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revision 863, Thu Aug 18 21:31:31 2005 UTC revision 1455, Mon Aug 28 15:35:44 2006 UTC
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1    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
4            in all cases.
5    
6    2006-08-27  Douglas Bates  <bates@R-project.org>
7    
8            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
9            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
10    
11    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
14            subclasses of "ddenseMatrix"
15            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
16            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
17            instead of half dozen specialized ones.
18    
19    2006-08-25  Douglas Bates  <bates@R-project.org>
20    
21            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
22            <tillard@cirad.fr> - ordering standard errors to match effects.
23    
24    2006-08-24  Douglas Bates  <bates@R-project.org>
25    
26            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
27            on R_ldl.
28            * R/lCholCMatrix.R,
29            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
30            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
31            * many files in ./R and ./src: Use more general version of
32            dup_mMatrix_as_dgeMatrix to simplify method definitions.
33            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
34            dtpMatrix, dspMatrix and dppMatrix conversions.
35    
36    
37    2006-08-23  Douglas Bates  <bates@R-project.org>
38    
39            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
40            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
41            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
42            dgeMatrix_crossprod (may need to do this in other places).
43            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
44            generic and method for dsCMatrix.  Use CHOLMOD for chol().
45    
46    2006-08-22  Douglas Bates  <bates@R-project.org>
47    
48            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
49            types of classed Matrices, matrices or numeric or logical vectors.
50            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
51            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
52            to Mutils.h (as an inline) and change name to Matrix_check_class;
53            fixes in as_cholmod_factor and chm_factor_to_SEXP.
54            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
55            dsCMatrix_matrix_solve.  Comment out vestigial functions.
56            * src/Csparse.c: use diag_P and uplo_P macros.
57    
58    2006-08-21  Douglas Bates  <bates@R-project.org>
59    
60            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
61            valgrind.
62            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
63            inverses.
64            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
65            -Wall warnings.
66            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
67            Use dup_mMatrix_as_dgeMatrix.
68    
69    2006-08-20  Douglas Bates  <bates@R-project.org>
70    
71            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
72            * tests/sparseQR.R: Added
73            * man/sparseQR-class.Rd: Document methods for qr.* generics
74            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
75    
76    2006-08-19  Douglas Bates  <bates@R-project.org>
77    
78            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
79            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
80            and qr.fitted.
81            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
82            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
83    
84    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
87            the base version has no "..." argument.
88    
89            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
90    
91            * R/Matrix.R: define and
92            * NAMESPACE: export as.numeric() and as.logical() methods.
93                    Let's hope these do not badly slow down something...
94            Finally export the zapsmall() method.
95    
96    2006-08-17  Douglas Bates  <bates@R-project.org>
97    
98            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
99            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
100            * src/dtCMatrix.c :Remove code that is no longer used
101            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
102    
103    2006-08-14  Douglas Bates  <bates@R-project.org>
104    
105            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
106            Csparse_to_logical and Csparse_symmetric_to_general.
107            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
108            coercion methods between CsparseMatrix and TsparseMatrix.
109    
110    2006-08-14  Douglas Bates  <bates@R-project.org>
111    
112            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
113            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
114            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
115            possible.
116    
117    2006-08-12  Douglas Bates  <bates@R-project.org>
118    
119            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
120              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
121              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
122              generalize conversions between TsparseMatrix, CsparseMatrix,
123              denseMatrix and matrix.  Preserve triangularity property and
124              propagate Dimnames in the easy cases.
125    
126    2006-08-10  Douglas Bates  <bates@R-project.org>
127    
128            * src/lmer.c: adjust checks in glmer_init for S4SXP
129            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
130            before S4SXP but for the wrong reasons.
131    
132    2006-08-08  Douglas Bates  <bates@R-project.org>
133    
134            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
135            Later modified to return the upper triangle only.
136            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
137    
138    2006-08-07  Douglas Bates  <bates@R-project.org>
139    
140            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
141            R-level conversion to a sparse symmetric class.
142            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
143            Remove conversion to sparse symmetric classes (now done in C code).
144    
145    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
148            * man/band.Rd:  adapt the \dontshow{} unit test.
149    
150    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Version): 0.995-14  for CRAN
153    
154            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
155    
156            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
157            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
158    
159            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
160            * R/Tsparse.R (tril, triu, band): methods
161            * R/dgRMatrix.R (tril, ...):    ditto
162            * man/band.Rd:                  ditto
163    
164    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Matrix.R (head, tail): directly use utils:::head.matrix
167                    to be up-to-date automatically.
168    
169    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
172    
173            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
174            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
175            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
176            such that the S4 objects are always created by the current version
177            of R and 'Matrix' class definitions.
178    
179    2006-08-01  Douglas Bates  <bates@R-project.org>
180    
181            * R/lmer.R (LMEoptimize method), tests/lmer.R,
182            inst/external/test3comp.rda: Added warnings for convergence on
183            boundary and test cases.
184    
185            * src/lmer.c (mer_postVar): Modified to return the variances that
186            are marginal to the fixed effects, not conditional on them (which
187            is what the bVar slot contents represent).
188    
189    2006-07-31  Douglas Bates  <bates@R-project.org>
190    
191            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
192            function which calls the C function mer_hat_trace2.
193    
194            * man/ranef.Rd: Include description of "postVar" argument and
195            producing a caterpillar plot.
196    
197    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * NAMESPACE:    change  "correlation" to "corMatrix"
200            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
201            * R/dpoMatrix.R: ditto
202            * R/lmer.R:      ditto
203    
204    2006-07-28  Douglas Bates  <bates@R-project.org>
205    
206            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
207            RZXinv slot's contents into a separate internal function that can
208            be used in mer_hat_trace.
209    
210    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
213            via new smart
214            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
215            utility functions.
216    
217    
218    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Csparse.R (tril, triu, band): do return *triangular* classed
221            matrices when appropriate; band() even symmetric ones.
222            (replCmat): extend to potentially all "CsparseMatrix"
223            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
224            allow subassignment for special sparse matrices.
225    
226            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
227    
228            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
229            argument; in glmer_*(): print only if(verbose).
230    
231            speed-optimize a few places by moving REAL(.) out of loops.
232    
233            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
234    
235    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
238                    since that wrongly triggers also for M[ logi , ]
239    
240            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
241            a symmetric matrix that results in a non-symmetric one.
242            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
243    
244            * R/dMatrix.R: make round(M) work as round(M, 0)
245    
246            * R/dgTMatrix.R (image): coordinate system and axis now use
247            1-based indices, not 0-based ones.
248    
249            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
250            * tests/indexing.R: test it.
251    
252            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
253            * man/isSymmetric-methods.Rd: and document it.
254    
255            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
256            * man/SparseM-conv.Rd: docu them
257    
258            * tests/other-pkgs.R: renamed from tests/graph.R and add example
259                    for 'SparseM' conversions
260    
261    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
262    
263            * R/Matrix.R (head): added head() and tail() methods.
264    
265    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * DESCRIPTION (Version): 0.995-12 released to CRAN
268    
269    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * tests/simple.R: add check for correct dsT -> dgT coercion;
272                    add check for correct printing of symmetric sparse matrices.
273    
274            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
275            for sparse symmetric matrices.
276    
277            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
278            diagonal twice.
279    
280    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
281    
282            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
283            being applied to the x slot (detected by Brian Ripley).
284    
285    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
288    
289            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
290    
291    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * src/lgCMatrix.c (lgCMatrix_diag): new function
294            * R/lgCMatrix.R (diag): for new method
295    
296            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
297                 ==> construction of illegal "*gTMatrix" via new() should
298                 now be much less easy:
299            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
300    
301            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
302                    directly.
303            * man/Matrix.Rd: documents it.
304    
305    2006-07-06  Douglas Bates  <bates@R-project.org>
306    
307            * src/pedigree.c (pedigree_inbreeding): Correction in
308            initialization.  This function is not currently being used and is
309            not fully tested.
310    
311            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
312            Introduced the glmer class.  Added code for mcmcmsamp on glmer
313            objects.  Modified validity check on pedigree objects to account
314            for nonparallel patterns of missingness of parents.
315    
316            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
317            class.
318    
319    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/pMatrix.R: coercion pMatrix -> Tsparse
322    
323    2006-06-12  Douglas Bates  <bates@R-project.org>
324    
325            * DESCRIPTION (Version): 0.995-11 released to CRAN
326    
327            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
328            the output from mcmcsamp.
329    
330    2006-06-10  Douglas Bates  <bates@R-project.org>
331    
332            * R/lmer.R (simulestimate): added C code for calculating the trace
333            of the hat matrix.
334    
335    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
338            classes.
339            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
340    
341    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/dgTMatrix.R (colSums): etc. All four of
344            colSums(), rowSums(), colMeans(), rowMeans() now should work for
345            all "Matrices".
346    
347    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
348    
349            * R/lmer.R (panel.ci): Add a reference line at zero and a
350            background grid to the qqmath plot of ranef.lmer.
351    
352    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
353    
354            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
355            grouping factors to be specified in the formula as (1|foo/bar).
356    
357    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
358    
359            * R/lmer.R (findbars and others): Change check of is.numeric to
360            !is.language to resolve the bug reported by Jacob Wegelin.
361    
362            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
363            code to evaluate inbreeding coefficients without calculating T,
364            based on code in Sargolzaei and Iwaisaki's paper.
365    
366    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
367    
368            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
369            generic and mer methods for isNested and denomDF. This denomDF was
370            an attempt to emulate that in lme but I don't think that makes
371            sense.  Use the trace of the hat matrix instead.
372    
373    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
376            the C code depending on a slot structure that's no longer valid.
377            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
378    
379    
380    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
381    
382            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
383            of lowerTriMatrix generic and methods to tril (also upper to triu)
384            and added a general band extractor.
385    
386    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * R/pedigree.R (pedigree): Replace sire and dam values outside the
389            allowable range with NAs. Added a corresponding check in the
390            validity check for the pedigree class.
391    
392            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
393            crossprod methods now inherits from symmetricMatrix.
394    
395    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
396    
397            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
398            generics lowerTriMatrix and upperTriMatrix along with methods for
399            the Csparse virtual class.  Also added a C function Csparse_band
400            that implements these methods by calling cholmod_band.
401    
402    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
405            erased when it was NULL.  This led to invalid subselections!
406    
407    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
408    
409            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
410            in method for "t" so as not to lose the unit diagonal property.
411    
412    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
413    
414            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
415            and methods.  This is now an option to the ranef method for the
416            mer class.
417    
418            * src/cs_utils.c: Ensure that the nz component is -1 for a
419            compressed column-oriented matrix.  Minor formatting cleanup.
420    
421            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
422            objects.
423    
424    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
427            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
428    
429    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
430    
431            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
432            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
433    
434            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
435            for the dtCMatrix class.
436    
437    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
438    
439            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
440            and methods for it.
441    
442    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
445            arguments, such that M %*% 1:6 now works
446            * Tests/matprod.R: test the above
447    
448    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
451            the ranef.lmer class.
452    
453            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
454            methods to extract the posterior variances from the bVar slot.
455    
456    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
459            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
460    
461            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
462            * tests/simple: (extended)
463    
464            * R/sparseMatrix.R (isTriangular): now using much improved
465            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
466    
467    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
468    
469            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
470            (problem report from Franklin Parlamis).  This should be done
471            generally.
472    
473    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
474    
475            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
476            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
477            update the plot methods.
478    
479    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
480    
481            * R/lmer.R (resid and ranef methods):  Added methods for the
482            "residuals" and "resid" generic but only for linear mixed model
483            fits.  Changed the ranef method to return a list of data frames so
484            that the plot methods now work.
485    
486    2006-03-16  Douglas Bates  <bates@bates2>
487    
488            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
489            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
490    
491            * DESCRIPTION (Date): New release
492    
493    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
494    
495            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
496    
497            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
498            * man/KNex.Rd: and other help files
499            * tests/*.R: several ones needed adaption
500            * inst/doc/Comparisons.Rnw: ditto
501    
502    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
505    
506            * tests/indexing.R: tests for new [<- methods for sparse matrices.
507    
508    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
511    
512            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
513    
514    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/dMatrix.R: enable things like  M [ M < 10 ]
517            * R/dgeMatrix.R: implement it
518    
519    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/AllClass.R: define "summary.mer" and "*.lmer"
522            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
523            * R/lmer.R (show): now works with summary()
524    
525    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
528            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
529                    support the above
530    
531    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
532    
533            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
534            Use glmFit$prior.weights for weights in a glmm.
535            Allow an option usePQL = FALSE to skip the PQL steps for the
536            Laplace method (and, in time, the AGQ method).
537    
538            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
539            into a separate function internal_mer_Xfactor to be able to call
540            it from internal_bhat.
541    
542    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * tests/Class+Meth.R (tstMatrixClass): function for much better
545            testing; now again of all actual classes.
546    
547            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
548                    use macros and define make_d_matrix_* and make_i_matrix_*
549                    where _i_ is for the ldense routines:
550    
551            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
552            * src/ldense.c (lsyMatrix_as_lgeMatrix):
553    
554            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
555    
556    
557    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
560                    many different kinds of matrices.
561            * R/*.R: quite a few new methods were needed for R CMD check with
562                    new Matrix().  Very good for users playing around.
563    
564    
565    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * src/dgeMatrix.c (dMatrix_validate): new
568            * src/Mutils.c (dense_nonpacked_validate): new
569    
570            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
571    
572    
573    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
574    
575            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
576    
577    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
578    
579            * DESCRIPTION (Version): 0.99-6 released to CRAN
580    
581            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
582            segfault in cases with multiple non-nested grouping factors.
583    
584    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
587                    (Depends): also on 'utils'
588    
589            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
590            * R/diagMatrix.R (Diagonal): constructor and methods for
591            diagonal matrices
592    
593            * R/ltTMatrix.R: new "minimal methods"
594    
595    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
598            all methods (and help files).
599    
600    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
603                    for case (dimn.  op  no_dimn.)
604    
605    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
606    
607            * DESCRIPTION (Version): 0.99-2  released to CRAN
608    
609    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
610    
611            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
612            by Julian Faraway.
613    
614    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Auxiliaries.R (try_as): new utility
617            * R/sparseMatrix.R: use try_as() in coercion to original class
618    
619    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
622    
623    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/Auxiliaries.R (dimNamesCheck): added
626    
627            * R/Matrix.R (as.array), (as.vector): new
628    
629    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
632                    default.
633            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
634                    "pMatrix" now contains "sparseMatrix"
635    
636    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * tests/Class+Meth.R: new tests; t(t(m)) == m
639    
640            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
641    
642            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
643            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
644    
645            * R/dspMatrix.R: typo in "t" method
646    
647    2005-09-18  Douglas Bates  <bates@wisc.edu>
648    
649            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
650            * R/Tsparse.R: instead of R/gTMatrix.R
651            * R/Csparse.R: new
652            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
653            * src/Tsparse.c: new; many trivial methods calling cholmod_()
654            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
655                            via cholmod
656    
657    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/Auxiliaries.R (non0ind): new function using new C code
660            * src/dgCMatrix.c (compressed_non_0_ij): new utility
661    
662    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
663    
664            * src/chm_common.h: header file required by all C sources that
665            call CHOLMOD functions.  It defines a cholmod_common structure
666            called 'c' whose address is passed as the last argument to
667            (virtually) every CHOLMOD function.
668    
669            * src/Pattern.c: Simple example of the use of CHOLMOD.
670    
671            * src/init.c: initialize and finalize the cholmod_common structure.
672    
673            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
674            LDL and CCOLAMD from the U. of Florida sparse matrix library.
675    
676    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * inst/test-tools.R: new file collecting the utility functions used
679                    in ./tests/*.R
680    
681            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
682            * R/Matrix.R (cbind2): methods for NULL and missing
683    
684    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/AllClass.R: new "index" class for "[" and "[<-":
687                    First cut at "symmetricMatrix" and "triangularMatrix"
688            * R/gTMatrix.R (.ind.prep): new function;
689                    Logical and character indexing now work too.
690            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
691            * tests/indexing.R: new, including *.Rout.save
692            * tests/dgTMatrix.R: new
693    
694    2005-08-29  Douglas Bates  <bates@wisc.edu>
695    
696            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
697            indicator pos not being updated.  Also enforced upper triangular
698            for symmetric case.  Need to coerce edges component of elements of
699            edge list - grr! (Why don't they define their classes cleanly?)
700    
701    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/Matrix.R:  added first "[<-" methods; not yet functional
704            * R/denseMatrix.R: ditto
705            * man/Subassign-methods.Rd: new help file for these
706    
707    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * DESCRIPTION (Version): 0.98-6
710    
711            * R/denseMatrix.R: new file for "[" fallback methods for all dense
712            matrices.
713    
714    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
717                    as( <logical>, "matrix")
718    
719            * R/pMatrix.R: coercion to "lgTMatrix"
720    
721            * R/gTMatrix.R: new virtual class to define "[" methods for.
722            * man/gTMatrix-class.Rd:
723            * General slight re-organization of where "[" methods are defined.
724              more to come.
725    
726    2005-08-18  Douglas Bates  <bates@wisc.edu>
727    
728            * DESCRIPTION (Version): 0.98-5  released to CRAN
729    
730            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
731            * .....
732    
733  2005-08-18  Douglas Bates  <bates@localhost.localdomain>  2005-08-18  Douglas Bates  <bates@localhost.localdomain>
734    
735          * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer          * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer

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