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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1543, Sat Sep 9 13:44:15 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    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
9            for exported functions
10            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
11            Remove partitioning algorithms for sparse matrix reordering.  The
12            copyright on the Metis code was problematic and the methods were
13            rarely used.
14            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
15            operations are now done entirely in CHOLMOD code.
16    
17    2006-09-06  Douglas Bates  <bates@R-project.org>
18    
19            * src/Mutils.h: Remove functions that are no longer used.
20    
21    2006-09-04  Douglas Bates  <bates@R-project.org>
22    
23            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
24            * src/DEPS.mkf: update
25    
26    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * created branches/Matrix-for-R-2.3.x;  on trunk: do
29            * DESCRIPTION (Version): 0.9975-0
30            (Depends): R (>= 2.4.0)
31    
32    2006-09-01  Douglas Bates  <bates@R-project.org>
33    
34            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
35    
36    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
39            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
40    
41            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
42    
43    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
46            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
47            * R/dsparseMatrix.R: dito
48            * R/Csparse.R: dito
49    
50    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dMatrix.R (Compare): improve availability of "<", etc
53            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
54    
55    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
58            of a 0-index which was used as 1-index (..hmm)
59    
60            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
61    
62            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
63            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
64            (.is.diagonal): dito
65    
66            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
67    
68            * R/Matrix.R (Matrix): also work for NA data
69    
70    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
73            in all cases.
74    
75    2006-08-27  Douglas Bates  <bates@R-project.org>
76    
77            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
78            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
79    
80    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
83            subclasses of "ddenseMatrix"
84            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
85            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
86            instead of half dozen specialized ones.
87    
88    2006-08-25  Douglas Bates  <bates@R-project.org>
89    
90            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
91            <tillard@cirad.fr> - ordering standard errors to match effects.
92    
93    2006-08-24  Douglas Bates  <bates@R-project.org>
94    
95            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
96            on R_ldl.
97            * R/lCholCMatrix.R,
98            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
99            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
100            * many files in ./R and ./src: Use more general version of
101            dup_mMatrix_as_dgeMatrix to simplify method definitions.
102            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
103            dtpMatrix, dspMatrix and dppMatrix conversions.
104    
105    
106    2006-08-23  Douglas Bates  <bates@R-project.org>
107    
108            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
109            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
110            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
111            dgeMatrix_crossprod (may need to do this in other places).
112            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
113            generic and method for dsCMatrix.  Use CHOLMOD for chol().
114    
115    2006-08-22  Douglas Bates  <bates@R-project.org>
116    
117            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
118            types of classed Matrices, matrices or numeric or logical vectors.
119            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
120            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
121            to Mutils.h (as an inline) and change name to Matrix_check_class;
122            fixes in as_cholmod_factor and chm_factor_to_SEXP.
123            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
124            dsCMatrix_matrix_solve.  Comment out vestigial functions.
125            * src/Csparse.c: use diag_P and uplo_P macros.
126    
127    2006-08-21  Douglas Bates  <bates@R-project.org>
128    
129            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
130            valgrind.
131            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
132            inverses.
133            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
134            -Wall warnings.
135            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
136            Use dup_mMatrix_as_dgeMatrix.
137    
138    2006-08-20  Douglas Bates  <bates@R-project.org>
139    
140            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
141            * tests/sparseQR.R: Added
142            * man/sparseQR-class.Rd: Document methods for qr.* generics
143            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
144    
145    2006-08-19  Douglas Bates  <bates@R-project.org>
146    
147            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
148            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
149            and qr.fitted.
150            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
151            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
152    
153    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
156            the base version has no "..." argument.
157    
158            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
159    
160            * R/Matrix.R: define and
161            * NAMESPACE: export as.numeric() and as.logical() methods.
162                    Let's hope these do not badly slow down something...
163            Finally export the zapsmall() method.
164    
165    2006-08-17  Douglas Bates  <bates@R-project.org>
166    
167            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
168            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
169            * src/dtCMatrix.c :Remove code that is no longer used
170            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
171    
172    2006-08-14  Douglas Bates  <bates@R-project.org>
173    
174            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
175            Csparse_to_logical and Csparse_symmetric_to_general.
176            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
177            coercion methods between CsparseMatrix and TsparseMatrix.
178    
179    2006-08-14  Douglas Bates  <bates@R-project.org>
180    
181            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
182            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
183            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
184            possible.
185    
186    2006-08-12  Douglas Bates  <bates@R-project.org>
187    
188            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
189              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
190              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
191              generalize conversions between TsparseMatrix, CsparseMatrix,
192              denseMatrix and matrix.  Preserve triangularity property and
193              propagate Dimnames in the easy cases.
194    
195    2006-08-10  Douglas Bates  <bates@R-project.org>
196    
197            * src/lmer.c: adjust checks in glmer_init for S4SXP
198            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
199            before S4SXP but for the wrong reasons.
200    
201    2006-08-08  Douglas Bates  <bates@R-project.org>
202    
203            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
204            Later modified to return the upper triangle only.
205            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
206    
207    2006-08-07  Douglas Bates  <bates@R-project.org>
208    
209            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
210            R-level conversion to a sparse symmetric class.
211            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
212            Remove conversion to sparse symmetric classes (now done in C code).
213    
214    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
217            * man/band.Rd:  adapt the \dontshow{} unit test.
218    
219    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * DESCRIPTION (Version): 0.995-14  for CRAN
222    
223            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
224    
225            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
226            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
227    
228            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
229            * R/Tsparse.R (tril, triu, band): methods
230            * R/dgRMatrix.R (tril, ...):    ditto
231            * man/band.Rd:                  ditto
232    
233    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Matrix.R (head, tail): directly use utils:::head.matrix
236                    to be up-to-date automatically.
237    
238    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
241    
242            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
243            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
244            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
245            such that the S4 objects are always created by the current version
246            of R and 'Matrix' class definitions.
247    
248    2006-08-01  Douglas Bates  <bates@R-project.org>
249    
250            * R/lmer.R (LMEoptimize method), tests/lmer.R,
251            inst/external/test3comp.rda: Added warnings for convergence on
252            boundary and test cases.
253    
254            * src/lmer.c (mer_postVar): Modified to return the variances that
255            are marginal to the fixed effects, not conditional on them (which
256            is what the bVar slot contents represent).
257    
258    2006-07-31  Douglas Bates  <bates@R-project.org>
259    
260            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
261            function which calls the C function mer_hat_trace2.
262    
263            * man/ranef.Rd: Include description of "postVar" argument and
264            producing a caterpillar plot.
265    
266    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * NAMESPACE:    change  "correlation" to "corMatrix"
269            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
270            * R/dpoMatrix.R: ditto
271            * R/lmer.R:      ditto
272    
273    2006-07-28  Douglas Bates  <bates@R-project.org>
274    
275            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
276            RZXinv slot's contents into a separate internal function that can
277            be used in mer_hat_trace.
278    
279    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
282            via new smart
283            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
284            utility functions.
285    
286    
287    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Csparse.R (tril, triu, band): do return *triangular* classed
290            matrices when appropriate; band() even symmetric ones.
291            (replCmat): extend to potentially all "CsparseMatrix"
292            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
293            allow subassignment for special sparse matrices.
294    
295            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
296    
297            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
298            argument; in glmer_*(): print only if(verbose).
299    
300            speed-optimize a few places by moving REAL(.) out of loops.
301    
302            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
303    
304    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
307                    since that wrongly triggers also for M[ logi , ]
308    
309            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
310            a symmetric matrix that results in a non-symmetric one.
311            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
312    
313            * R/dMatrix.R: make round(M) work as round(M, 0)
314    
315            * R/dgTMatrix.R (image): coordinate system and axis now use
316            1-based indices, not 0-based ones.
317    
318            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
319            * tests/indexing.R: test it.
320    
321            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
322            * man/isSymmetric-methods.Rd: and document it.
323    
324            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
325            * man/SparseM-conv.Rd: docu them
326    
327            * tests/other-pkgs.R: renamed from tests/graph.R and add example
328                    for 'SparseM' conversions
329    
330    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
331    
332            * R/Matrix.R (head): added head() and tail() methods.
333    
334    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * DESCRIPTION (Version): 0.995-12 released to CRAN
337    
338    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * tests/simple.R: add check for correct dsT -> dgT coercion;
341                    add check for correct printing of symmetric sparse matrices.
342    
343            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
344            for sparse symmetric matrices.
345    
346            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
347            diagonal twice.
348    
349    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
350    
351            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
352            being applied to the x slot (detected by Brian Ripley).
353    
354    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
357    
358            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
359    
360    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * src/lgCMatrix.c (lgCMatrix_diag): new function
363            * R/lgCMatrix.R (diag): for new method
364    
365            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
366                 ==> construction of illegal "*gTMatrix" via new() should
367                 now be much less easy:
368            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
369    
370            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
371                    directly.
372            * man/Matrix.Rd: documents it.
373    
374    2006-07-06  Douglas Bates  <bates@R-project.org>
375    
376            * src/pedigree.c (pedigree_inbreeding): Correction in
377            initialization.  This function is not currently being used and is
378            not fully tested.
379    
380            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
381            Introduced the glmer class.  Added code for mcmcmsamp on glmer
382            objects.  Modified validity check on pedigree objects to account
383            for nonparallel patterns of missingness of parents.
384    
385            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
386            class.
387    
388    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/pMatrix.R: coercion pMatrix -> Tsparse
391    
392    2006-06-12  Douglas Bates  <bates@R-project.org>
393    
394            * DESCRIPTION (Version): 0.995-11 released to CRAN
395    
396            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
397            the output from mcmcsamp.
398    
399    2006-06-10  Douglas Bates  <bates@R-project.org>
400    
401            * R/lmer.R (simulestimate): added C code for calculating the trace
402            of the hat matrix.
403    
404    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
407            classes.
408            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
409    
410    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/dgTMatrix.R (colSums): etc. All four of
413            colSums(), rowSums(), colMeans(), rowMeans() now should work for
414            all "Matrices".
415    
416    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * R/lmer.R (panel.ci): Add a reference line at zero and a
419            background grid to the qqmath plot of ranef.lmer.
420    
421    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
422    
423            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
424            grouping factors to be specified in the formula as (1|foo/bar).
425    
426    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
427    
428            * R/lmer.R (findbars and others): Change check of is.numeric to
429            !is.language to resolve the bug reported by Jacob Wegelin.
430    
431            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
432            code to evaluate inbreeding coefficients without calculating T,
433            based on code in Sargolzaei and Iwaisaki's paper.
434    
435    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
436    
437            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
438            generic and mer methods for isNested and denomDF. This denomDF was
439            an attempt to emulate that in lme but I don't think that makes
440            sense.  Use the trace of the hat matrix instead.
441    
442    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
445            the C code depending on a slot structure that's no longer valid.
446            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
447    
448    
449    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
450    
451            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
452            of lowerTriMatrix generic and methods to tril (also upper to triu)
453            and added a general band extractor.
454    
455    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
456    
457            * R/pedigree.R (pedigree): Replace sire and dam values outside the
458            allowable range with NAs. Added a corresponding check in the
459            validity check for the pedigree class.
460    
461            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
462            crossprod methods now inherits from symmetricMatrix.
463    
464    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
465    
466            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
467            generics lowerTriMatrix and upperTriMatrix along with methods for
468            the Csparse virtual class.  Also added a C function Csparse_band
469            that implements these methods by calling cholmod_band.
470    
471    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
474            erased when it was NULL.  This led to invalid subselections!
475    
476    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
477    
478            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
479            in method for "t" so as not to lose the unit diagonal property.
480    
481    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
482    
483            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
484            and methods.  This is now an option to the ranef method for the
485            mer class.
486    
487            * src/cs_utils.c: Ensure that the nz component is -1 for a
488            compressed column-oriented matrix.  Minor formatting cleanup.
489    
490            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
491            objects.
492    
493    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
494    
495            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
496            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
497    
498    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
499    
500            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
501            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
502    
503            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
504            for the dtCMatrix class.
505    
506    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
507    
508            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
509            and methods for it.
510    
511    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
514            arguments, such that M %*% 1:6 now works
515            * Tests/matprod.R: test the above
516    
517    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
520            the ranef.lmer class.
521    
522            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
523            methods to extract the posterior variances from the bVar slot.
524    
525    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
528            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
529    
530            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
531            * tests/simple: (extended)
532    
533            * R/sparseMatrix.R (isTriangular): now using much improved
534            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
535    
536    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
537    
538            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
539            (problem report from Franklin Parlamis).  This should be done
540            generally.
541    
542    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
543    
544            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
545            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
546            update the plot methods.
547    
548    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
549    
550            * R/lmer.R (resid and ranef methods):  Added methods for the
551            "residuals" and "resid" generic but only for linear mixed model
552            fits.  Changed the ranef method to return a list of data frames so
553            that the plot methods now work.
554    
555    2006-03-16  Douglas Bates  <bates@bates2>
556    
557            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
558            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
559    
560            * DESCRIPTION (Date): New release
561    
562    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
565    
566            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
567            * man/KNex.Rd: and other help files
568            * tests/*.R: several ones needed adaption
569            * inst/doc/Comparisons.Rnw: ditto
570    
571    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
574    
575            * tests/indexing.R: tests for new [<- methods for sparse matrices.
576    
577    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
580    
581            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
582    
583    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/dMatrix.R: enable things like  M [ M < 10 ]
586            * R/dgeMatrix.R: implement it
587    
588    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/AllClass.R: define "summary.mer" and "*.lmer"
591            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
592            * R/lmer.R (show): now works with summary()
593    
594    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
597            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
598                    support the above
599    
600  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
601    
602          * 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 770 
770  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
773          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
774          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
775    
776  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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