLMOD code.
186    
187    2006-09-06  Douglas Bates  <bates@R-project.org>
188    
189            * src/Mutils.h: Remove functions that are no longer used.
190    
191    2006-09-04  Douglas Bates  <bates@R-project.org>
192    
193            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
194            * src/DEPS.mkf: update
195    
196    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * created branches/Matrix-for-R-2.3.x;  on trunk: do
199            * DESCRIPTION (Version): 0.9975-0
200            (Depends): R (>= 2.4.0)
201    
202    2006-09-01  Douglas Bates  <bates@R-project.org>
203    
204            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
205    
206    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
209            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
210    
211            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
212    
213    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
216            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
217            * R/dsparseMatrix.R: ditto
218            * R/Csparse.R: ditto
219    
220    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/dMatrix.R (Compare): improve availability of "<", etc
223            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
224    
225    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
228            of a 0-index which was used as 1-index (..hmm)
229    
230            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
231    
232            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
233            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
234            (.is.diagonal): ditto
235    
236            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
237    
238            * R/Matrix.R (Matrix): also work for NA data
239    
240    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
243            in all cases.
244    
245    2006-08-27  Douglas Bates  <bates@R-project.org>
246    
247            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
248            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
249    
250    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
253            subclasses of "ddenseMatrix"
254            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
255            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
256            instead of half dozen specialized ones.
257    
258    2006-08-25  Douglas Bates  <bates@R-project.org>
259    
260            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
261            <tillard@cirad.fr> - ordering standard errors to match effects.
262    
263    2006-08-24  Douglas Bates  <bates@R-project.org>
264    
265            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
266            on R_ldl.
267            * R/lCholCMatrix.R,
268            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
269            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
270            * many files in ./R and ./src: Use more general version of
271            dup_mMatrix_as_dgeMatrix to simplify method definitions.
272            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
273            dtpMatrix, dspMatrix and dppMatrix conversions.
274    
275    
276    2006-08-23  Douglas Bates  <bates@R-project.org>
277    
278            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
279            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
280            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
281            dgeMatrix_crossprod (may need to do this in other places).
282            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
283            generic and method for dsCMatrix.  Use CHOLMOD for chol().
284    
285    2006-08-22  Douglas Bates  <bates@R-project.org>
286    
287            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
288            types of classed Matrices, matrices or numeric or logical vectors.
289            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
290            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
291            to Mutils.h (as an inline) and change name to Matrix_check_class;
292            fixes in as_cholmod_factor and chm_factor_to_SEXP.
293            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
294            dsCMatrix_matrix_solve.  Comment out vestigial functions.
295            * src/Csparse.c: use diag_P and uplo_P macros.
296    
297    2006-08-21  Douglas Bates  <bates@R-project.org>
298    
299            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
300            valgrind.
301            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
302            inverses.
303            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
304            -Wall warnings.
305            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
306            Use dup_mMatrix_as_dgeMatrix.
307    
308    2006-08-20  Douglas Bates  <bates@R-project.org>
309    
310            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
311            * tests/sparseQR.R: Added
312            * man/sparseQR-class.Rd: Document methods for qr.* generics
313            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
314    
315    2006-08-19  Douglas Bates  <bates@R-project.org>
316    
317            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
318            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
319            and qr.fitted.
320            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
321            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
322    
323    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
326            the base version has no "..." argument.
327    
328            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
329    
330            * R/Matrix.R: define and
331            * NAMESPACE: export as.numeric() and as.logical() methods.
332                    Let's hope these do not badly slow down something...
333            Finally export the zapsmall() method.
334    
335    2006-08-17  Douglas Bates  <bates@R-project.org>
336    
337            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
338            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
339            * src/dtCMatrix.c :Remove code that is no longer used
340            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
341    
342    2006-08-14  Douglas Bates  <bates@R-project.org>
343    
344            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
345            Csparse_to_logical and Csparse_symmetric_to_general.
346            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
347            coercion methods between CsparseMatrix and TsparseMatrix.
348    
349    2006-08-14  Douglas Bates  <bates@R-project.org>
350    
351            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
352            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
353            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
354            possible.
355    
356    2006-08-12  Douglas Bates  <bates@R-project.org>
357    
358            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
359              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
360              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
361              generalize conversions between TsparseMatrix, CsparseMatrix,
362              denseMatrix and matrix.  Preserve triangularity property and
363              propagate Dimnames in the easy cases.
364    
365    2006-08-10  Douglas Bates  <bates@R-project.org>
366    
367            * src/lmer.c: adjust checks in glmer_init for S4SXP
368            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
369            before S4SXP but for the wrong reasons.
370    
371    2006-08-08  Douglas Bates  <bates@R-project.org>
372    
373            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
374            Later modified to return the upper triangle only.
375            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
376    
377    2006-08-07  Douglas Bates  <bates@R-project.org>
378    
379            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
380            R-level conversion to a sparse symmetric class.
381            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
382            Remove conversion to sparse symmetric classes (now done in C code).
383    
384    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
387            * man/band.Rd:  adapt the \dontshow{} unit test.
388    
389    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * DESCRIPTION (Version): 0.995-14  for CRAN
392    
393            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
394    
395            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
396            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
397    
398            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
399            * R/Tsparse.R (tril, triu, band): methods
400            * R/dgRMatrix.R (tril, ...):    ditto
401            * man/band.Rd:                  ditto
402    
403    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/Matrix.R (head, tail): directly use utils:::head.matrix
406                    to be up-to-date automatically.
407    
408    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
411    
412            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
413            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
414            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
415            such that the S4 objects are always created by the current version
416            of R and 'Matrix' class definitions.
417    
418    2006-08-01  Douglas Bates  <bates@R-project.org>
419    
420            * R/lmer.R (LMEoptimize method), tests/lmer.R,
421            inst/external/test3comp.rda: Added warnings for convergence on
422            boundary and test cases.
423    
424            * src/lmer.c (mer_postVar): Modified to return the variances that
425            are marginal to the fixed effects, not conditional on them (which
426            is what the bVar slot contents represent).
427    
428    2006-07-31  Douglas Bates  <bates@R-project.org>
429    
430            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
431            function which calls the C function mer_hat_trace2.
432    
433            * man/ranef.Rd: Include description of "postVar" argument and
434            producing a caterpillar plot.
435    
436    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * NAMESPACE:    change  "correlation" to "corMatrix"
439            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
440            * R/dpoMatrix.R: ditto
441            * R/lmer.R:      ditto
442    
443    2006-07-28  Douglas Bates  <bates@R-project.org>
444    
445            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
446            RZXinv slot's contents into a separate internal function that can
447            be used in mer_hat_trace.
448    
449    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
452            via new smart
453            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
454            utility functions.
455    
456    
457    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/Csparse.R (tril, triu, band): do return *triangular* classed
460            matrices when appropriate; band() even symmetric ones.
461            (replCmat): extend to potentially all "CsparseMatrix"
462            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
463            allow subassignment for special sparse matrices.
464    
465            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
466    
467            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
468            argument; in glmer_*(): print only if(verbose).
469    
470            speed-optimize a few places by moving REAL(.) out of loops.
471    
472            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
473    
474    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
477                    since that wrongly triggers also for M[ logi , ]
478    
479            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
480            a symmetric matrix that results in a non-symmetric one.
481            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
482    
483            * R/dMatrix.R: make round(M) work as round(M, 0)
484    
485            * R/dgTMatrix.R (image): coordinate system and axis now use
486            1-based indices, not 0-based ones.
487    
488            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
489            * tests/indexing.R: test it.
490    
491            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
492            * man/isSymmetric-methods.Rd: and document it.
493    
494            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
495            * man/SparseM-conv.Rd: docu them
496    
497            * tests/other-pkgs.R: renamed from tests/graph.R and add example
498                    for 'SparseM' conversions
499    
500    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
501    
502            * R/Matrix.R (head): added head() and tail() methods.
503    
504    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * DESCRIPTION (Version): 0.995-12 released to CRAN
507    
508    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * tests/simple.R: add check for correct dsT -> dgT coercion;
511                    add check for correct printing of symmetric sparse matrices.
512    
513            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
514            for sparse symmetric matrices.
515    
516            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
517            diagonal twice.
518    
519    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
520    
521            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
522            being applied to the x slot (detected by Brian Ripley).
523    
524    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
527    
528            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
529    
530    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * src/lgCMatrix.c (lgCMatrix_diag): new function
533            * R/lgCMatrix.R (diag): for new method
534    
535            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
536                 ==> construction of illegal "*gTMatrix" via new() should
537                 now be much less easy:
538            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
539    
540            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
541                    directly.
542            * man/Matrix.Rd: documents it.
543    
544    2006-07-06  Douglas Bates  <bates@R-project.org>
545    
546            * src/pedigree.c (pedigree_inbreeding): Correction in
547            initialization.  This function is not currently being used and is
548            not fully tested.
549    
550            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
551            Introduced the glmer class.  Added code for mcmcmsamp on glmer
552            objects.  Modified validity check on pedigree objects to account
553            for nonparallel patterns of missingness of parents.
554    
555            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
556            class.
557    
558    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/pMatrix.R: coercion pMatrix -> Tsparse
561    
562    2006-06-12  Douglas Bates  <bates@R-project.org>
563    
564            * DESCRIPTION (Version): 0.995-11 released to CRAN
565    
566            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
567            the output from mcmcsamp.
568    
569  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
570    
571          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
572            of the hat matrix.
573    
574  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
577          classes.          classes.
578            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
579    
580  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
# Line 43  Line 613 
613    
614          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
615          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
616          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
617    
618    
619  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 736 
736          * 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)
737          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
738          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
739          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
740    
741  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
# Line 370  Line 940 
940  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
943          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
944          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
945    
946  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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