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revision 809, Tue Jul 12 23:00:50 2005 UTC revision 1271, Thu May 18 06:47:09 2006 UTC
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1  2005-07-12  Douglas Bates  <bates@localhost.localdomain>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
4            the C code depending on a slot structure that's no longer valid.
5            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
6    
7    
8    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
9    
10            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
11            of lowerTriMatrix generic and methods to tril (also upper to triu)
12            and added a general band extractor.
13    
14    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
15    
16            * R/pedigree.R (pedigree): Replace sire and dam values outside the
17            allowable range with NAs. Added a corresponding check in the
18            validity check for the pedigree class.
19    
20            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
21            crossprod methods now inherits from symmetricMatrix.
22    
23    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
24    
25            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
26            generics lowerTriMatrix and upperTriMatrix along with methods for
27            the Csparse virtual class.  Also added a C function Csparse_band
28            that implements these methods by calling cholmod_band.
29    
30    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
33            erased when it was NULL.  This led to invalid subselections!
34    
35    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
38            in method for "t" so as not to lose the unit diagonal property.
39    
40    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
43            and methods.  This is now an option to the ranef method for the
44            mer class.
45    
46            * src/cs_utils.c: Ensure that the nz component is -1 for a
47            compressed column-oriented matrix.  Minor formatting cleanup.
48    
49            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
50            objects.
51    
52    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
55            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
56    
57    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
58    
59            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
60            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
61    
62            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
63            for the dtCMatrix class.
64    
65    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
68            and methods for it.
69    
70    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
73            arguments, such that M %*% 1:6 now works
74            * Tests/matprod.R: test the above
75    
76    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
77    
78            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
79            the ranef.lmer class.
80    
81            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
82            methods to extract the posterior variances from the bVar slot.
83    
84    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
87            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
88    
89            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
90            * tests/simple: (extended)
91    
92            * R/sparseMatrix.R (isTriangular): now using much improved
93            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
94    
95    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
96    
97            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
98            (problem report from Franklin Parlamis).  This should be done
99            generally.
100    
101    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
102    
103            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
104            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
105            update the plot methods.
106    
107    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * R/lmer.R (resid and ranef methods):  Added methods for the
110            "residuals" and "resid" generic but only for linear mixed model
111            fits.  Changed the ranef method to return a list of data frames so
112            that the plot methods now work.
113    
114    2006-03-16  Douglas Bates  <bates@bates2>
115    
116            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
117            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
118    
119            * DESCRIPTION (Date): New release
120    
121    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
124    
125            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
126            * man/KNex.Rd: and other help files
127            * tests/*.R: several ones needed adaption
128            * inst/doc/Comparisons.Rnw: dito
129    
130    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
133    
134            * tests/indexing.R: tests for new [<- methods for sparse matrices.
135    
136    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
139    
140            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
141    
142    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dMatrix.R: enable things like  M [ M < 10 ]
145            * R/dgeMatrix.R: implement it
146    
147    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/AllClass.R: define "summary.mer" and "*.lmer"
150            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
151            * R/lmer.R (show): now works with summary()
152    
153    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
156            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
157                    support the above
158    
159    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
162            Use glmFit$prior.weights for weights in a glmm.
163            Allow an option usePQL = FALSE to skip the PQL steps for the
164            Laplace method (and, in time, the AGQ method).
165    
166            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
167            into a separate function internal_mer_Xfactor to be able to call
168            it from internal_bhat.
169    
170    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/Class+Meth.R (tstMatrixClass): function for much better
173            testing; now again of all actual classes.
174    
175            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
176                    use macros and define make_d_matrix_* and make_i_matrix_*
177                    where _i_ is for the ldense routines:
178    
179            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
180            * src/ldense.c (lsyMatrix_as_lgeMatrix):
181    
182            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
183    
184    
185    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
188                    many different kinds of matrices.
189            * R/*.R: quite a few new methods were needed for R CMD check with
190                    new Matrix().  Very good for users playing around.
191    
192    
193    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/dgeMatrix.c (dMatrix_validate): new
196            * src/Mutils.c (dense_nonpacked_validate): new
197    
198            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
199    
200    
201    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
202    
203            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
204    
205    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
206    
207            * DESCRIPTION (Version): 0.99-6 released to CRAN
208    
209            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
210            segfault in cases with multiple non-nested grouping factors.
211    
212    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
215                    (Depends): also on 'utils'
216    
217            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
218            * R/diagMatrix.R (Diagonal): constructor and methods for
219            diagonal matrices
220    
221            * R/ltTMatrix.R: new "minimal methods"
222    
223    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
226            all methods (and help files).
227    
228    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
231                    for case (dimn.  op  no_dimn.)
232    
233    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
234    
235            * DESCRIPTION (Version): 0.99-2  released to CRAN
236    
237    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
240            by Julian Faraway.
241    
242    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/Auxiliaries.R (try_as): new utility
245            * R/sparseMatrix.R: use try_as() in coercion to original class
246    
247    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
250    
251    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (dimNamesCheck): added
254    
255            * R/Matrix.R (as.array), (as.vector): new
256    
257    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
260                    default.
261            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
262                    "pMatrix" now contains "sparseMatrix"
263    
264    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/Class+Meth.R: new tests; t(t(m)) == m
267    
268            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
269    
270            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
271            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
272    
273            * R/dspMatrix.R: typo in "t" method
274    
275    2005-09-18  Douglas Bates  <bates@wisc.edu>
276    
277            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
278            * R/Tsparse.R: instead of R/gTMatrix.R
279            * R/Csparse.R: new
280            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
281            * src/Tsparse.c: new; many trivial methods calling cholmod_()
282            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
283                            via cholmod
284    
285    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/Auxiliaries.R (non0ind): new function using new C code
288            * src/dgCMatrix.c (compressed_non_0_ij): new utility
289    
290    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
291    
292            * src/chm_common.h: header file required by all C sources that
293            call CHOLMOD functions.  It defines a cholmod_common structure
294            called 'c' whose address is passed as the last argument to
295            (virtually) every CHOLMOD function.
296    
297            * src/Pattern.c: Simple example of the use of CHOLMOD.
298    
299            * src/init.c: initialize and finalize the cholmod_common structure.
300    
301            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
302            LDL and CCOLAMD from the U. of Florida sparse matrix library.
303    
304    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * inst/test-tools.R: new file collecting the utility functions used
307                    in ./tests/*.R
308    
309            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
310            * R/Matrix.R (cbind2): methods for NULL and missing
311    
312    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/AllClass.R: new "index" class for "[" and "[<-":
315                    First cut at "symmetricMatrix" and "triangularMatrix"
316            * R/gTMatrix.R (.ind.prep): new function;
317                    Logical and character indexing now work too.
318            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
319            * tests/indexing.R: new, including *.Rout.save
320            * tests/dgTMatrix.R: new
321    
322    2005-08-29  Douglas Bates  <bates@wisc.edu>
323    
324            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
325            indicator pos not being updated.  Also enforced upper triangular
326            for symmetric case.  Need to coerce edges component of elements of
327            edge list - grr! (Why don't they define their classes cleanly?)
328    
329    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R:  added first "[<-" methods; not yet functional
332            * R/denseMatrix.R: dito
333            * man/Subassign-methods.Rd: new help file for these
334    
335    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * DESCRIPTION (Version): 0.98-6
338    
339            * R/denseMatrix.R: new file for "[" fallback methods for all dense
340            matrices.
341    
342    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
345                    as( <logical>, "matrix")
346    
347            * R/pMatrix.R: coercion to "lgTMatrix"
348    
349            * R/gTMatrix.R: new virtual class to define "[" methods for.
350            * man/gTMatrix-class.Rd:
351            * General slight re-organization of where "[" methods are defined.
352              more to come.
353    
354    2005-08-18  Douglas Bates  <bates@wisc.edu>
355    
356            * DESCRIPTION (Version): 0.98-5  released to CRAN
357    
358            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
359            * .....
360    
361    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
362    
363            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
364            or glmer objects.
365    
366    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
369    
370    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
371    
372            * R/HBMM.R: finish re-writing R-only code.
373    
374    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
375    
376            * man/externalFormats.Rd: move documentation for writeHB and
377            writeMM here.
378    
379            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
380            (suggested by Paul Roecker).
381    
382            * tests/validObj.R (assertError): Comment out test that is failing
383            after recent changes in r-devel.
384    
385    
386    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/AllClass.R: intermediate virtual class "denseMatrix"
389            * man/denseMatrix-class.Rd
390            * NAMESPACE: export it, and also export
391            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
392    
393    2005-08-10  Douglas Bates  <bates@wisc.edu>
394    
395            * DESCRIPTION (Version): 0.98-3 to CRAN
396    
397            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
398            matrix_solve code (which was really, really wrong).
399    
400    2005-08-07  Douglas Bates  <bates@wisc.edu>
401    
402            * DESCRIPTION (Version): 0.98-2
403    
404            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
405    
406            * R/lmer.R (abbrvNms): new
407            * R/lmer.R (mcmcsamp): allow transformed parameters
408            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
409            for the Harwell-Boeing and the MatrixMarket formats.
410    
411    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * man/dtrMatrix-class.Rd: add examples
414            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
415    
416            * TODO: note the dtpMatrix (docu) bug
417    
418            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
419            in order to ensure that new as.matrix() is used by old functions,
420            e.g., svd(), qr(), eigen(), dist(),..;
421                  apply(), also matplot() or pairs().
422    
423    
424    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
427              add comments about 'control' / lmerControl() arguments
428    
429    2005-07-27  Douglas Bates  <bates@wisc.edu>
430    
431            * man/sleepstudy.Rd: Added the sleep data set.
432            * DESCRIPTION (Version): 0.98-1  released to CRAN
433    
434    2005-07-12  Douglas Bates  <bates@wisc.edu>
435            * man/sleepstudy.Rd: Added the sleep data set.
436    
437          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
438          .Call calls that were producing spurious output.          .Call calls that were producing spurious output.
439    
440  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-07-05  Douglas Bates  <bates@wisc.edu>
441    
442          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
443          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
444          Lancelot).          Lancelot).
445    
446  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
447    
448          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
449          unidimensional case.          unidimensional case.
450    
451  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
452    
453          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
454    
455          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
456    
457  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
458    
459          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
460          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
461    
462  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
463    
464          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
465    
466  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
467    
468          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
469          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
470    
471  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
472    
473          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
474          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 43  Line 477 
477          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
478          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
479    
480  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
481    
482          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
483          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
484    
485  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
486    
487          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
488          multiplication operation.          multiplication operation.
# Line 61  Line 495 
495    
496          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
497    
498  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
499    
500          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
501    
502          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
503    
504    
505  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
506    
507          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
508    
# Line 77  Line 511 
511          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
512          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
513    
514  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
515    
516          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
517    
# Line 103  Line 537 
537          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
538            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
539    
540  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
541    
542          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
543          * ....          * ....
544    
545  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
546    
547          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
548    
# Line 123  Line 557 
557            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
558          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
559    
560  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
561    
562          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
563    
564  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
565    
566          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
567    
568  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
569    
570          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
571          the package.          the package.
# Line 179  Line 613 
613    
614          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
615    
616  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
617    
618          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
619          for the geMatrix class.          for the geMatrix class.
620    
621  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
622    
623          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
624    
625          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
626    
627  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
628    
629          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
630          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
631    
632  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
633    
634          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
635    
636  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
637    
638          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
639          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
640    
641  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
642    
643          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
644    
645          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
646          for tripletMatrix to matrix.          for tripletMatrix to matrix.
647    
648  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
649    
650          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
651          no longer used.          no longer used.
# Line 223  Line 657 
657          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
658          Fixes part but not all of #15.          Fixes part but not all of #15.
659    
660  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
661    
662          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
663          scalar grouping factors corrected.          scalar grouping factors corrected.
664    
665  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
666    
667          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
668    
669  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
670    
671          * 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
672          .h file can be included.          .h file can be included.
673    
674  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
675    
676          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
677          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
678    
679          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
680    
681  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
682    
683          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
684    
685  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
686    
687          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
688    
689  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
690    
691          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
692    
693  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
694    
695          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
696    
697  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
698    
699          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
700          routines.          routines.
701    
702  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
703    
704          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
705    
706  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
707    
708          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
709    

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