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revision 820, Wed Jul 27 23:07:04 2005 UTC revision 1298, Sat Jun 10 19:56:18 2006 UTC
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1  2005-07-27  Douglas Bates  <bates@localhost.localdomain>  2006-06-10  Douglas Bates  <bates@R-project.org>
2    
3          * man/sleep.Rd: Added the sleep data set.          * R/lmer.R (simulestimate): added
4    
5  2005-07-12  Douglas Bates  <bates@localhost.localdomain>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
8            classes.
9    
10    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/dgTMatrix.R (colSums): etc. All four of
13            colSums(), rowSums(), colMeans(), rowMeans() now should work for
14            all "Matrices".
15    
16    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
17    
18            * R/lmer.R (panel.ci): Add a reference line at zero and a
19            background grid to the qqmath plot of ranef.lmer.
20    
21    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
24            grouping factors to be specified in the formula as (1|foo/bar).
25    
26    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/lmer.R (findbars and others): Change check of is.numeric to
29            !is.language to resolve the bug reported by Jacob Wegelin.
30    
31            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
32            code to evaluate inbreeding coefficients without calculating T,
33            based on code in Sargolzaei and Iwaisaki's paper.
34    
35    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
38            generic and mer methods for isNested and denomDF. This denomDF was
39            an attempt to emulate that in lme but I don't think that makes
40            sense.  Use the trace of the hat matrix instead.
41    
42    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
45            the C code depending on a slot structure that's no longer valid.
46            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
47    
48    
49    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
50    
51            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
52            of lowerTriMatrix generic and methods to tril (also upper to triu)
53            and added a general band extractor.
54    
55    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * R/pedigree.R (pedigree): Replace sire and dam values outside the
58            allowable range with NAs. Added a corresponding check in the
59            validity check for the pedigree class.
60    
61            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
62            crossprod methods now inherits from symmetricMatrix.
63    
64    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
67            generics lowerTriMatrix and upperTriMatrix along with methods for
68            the Csparse virtual class.  Also added a C function Csparse_band
69            that implements these methods by calling cholmod_band.
70    
71    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
74            erased when it was NULL.  This led to invalid subselections!
75    
76    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
77    
78            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
79            in method for "t" so as not to lose the unit diagonal property.
80    
81    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
84            and methods.  This is now an option to the ranef method for the
85            mer class.
86    
87            * src/cs_utils.c: Ensure that the nz component is -1 for a
88            compressed column-oriented matrix.  Minor formatting cleanup.
89    
90            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
91            objects.
92    
93    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
96            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
97    
98    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
101            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
102    
103            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
104            for the dtCMatrix class.
105    
106    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
107    
108            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
109            and methods for it.
110    
111    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
114            arguments, such that M %*% 1:6 now works
115            * Tests/matprod.R: test the above
116    
117    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
120            the ranef.lmer class.
121    
122            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
123            methods to extract the posterior variances from the bVar slot.
124    
125    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
128            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
129    
130            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
131            * tests/simple: (extended)
132    
133            * R/sparseMatrix.R (isTriangular): now using much improved
134            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
135    
136    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
139            (problem report from Franklin Parlamis).  This should be done
140            generally.
141    
142    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
143    
144            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
145            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
146            update the plot methods.
147    
148    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * R/lmer.R (resid and ranef methods):  Added methods for the
151            "residuals" and "resid" generic but only for linear mixed model
152            fits.  Changed the ranef method to return a list of data frames so
153            that the plot methods now work.
154    
155    2006-03-16  Douglas Bates  <bates@bates2>
156    
157            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
158            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
159    
160            * DESCRIPTION (Date): New release
161    
162    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
165    
166            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
167            * man/KNex.Rd: and other help files
168            * tests/*.R: several ones needed adaption
169            * inst/doc/Comparisons.Rnw: dito
170    
171    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
174    
175            * tests/indexing.R: tests for new [<- methods for sparse matrices.
176    
177    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
180    
181            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
182    
183    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/dMatrix.R: enable things like  M [ M < 10 ]
186            * R/dgeMatrix.R: implement it
187    
188    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/AllClass.R: define "summary.mer" and "*.lmer"
191            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
192            * R/lmer.R (show): now works with summary()
193    
194    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
197            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
198                    support the above
199    
200    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
201    
202            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
203            Use glmFit$prior.weights for weights in a glmm.
204            Allow an option usePQL = FALSE to skip the PQL steps for the
205            Laplace method (and, in time, the AGQ method).
206    
207            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
208            into a separate function internal_mer_Xfactor to be able to call
209            it from internal_bhat.
210    
211    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * tests/Class+Meth.R (tstMatrixClass): function for much better
214            testing; now again of all actual classes.
215    
216            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
217                    use macros and define make_d_matrix_* and make_i_matrix_*
218                    where _i_ is for the ldense routines:
219    
220            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
221            * src/ldense.c (lsyMatrix_as_lgeMatrix):
222    
223            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
224    
225    
226    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
229                    many different kinds of matrices.
230            * R/*.R: quite a few new methods were needed for R CMD check with
231                    new Matrix().  Very good for users playing around.
232    
233    
234    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/dgeMatrix.c (dMatrix_validate): new
237            * src/Mutils.c (dense_nonpacked_validate): new
238    
239            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
240    
241    
242    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
245    
246    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * DESCRIPTION (Version): 0.99-6 released to CRAN
249    
250            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
251            segfault in cases with multiple non-nested grouping factors.
252    
253    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
256                    (Depends): also on 'utils'
257    
258            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
259            * R/diagMatrix.R (Diagonal): constructor and methods for
260            diagonal matrices
261    
262            * R/ltTMatrix.R: new "minimal methods"
263    
264    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
267            all methods (and help files).
268    
269    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
272                    for case (dimn.  op  no_dimn.)
273    
274    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * DESCRIPTION (Version): 0.99-2  released to CRAN
277    
278    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
281            by Julian Faraway.
282    
283    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Auxiliaries.R (try_as): new utility
286            * R/sparseMatrix.R: use try_as() in coercion to original class
287    
288    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
291    
292    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/Auxiliaries.R (dimNamesCheck): added
295    
296            * R/Matrix.R (as.array), (as.vector): new
297    
298    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
301                    default.
302            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
303                    "pMatrix" now contains "sparseMatrix"
304    
305    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * tests/Class+Meth.R: new tests; t(t(m)) == m
308    
309            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
310    
311            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
312            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
313    
314            * R/dspMatrix.R: typo in "t" method
315    
316    2005-09-18  Douglas Bates  <bates@wisc.edu>
317    
318            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
319            * R/Tsparse.R: instead of R/gTMatrix.R
320            * R/Csparse.R: new
321            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
322            * src/Tsparse.c: new; many trivial methods calling cholmod_()
323            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
324                            via cholmod
325    
326    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Auxiliaries.R (non0ind): new function using new C code
329            * src/dgCMatrix.c (compressed_non_0_ij): new utility
330    
331    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
332    
333            * src/chm_common.h: header file required by all C sources that
334            call CHOLMOD functions.  It defines a cholmod_common structure
335            called 'c' whose address is passed as the last argument to
336            (virtually) every CHOLMOD function.
337    
338            * src/Pattern.c: Simple example of the use of CHOLMOD.
339    
340            * src/init.c: initialize and finalize the cholmod_common structure.
341    
342            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
343            LDL and CCOLAMD from the U. of Florida sparse matrix library.
344    
345    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * inst/test-tools.R: new file collecting the utility functions used
348                    in ./tests/*.R
349    
350            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
351            * R/Matrix.R (cbind2): methods for NULL and missing
352    
353    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/AllClass.R: new "index" class for "[" and "[<-":
356                    First cut at "symmetricMatrix" and "triangularMatrix"
357            * R/gTMatrix.R (.ind.prep): new function;
358                    Logical and character indexing now work too.
359            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
360            * tests/indexing.R: new, including *.Rout.save
361            * tests/dgTMatrix.R: new
362    
363    2005-08-29  Douglas Bates  <bates@wisc.edu>
364    
365            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
366            indicator pos not being updated.  Also enforced upper triangular
367            for symmetric case.  Need to coerce edges component of elements of
368            edge list - grr! (Why don't they define their classes cleanly?)
369    
370    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/Matrix.R:  added first "[<-" methods; not yet functional
373            * R/denseMatrix.R: dito
374            * man/Subassign-methods.Rd: new help file for these
375    
376    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * DESCRIPTION (Version): 0.98-6
379    
380            * R/denseMatrix.R: new file for "[" fallback methods for all dense
381            matrices.
382    
383    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
386                    as( <logical>, "matrix")
387    
388            * R/pMatrix.R: coercion to "lgTMatrix"
389    
390            * R/gTMatrix.R: new virtual class to define "[" methods for.
391            * man/gTMatrix-class.Rd:
392            * General slight re-organization of where "[" methods are defined.
393              more to come.
394    
395    2005-08-18  Douglas Bates  <bates@wisc.edu>
396    
397            * DESCRIPTION (Version): 0.98-5  released to CRAN
398    
399            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
400            * .....
401    
402    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
403    
404            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
405            or glmer objects.
406    
407    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
410    
411    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
412    
413            * R/HBMM.R: finish re-writing R-only code.
414    
415    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
416    
417            * man/externalFormats.Rd: move documentation for writeHB and
418            writeMM here.
419    
420            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
421            (suggested by Paul Roecker).
422    
423            * tests/validObj.R (assertError): Comment out test that is failing
424            after recent changes in r-devel.
425    
426    
427    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/AllClass.R: intermediate virtual class "denseMatrix"
430            * man/denseMatrix-class.Rd
431            * NAMESPACE: export it, and also export
432            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
433    
434    2005-08-10  Douglas Bates  <bates@wisc.edu>
435    
436            * DESCRIPTION (Version): 0.98-3 to CRAN
437    
438            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
439            matrix_solve code (which was really, really wrong).
440    
441    2005-08-07  Douglas Bates  <bates@wisc.edu>
442    
443            * DESCRIPTION (Version): 0.98-2
444    
445            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
446    
447            * R/lmer.R (abbrvNms): new
448            * R/lmer.R (mcmcsamp): allow transformed parameters
449            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
450            for the Harwell-Boeing and the MatrixMarket formats.
451    
452    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * man/dtrMatrix-class.Rd: add examples
455            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
456    
457            * TODO: note the dtpMatrix (docu) bug
458    
459            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
460            in order to ensure that new as.matrix() is used by old functions,
461            e.g., svd(), qr(), eigen(), dist(),..;
462                  apply(), also matplot() or pairs().
463    
464    
465    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
468              add comments about 'control' / lmerControl() arguments
469    
470    2005-07-27  Douglas Bates  <bates@wisc.edu>
471    
472            * man/sleepstudy.Rd: Added the sleep data set.
473            * DESCRIPTION (Version): 0.98-1  released to CRAN
474    
475    2005-07-12  Douglas Bates  <bates@wisc.edu>
476            * man/sleepstudy.Rd: Added the sleep data set.
477    
478          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
479          .Call calls that were producing spurious output.          .Call calls that were producing spurious output.
480    
481  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-07-05  Douglas Bates  <bates@wisc.edu>
482    
483          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
484          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
485          Lancelot).          Lancelot).
486    
487  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
488    
489          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
490          unidimensional case.          unidimensional case.
491    
492  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
493    
494          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
495    
496          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
497    
498  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
499    
500          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
501          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
502    
503  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
504    
505          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
506    
507  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
508    
509          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
510          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
511    
512  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
513    
514          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
515          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 47  Line 518 
518          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
519          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
520    
521  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
522    
523          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
524          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
525    
526  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
527    
528          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
529          multiplication operation.          multiplication operation.
# Line 65  Line 536 
536    
537          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
538    
539  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
540    
541          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
542    
543          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
544    
545    
546  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
547    
548          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
549    
# Line 81  Line 552 
552          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
553          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
554    
555  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
556    
557          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
558    
# Line 107  Line 578 
578          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
579            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
580    
581  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
582    
583          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
584          * ....          * ....
585    
586  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
587    
588          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
589    
# Line 127  Line 598 
598            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
599          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
600    
601  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
602    
603          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
604    
605  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
606    
607          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
608    
609  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
610    
611          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
612          the package.          the package.
# Line 183  Line 654 
654    
655          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
656    
657  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
658    
659          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
660          for the geMatrix class.          for the geMatrix class.
661    
662  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
663    
664          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
665    
666          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
667    
668  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
669    
670          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
671          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
672    
673  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
674    
675          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
676    
677  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
678    
679          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
680          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
681    
682  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
683    
684          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
685    
686          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
687          for tripletMatrix to matrix.          for tripletMatrix to matrix.
688    
689  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
690    
691          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
692          no longer used.          no longer used.
# Line 227  Line 698 
698          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
699          Fixes part but not all of #15.          Fixes part but not all of #15.
700    
701  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
702    
703          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
704          scalar grouping factors corrected.          scalar grouping factors corrected.
705    
706  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
707    
708          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
709    
710  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
711    
712          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
713          .h file can be included.          .h file can be included.
714    
715  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
716    
717          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
718          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
719    
720          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
721    
722  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
723    
724          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
725    
726  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
727    
728          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
729    
730  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
731    
732          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
733    
734  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
735    
736          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
737    
738  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
739    
740          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
741          routines.          routines.
742    
743  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
744    
745          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
746    
747  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
748    
749          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
750    

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