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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1544, Sat Sep 9 14:04:24 2006 UTC
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1    2006-09-09  Douglas Bates  <bates@R-project.org>
2    
3            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
4            fixed
5    
6    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
9    
10            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
11            * man/tcrossprod.Rd: dito
12    
13    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
16            for exported functions
17            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
18            Remove partitioning algorithms for sparse matrix reordering.  The
19            copyright on the Metis code was problematic and the methods were
20            rarely used.
21            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
22            operations are now done entirely in CHOLMOD code.
23    
24    2006-09-06  Douglas Bates  <bates@R-project.org>
25    
26            * src/Mutils.h: Remove functions that are no longer used.
27    
28    2006-09-04  Douglas Bates  <bates@R-project.org>
29    
30            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
31            * src/DEPS.mkf: update
32    
33    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * created branches/Matrix-for-R-2.3.x;  on trunk: do
36            * DESCRIPTION (Version): 0.9975-0
37            (Depends): R (>= 2.4.0)
38    
39    2006-09-01  Douglas Bates  <bates@R-project.org>
40    
41            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
42    
43    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
46            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
47    
48            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
49    
50    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
53            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
54            * R/dsparseMatrix.R: dito
55            * R/Csparse.R: dito
56    
57    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/dMatrix.R (Compare): improve availability of "<", etc
60            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
61    
62    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
65            of a 0-index which was used as 1-index (..hmm)
66    
67            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
68    
69            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
70            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
71            (.is.diagonal): dito
72    
73            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
74    
75            * R/Matrix.R (Matrix): also work for NA data
76    
77    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
80            in all cases.
81    
82    2006-08-27  Douglas Bates  <bates@R-project.org>
83    
84            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
85            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
86    
87    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
90            subclasses of "ddenseMatrix"
91            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
92            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
93            instead of half dozen specialized ones.
94    
95    2006-08-25  Douglas Bates  <bates@R-project.org>
96    
97            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
98            <tillard@cirad.fr> - ordering standard errors to match effects.
99    
100    2006-08-24  Douglas Bates  <bates@R-project.org>
101    
102            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
103            on R_ldl.
104            * R/lCholCMatrix.R,
105            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
106            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
107            * many files in ./R and ./src: Use more general version of
108            dup_mMatrix_as_dgeMatrix to simplify method definitions.
109            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
110            dtpMatrix, dspMatrix and dppMatrix conversions.
111    
112    
113    2006-08-23  Douglas Bates  <bates@R-project.org>
114    
115            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
116            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
117            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
118            dgeMatrix_crossprod (may need to do this in other places).
119            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
120            generic and method for dsCMatrix.  Use CHOLMOD for chol().
121    
122    2006-08-22  Douglas Bates  <bates@R-project.org>
123    
124            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
125            types of classed Matrices, matrices or numeric or logical vectors.
126            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
127            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
128            to Mutils.h (as an inline) and change name to Matrix_check_class;
129            fixes in as_cholmod_factor and chm_factor_to_SEXP.
130            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
131            dsCMatrix_matrix_solve.  Comment out vestigial functions.
132            * src/Csparse.c: use diag_P and uplo_P macros.
133    
134    2006-08-21  Douglas Bates  <bates@R-project.org>
135    
136            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
137            valgrind.
138            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
139            inverses.
140            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
141            -Wall warnings.
142            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
143            Use dup_mMatrix_as_dgeMatrix.
144    
145    2006-08-20  Douglas Bates  <bates@R-project.org>
146    
147            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
148            * tests/sparseQR.R: Added
149            * man/sparseQR-class.Rd: Document methods for qr.* generics
150            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
151    
152    2006-08-19  Douglas Bates  <bates@R-project.org>
153    
154            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
155            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
156            and qr.fitted.
157            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
158            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
159    
160    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
163            the base version has no "..." argument.
164    
165            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
166    
167            * R/Matrix.R: define and
168            * NAMESPACE: export as.numeric() and as.logical() methods.
169                    Let's hope these do not badly slow down something...
170            Finally export the zapsmall() method.
171    
172    2006-08-17  Douglas Bates  <bates@R-project.org>
173    
174            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
175            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
176            * src/dtCMatrix.c :Remove code that is no longer used
177            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
178    
179    2006-08-14  Douglas Bates  <bates@R-project.org>
180    
181            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
182            Csparse_to_logical and Csparse_symmetric_to_general.
183            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
184            coercion methods between CsparseMatrix and TsparseMatrix.
185    
186    2006-08-14  Douglas Bates  <bates@R-project.org>
187    
188            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
189            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
190            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
191            possible.
192    
193    2006-08-12  Douglas Bates  <bates@R-project.org>
194    
195            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
196              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
197              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
198              generalize conversions between TsparseMatrix, CsparseMatrix,
199              denseMatrix and matrix.  Preserve triangularity property and
200              propagate Dimnames in the easy cases.
201    
202    2006-08-10  Douglas Bates  <bates@R-project.org>
203    
204            * src/lmer.c: adjust checks in glmer_init for S4SXP
205            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
206            before S4SXP but for the wrong reasons.
207    
208    2006-08-08  Douglas Bates  <bates@R-project.org>
209    
210            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
211            Later modified to return the upper triangle only.
212            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
213    
214    2006-08-07  Douglas Bates  <bates@R-project.org>
215    
216            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
217            R-level conversion to a sparse symmetric class.
218            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
219            Remove conversion to sparse symmetric classes (now done in C code).
220    
221    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
224            * man/band.Rd:  adapt the \dontshow{} unit test.
225    
226    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION (Version): 0.995-14  for CRAN
229    
230            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
231    
232            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
233            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
234    
235            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
236            * R/Tsparse.R (tril, triu, band): methods
237            * R/dgRMatrix.R (tril, ...):    ditto
238            * man/band.Rd:                  ditto
239    
240    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Matrix.R (head, tail): directly use utils:::head.matrix
243                    to be up-to-date automatically.
244    
245    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
248    
249            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
250            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
251            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
252            such that the S4 objects are always created by the current version
253            of R and 'Matrix' class definitions.
254    
255    2006-08-01  Douglas Bates  <bates@R-project.org>
256    
257            * R/lmer.R (LMEoptimize method), tests/lmer.R,
258            inst/external/test3comp.rda: Added warnings for convergence on
259            boundary and test cases.
260    
261            * src/lmer.c (mer_postVar): Modified to return the variances that
262            are marginal to the fixed effects, not conditional on them (which
263            is what the bVar slot contents represent).
264    
265    2006-07-31  Douglas Bates  <bates@R-project.org>
266    
267            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
268            function which calls the C function mer_hat_trace2.
269    
270            * man/ranef.Rd: Include description of "postVar" argument and
271            producing a caterpillar plot.
272    
273    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * NAMESPACE:    change  "correlation" to "corMatrix"
276            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
277            * R/dpoMatrix.R: ditto
278            * R/lmer.R:      ditto
279    
280    2006-07-28  Douglas Bates  <bates@R-project.org>
281    
282            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
283            RZXinv slot's contents into a separate internal function that can
284            be used in mer_hat_trace.
285    
286    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
289            via new smart
290            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
291            utility functions.
292    
293    
294    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Csparse.R (tril, triu, band): do return *triangular* classed
297            matrices when appropriate; band() even symmetric ones.
298            (replCmat): extend to potentially all "CsparseMatrix"
299            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
300            allow subassignment for special sparse matrices.
301    
302            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
303    
304            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
305            argument; in glmer_*(): print only if(verbose).
306    
307            speed-optimize a few places by moving REAL(.) out of loops.
308    
309            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
310    
311    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
314                    since that wrongly triggers also for M[ logi , ]
315    
316            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
317            a symmetric matrix that results in a non-symmetric one.
318            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
319    
320            * R/dMatrix.R: make round(M) work as round(M, 0)
321    
322            * R/dgTMatrix.R (image): coordinate system and axis now use
323            1-based indices, not 0-based ones.
324    
325            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
326            * tests/indexing.R: test it.
327    
328            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
329            * man/isSymmetric-methods.Rd: and document it.
330    
331            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
332            * man/SparseM-conv.Rd: docu them
333    
334            * tests/other-pkgs.R: renamed from tests/graph.R and add example
335                    for 'SparseM' conversions
336    
337    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
338    
339            * R/Matrix.R (head): added head() and tail() methods.
340    
341    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * DESCRIPTION (Version): 0.995-12 released to CRAN
344    
345    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * tests/simple.R: add check for correct dsT -> dgT coercion;
348                    add check for correct printing of symmetric sparse matrices.
349    
350            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
351            for sparse symmetric matrices.
352    
353            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
354            diagonal twice.
355    
356    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
357    
358            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
359            being applied to the x slot (detected by Brian Ripley).
360    
361    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
364    
365            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
366    
367    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * src/lgCMatrix.c (lgCMatrix_diag): new function
370            * R/lgCMatrix.R (diag): for new method
371    
372            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
373                 ==> construction of illegal "*gTMatrix" via new() should
374                 now be much less easy:
375            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
376    
377            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
378                    directly.
379            * man/Matrix.Rd: documents it.
380    
381    2006-07-06  Douglas Bates  <bates@R-project.org>
382    
383            * src/pedigree.c (pedigree_inbreeding): Correction in
384            initialization.  This function is not currently being used and is
385            not fully tested.
386    
387            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
388            Introduced the glmer class.  Added code for mcmcmsamp on glmer
389            objects.  Modified validity check on pedigree objects to account
390            for nonparallel patterns of missingness of parents.
391    
392            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
393            class.
394    
395    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/pMatrix.R: coercion pMatrix -> Tsparse
398    
399    2006-06-12  Douglas Bates  <bates@R-project.org>
400    
401            * DESCRIPTION (Version): 0.995-11 released to CRAN
402    
403            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
404            the output from mcmcsamp.
405    
406    2006-06-10  Douglas Bates  <bates@R-project.org>
407    
408            * R/lmer.R (simulestimate): added C code for calculating the trace
409            of the hat matrix.
410    
411    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
414            classes.
415            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
416    
417    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/dgTMatrix.R (colSums): etc. All four of
420            colSums(), rowSums(), colMeans(), rowMeans() now should work for
421            all "Matrices".
422    
423    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
424    
425            * R/lmer.R (panel.ci): Add a reference line at zero and a
426            background grid to the qqmath plot of ranef.lmer.
427    
428    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
431            grouping factors to be specified in the formula as (1|foo/bar).
432    
433    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
434    
435            * R/lmer.R (findbars and others): Change check of is.numeric to
436            !is.language to resolve the bug reported by Jacob Wegelin.
437    
438            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
439            code to evaluate inbreeding coefficients without calculating T,
440            based on code in Sargolzaei and Iwaisaki's paper.
441    
442    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
443    
444            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
445            generic and mer methods for isNested and denomDF. This denomDF was
446            an attempt to emulate that in lme but I don't think that makes
447            sense.  Use the trace of the hat matrix instead.
448    
449    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
452            the C code depending on a slot structure that's no longer valid.
453            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
454    
455    
456    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
457    
458            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
459            of lowerTriMatrix generic and methods to tril (also upper to triu)
460            and added a general band extractor.
461    
462    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
463    
464            * R/pedigree.R (pedigree): Replace sire and dam values outside the
465            allowable range with NAs. Added a corresponding check in the
466            validity check for the pedigree class.
467    
468            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
469            crossprod methods now inherits from symmetricMatrix.
470    
471    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
474            generics lowerTriMatrix and upperTriMatrix along with methods for
475            the Csparse virtual class.  Also added a C function Csparse_band
476            that implements these methods by calling cholmod_band.
477    
478    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
481            erased when it was NULL.  This led to invalid subselections!
482    
483    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
484    
485            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
486            in method for "t" so as not to lose the unit diagonal property.
487    
488    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
491            and methods.  This is now an option to the ranef method for the
492            mer class.
493    
494            * src/cs_utils.c: Ensure that the nz component is -1 for a
495            compressed column-oriented matrix.  Minor formatting cleanup.
496    
497            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
498            objects.
499    
500    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
503            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
504    
505    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
506    
507            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
508            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
509    
510            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
511            for the dtCMatrix class.
512    
513    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
516            and methods for it.
517    
518    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
521            arguments, such that M %*% 1:6 now works
522            * Tests/matprod.R: test the above
523    
524    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
525    
526            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
527            the ranef.lmer class.
528    
529            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
530            methods to extract the posterior variances from the bVar slot.
531    
532    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
535            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
536    
537            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
538            * tests/simple: (extended)
539    
540            * R/sparseMatrix.R (isTriangular): now using much improved
541            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
542    
543    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
546            (problem report from Franklin Parlamis).  This should be done
547            generally.
548    
549    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
550    
551            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
552            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
553            update the plot methods.
554    
555    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
556    
557            * R/lmer.R (resid and ranef methods):  Added methods for the
558            "residuals" and "resid" generic but only for linear mixed model
559            fits.  Changed the ranef method to return a list of data frames so
560            that the plot methods now work.
561    
562    2006-03-16  Douglas Bates  <bates@bates2>
563    
564            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
565            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
566    
567            * DESCRIPTION (Date): New release
568    
569    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
572    
573            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
574            * man/KNex.Rd: and other help files
575            * tests/*.R: several ones needed adaption
576            * inst/doc/Comparisons.Rnw: ditto
577    
578    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
581    
582            * tests/indexing.R: tests for new [<- methods for sparse matrices.
583    
584    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
587    
588            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
589    
590    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/dMatrix.R: enable things like  M [ M < 10 ]
593            * R/dgeMatrix.R: implement it
594    
595    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/AllClass.R: define "summary.mer" and "*.lmer"
598            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
599            * R/lmer.R (show): now works with summary()
600    
601    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
604            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
605                    support the above
606    
607  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
608    
609          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 777 
777  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
780          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
781          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
782    
783  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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