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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1453, Sun Aug 27 16:16:35 2006 UTC
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1    2006-08-27  Douglas Bates  <bates@R-project.org>
2    
3            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
4            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
5    
6    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
9            subclasses of "ddenseMatrix"
10            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
11            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
12            instead of half dozen specialized ones.
13    
14    2006-08-25  Douglas Bates  <bates@R-project.org>
15    
16            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
17            <tillard@cirad.fr> - ordering standard errors to match effects.
18    
19    2006-08-24  Douglas Bates  <bates@R-project.org>
20    
21            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
22            on R_ldl.
23            * R/lCholCMatrix.R,
24            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
25            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
26            * many files in ./R and ./src: Use more general version of
27            dup_mMatrix_as_dgeMatrix to simplify method definitions.
28            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
29            dtpMatrix, dspMatrix and dppMatrix conversions.
30    
31    
32    2006-08-23  Douglas Bates  <bates@R-project.org>
33    
34            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
35            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
36            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
37            dgeMatrix_crossprod (may need to do this in other places).
38            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
39            generic and method for dsCMatrix.  Use CHOLMOD for chol().
40    
41    2006-08-22  Douglas Bates  <bates@R-project.org>
42    
43            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
44            types of classed Matrices, matrices or numeric or logical vectors.
45            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
46            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
47            to Mutils.h (as an inline) and change name to Matrix_check_class;
48            fixes in as_cholmod_factor and chm_factor_to_SEXP.
49            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
50            dsCMatrix_matrix_solve.  Comment out vestigial functions.
51            * src/Csparse.c: use diag_P and uplo_P macros.
52    
53    2006-08-21  Douglas Bates  <bates@R-project.org>
54    
55            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
56            valgrind.
57            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
58            inverses.
59            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
60            -Wall warnings.
61            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
62            Use dup_mMatrix_as_dgeMatrix.
63    
64    2006-08-20  Douglas Bates  <bates@R-project.org>
65    
66            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
67            * tests/sparseQR.R: Added
68            * man/sparseQR-class.Rd: Document methods for qr.* generics
69            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
70    
71    2006-08-19  Douglas Bates  <bates@R-project.org>
72    
73            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
74            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
75            and qr.fitted.
76            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
77            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
78    
79    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
82            the base version has no "..." argument.
83    
84            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
85    
86            * R/Matrix.R: define and
87            * NAMESPACE: export as.numeric() and as.logical() methods.
88                    Let's hope these do not badly slow down something...
89            Finally export the zapsmall() method.
90    
91    2006-08-17  Douglas Bates  <bates@R-project.org>
92    
93            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
94            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
95            * src/dtCMatrix.c :Remove code that is no longer used
96            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
97    
98    2006-08-14  Douglas Bates  <bates@R-project.org>
99    
100            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
101            Csparse_to_logical and Csparse_symmetric_to_general.
102            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
103            coercion methods between CsparseMatrix and TsparseMatrix.
104    
105    2006-08-14  Douglas Bates  <bates@R-project.org>
106    
107            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
108            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
109            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
110            possible.
111    
112    2006-08-12  Douglas Bates  <bates@R-project.org>
113    
114            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
115              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
116              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
117              generalize conversions between TsparseMatrix, CsparseMatrix,
118              denseMatrix and matrix.  Preserve triangularity property and
119              propagate Dimnames in the easy cases.
120    
121    2006-08-10  Douglas Bates  <bates@R-project.org>
122    
123            * src/lmer.c: adjust checks in glmer_init for S4SXP
124            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
125            before S4SXP but for the wrong reasons.
126    
127    2006-08-08  Douglas Bates  <bates@R-project.org>
128    
129            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
130            Later modified to return the upper triangle only.
131            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
132    
133    2006-08-07  Douglas Bates  <bates@R-project.org>
134    
135            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
136            R-level conversion to a sparse symmetric class.
137            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
138            Remove conversion to sparse symmetric classes (now done in C code).
139    
140    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
143            * man/band.Rd:  adapt the \dontshow{} unit test.
144    
145    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.995-14  for CRAN
148    
149            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
150    
151            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
152            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
153    
154            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
155            * R/Tsparse.R (tril, triu, band): methods
156            * R/dgRMatrix.R (tril, ...):    ditto
157            * man/band.Rd:                  ditto
158    
159    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R (head, tail): directly use utils:::head.matrix
162                    to be up-to-date automatically.
163    
164    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
167    
168            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
169            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
170            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
171            such that the S4 objects are always created by the current version
172            of R and 'Matrix' class definitions.
173    
174    2006-08-01  Douglas Bates  <bates@R-project.org>
175    
176            * R/lmer.R (LMEoptimize method), tests/lmer.R,
177            inst/external/test3comp.rda: Added warnings for convergence on
178            boundary and test cases.
179    
180            * src/lmer.c (mer_postVar): Modified to return the variances that
181            are marginal to the fixed effects, not conditional on them (which
182            is what the bVar slot contents represent).
183    
184    2006-07-31  Douglas Bates  <bates@R-project.org>
185    
186            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
187            function which calls the C function mer_hat_trace2.
188    
189            * man/ranef.Rd: Include description of "postVar" argument and
190            producing a caterpillar plot.
191    
192    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * NAMESPACE:    change  "correlation" to "corMatrix"
195            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
196            * R/dpoMatrix.R: ditto
197            * R/lmer.R:      ditto
198    
199    2006-07-28  Douglas Bates  <bates@R-project.org>
200    
201            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
202            RZXinv slot's contents into a separate internal function that can
203            be used in mer_hat_trace.
204    
205    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
208            via new smart
209            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
210            utility functions.
211    
212    
213    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Csparse.R (tril, triu, band): do return *triangular* classed
216            matrices when appropriate; band() even symmetric ones.
217            (replCmat): extend to potentially all "CsparseMatrix"
218            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
219            allow subassignment for special sparse matrices.
220    
221            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
222    
223            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
224            argument; in glmer_*(): print only if(verbose).
225    
226            speed-optimize a few places by moving REAL(.) out of loops.
227    
228            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
229    
230    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
233                    since that wrongly triggers also for M[ logi , ]
234    
235            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
236            a symmetric matrix that results in a non-symmetric one.
237            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
238    
239            * R/dMatrix.R: make round(M) work as round(M, 0)
240    
241            * R/dgTMatrix.R (image): coordinate system and axis now use
242            1-based indices, not 0-based ones.
243    
244            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
245            * tests/indexing.R: test it.
246    
247            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
248            * man/isSymmetric-methods.Rd: and document it.
249    
250            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
251            * man/SparseM-conv.Rd: docu them
252    
253            * tests/other-pkgs.R: renamed from tests/graph.R and add example
254                    for 'SparseM' conversions
255    
256    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
257    
258            * R/Matrix.R (head): added head() and tail() methods.
259    
260    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * DESCRIPTION (Version): 0.995-12 released to CRAN
263    
264    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/simple.R: add check for correct dsT -> dgT coercion;
267                    add check for correct printing of symmetric sparse matrices.
268    
269            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
270            for sparse symmetric matrices.
271    
272            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
273            diagonal twice.
274    
275    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
276    
277            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
278            being applied to the x slot (detected by Brian Ripley).
279    
280    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
283    
284            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
285    
286    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * src/lgCMatrix.c (lgCMatrix_diag): new function
289            * R/lgCMatrix.R (diag): for new method
290    
291            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
292                 ==> construction of illegal "*gTMatrix" via new() should
293                 now be much less easy:
294            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
295    
296            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
297                    directly.
298            * man/Matrix.Rd: documents it.
299    
300    2006-07-06  Douglas Bates  <bates@R-project.org>
301    
302            * src/pedigree.c (pedigree_inbreeding): Correction in
303            initialization.  This function is not currently being used and is
304            not fully tested.
305    
306            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
307            Introduced the glmer class.  Added code for mcmcmsamp on glmer
308            objects.  Modified validity check on pedigree objects to account
309            for nonparallel patterns of missingness of parents.
310    
311            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
312            class.
313    
314    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/pMatrix.R: coercion pMatrix -> Tsparse
317    
318    2006-06-12  Douglas Bates  <bates@R-project.org>
319    
320            * DESCRIPTION (Version): 0.995-11 released to CRAN
321    
322            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
323            the output from mcmcsamp.
324    
325    2006-06-10  Douglas Bates  <bates@R-project.org>
326    
327            * R/lmer.R (simulestimate): added C code for calculating the trace
328            of the hat matrix.
329    
330    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
333            classes.
334            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
335    
336    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/dgTMatrix.R (colSums): etc. All four of
339            colSums(), rowSums(), colMeans(), rowMeans() now should work for
340            all "Matrices".
341    
342    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * R/lmer.R (panel.ci): Add a reference line at zero and a
345            background grid to the qqmath plot of ranef.lmer.
346    
347    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
348    
349            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
350            grouping factors to be specified in the formula as (1|foo/bar).
351    
352    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
353    
354            * R/lmer.R (findbars and others): Change check of is.numeric to
355            !is.language to resolve the bug reported by Jacob Wegelin.
356    
357            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
358            code to evaluate inbreeding coefficients without calculating T,
359            based on code in Sargolzaei and Iwaisaki's paper.
360    
361    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
364            generic and mer methods for isNested and denomDF. This denomDF was
365            an attempt to emulate that in lme but I don't think that makes
366            sense.  Use the trace of the hat matrix instead.
367    
368    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
371            the C code depending on a slot structure that's no longer valid.
372            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
373    
374    
375    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
376    
377            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
378            of lowerTriMatrix generic and methods to tril (also upper to triu)
379            and added a general band extractor.
380    
381    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
382    
383            * R/pedigree.R (pedigree): Replace sire and dam values outside the
384            allowable range with NAs. Added a corresponding check in the
385            validity check for the pedigree class.
386    
387            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
388            crossprod methods now inherits from symmetricMatrix.
389    
390    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
391    
392            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
393            generics lowerTriMatrix and upperTriMatrix along with methods for
394            the Csparse virtual class.  Also added a C function Csparse_band
395            that implements these methods by calling cholmod_band.
396    
397    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
400            erased when it was NULL.  This led to invalid subselections!
401    
402    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
403    
404            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
405            in method for "t" so as not to lose the unit diagonal property.
406    
407    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
408    
409            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
410            and methods.  This is now an option to the ranef method for the
411            mer class.
412    
413            * src/cs_utils.c: Ensure that the nz component is -1 for a
414            compressed column-oriented matrix.  Minor formatting cleanup.
415    
416            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
417            objects.
418    
419    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
422            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
423    
424    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
425    
426            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
427            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
428    
429            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
430            for the dtCMatrix class.
431    
432    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
433    
434            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
435            and methods for it.
436    
437    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
440            arguments, such that M %*% 1:6 now works
441            * Tests/matprod.R: test the above
442    
443    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
444    
445            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
446            the ranef.lmer class.
447    
448            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
449            methods to extract the posterior variances from the bVar slot.
450    
451    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
454            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
455    
456            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
457            * tests/simple: (extended)
458    
459            * R/sparseMatrix.R (isTriangular): now using much improved
460            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
461    
462    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
463    
464            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
465            (problem report from Franklin Parlamis).  This should be done
466            generally.
467    
468    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
469    
470            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
471            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
472            update the plot methods.
473    
474    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
475    
476            * R/lmer.R (resid and ranef methods):  Added methods for the
477            "residuals" and "resid" generic but only for linear mixed model
478            fits.  Changed the ranef method to return a list of data frames so
479            that the plot methods now work.
480    
481    2006-03-16  Douglas Bates  <bates@bates2>
482    
483            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
484            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
485    
486            * DESCRIPTION (Date): New release
487    
488    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
491    
492            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
493            * man/KNex.Rd: and other help files
494            * tests/*.R: several ones needed adaption
495            * inst/doc/Comparisons.Rnw: ditto
496    
497    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
500    
501            * tests/indexing.R: tests for new [<- methods for sparse matrices.
502    
503    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
506    
507            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
508    
509    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/dMatrix.R: enable things like  M [ M < 10 ]
512            * R/dgeMatrix.R: implement it
513    
514    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/AllClass.R: define "summary.mer" and "*.lmer"
517            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
518            * R/lmer.R (show): now works with summary()
519    
520    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
523            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
524                    support the above
525    
526    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
527    
528            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
529            Use glmFit$prior.weights for weights in a glmm.
530            Allow an option usePQL = FALSE to skip the PQL steps for the
531            Laplace method (and, in time, the AGQ method).
532    
533            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
534            into a separate function internal_mer_Xfactor to be able to call
535            it from internal_bhat.
536    
537    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * tests/Class+Meth.R (tstMatrixClass): function for much better
540            testing; now again of all actual classes.
541    
542            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
543                    use macros and define make_d_matrix_* and make_i_matrix_*
544                    where _i_ is for the ldense routines:
545    
546            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
547            * src/ldense.c (lsyMatrix_as_lgeMatrix):
548    
549            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
550    
551    
552    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
555                    many different kinds of matrices.
556            * R/*.R: quite a few new methods were needed for R CMD check with
557                    new Matrix().  Very good for users playing around.
558    
559    
560    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * src/dgeMatrix.c (dMatrix_validate): new
563            * src/Mutils.c (dense_nonpacked_validate): new
564    
565            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
566    
567    
568    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
569    
570            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
571    
572    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
573    
574            * DESCRIPTION (Version): 0.99-6 released to CRAN
575    
576            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
577            segfault in cases with multiple non-nested grouping factors.
578    
579    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
582                    (Depends): also on 'utils'
583    
584            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
585            * R/diagMatrix.R (Diagonal): constructor and methods for
586            diagonal matrices
587    
588            * R/ltTMatrix.R: new "minimal methods"
589    
590    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
593            all methods (and help files).
594    
595    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
598                    for case (dimn.  op  no_dimn.)
599    
600    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * DESCRIPTION (Version): 0.99-2  released to CRAN
603    
604    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
605    
606            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
607            by Julian Faraway.
608    
609    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Auxiliaries.R (try_as): new utility
612            * R/sparseMatrix.R: use try_as() in coercion to original class
613    
614    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
617    
618    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/Auxiliaries.R (dimNamesCheck): added
621    
622            * R/Matrix.R (as.array), (as.vector): new
623    
624    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
627                    default.
628            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
629                    "pMatrix" now contains "sparseMatrix"
630    
631    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * tests/Class+Meth.R: new tests; t(t(m)) == m
634    
635            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
636    
637            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
638            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
639    
640            * R/dspMatrix.R: typo in "t" method
641    
642    2005-09-18  Douglas Bates  <bates@wisc.edu>
643    
644            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
645            * R/Tsparse.R: instead of R/gTMatrix.R
646            * R/Csparse.R: new
647            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
648            * src/Tsparse.c: new; many trivial methods calling cholmod_()
649            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
650                            via cholmod
651    
652    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/Auxiliaries.R (non0ind): new function using new C code
655            * src/dgCMatrix.c (compressed_non_0_ij): new utility
656    
657    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
658    
659            * src/chm_common.h: header file required by all C sources that
660            call CHOLMOD functions.  It defines a cholmod_common structure
661            called 'c' whose address is passed as the last argument to
662            (virtually) every CHOLMOD function.
663    
664            * src/Pattern.c: Simple example of the use of CHOLMOD.
665    
666            * src/init.c: initialize and finalize the cholmod_common structure.
667    
668            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
669            LDL and CCOLAMD from the U. of Florida sparse matrix library.
670    
671    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * inst/test-tools.R: new file collecting the utility functions used
674                    in ./tests/*.R
675    
676            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
677            * R/Matrix.R (cbind2): methods for NULL and missing
678    
679    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/AllClass.R: new "index" class for "[" and "[<-":
682                    First cut at "symmetricMatrix" and "triangularMatrix"
683            * R/gTMatrix.R (.ind.prep): new function;
684                    Logical and character indexing now work too.
685            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
686            * tests/indexing.R: new, including *.Rout.save
687            * tests/dgTMatrix.R: new
688    
689  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
690    
691          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 696 
696  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
699          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
700          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
701    
702  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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