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revision 820, Wed Jul 27 23:07:04 2005 UTC revision 1288, Thu Jun 1 20:41:20 2006 UTC
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1  2005-07-27  Douglas Bates  <bates@localhost.localdomain>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
2    
3          * man/sleep.Rd: Added the sleep data set.          * R/lmer.R (panel.ci): Add a reference line at zero and a
4            background grid to the qqmath plot of ranef.lmer.
5    
6  2005-07-12  Douglas Bates  <bates@localhost.localdomain>  2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
9            grouping factors to be specified in the formula as (1|foo/bar).
10    
11    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/lmer.R (findbars and others): Change check of is.numeric to
14            !is.language to resolve the bug reported by Jacob Wegelin.
15    
16            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
17            code to evaluate inbreeding coefficients without calculating T,
18            based on code in Sargolzaei and Iwaisaki's paper.
19    
20    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
23            generic and mer methods for isNested and denomDF. This denomDF was
24            an attempt to emulate that in lme but I don't think that makes
25            sense.  Use the trace of the hat matrix instead.
26    
27    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
30            the C code depending on a slot structure that's no longer valid.
31            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
32    
33    
34    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
35    
36            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
37            of lowerTriMatrix generic and methods to tril (also upper to triu)
38            and added a general band extractor.
39    
40    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * R/pedigree.R (pedigree): Replace sire and dam values outside the
43            allowable range with NAs. Added a corresponding check in the
44            validity check for the pedigree class.
45    
46            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
47            crossprod methods now inherits from symmetricMatrix.
48    
49    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
50    
51            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
52            generics lowerTriMatrix and upperTriMatrix along with methods for
53            the Csparse virtual class.  Also added a C function Csparse_band
54            that implements these methods by calling cholmod_band.
55    
56    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
59            erased when it was NULL.  This led to invalid subselections!
60    
61    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
64            in method for "t" so as not to lose the unit diagonal property.
65    
66    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
69            and methods.  This is now an option to the ranef method for the
70            mer class.
71    
72            * src/cs_utils.c: Ensure that the nz component is -1 for a
73            compressed column-oriented matrix.  Minor formatting cleanup.
74    
75            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
76            objects.
77    
78    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
81            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
82    
83    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
86            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
87    
88            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
89            for the dtCMatrix class.
90    
91    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
94            and methods for it.
95    
96    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
99            arguments, such that M %*% 1:6 now works
100            * Tests/matprod.R: test the above
101    
102    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
105            the ranef.lmer class.
106    
107            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
108            methods to extract the posterior variances from the bVar slot.
109    
110    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
113            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
114    
115            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
116            * tests/simple: (extended)
117    
118            * R/sparseMatrix.R (isTriangular): now using much improved
119            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
120    
121    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
124            (problem report from Franklin Parlamis).  This should be done
125            generally.
126    
127    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
130            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
131            update the plot methods.
132    
133    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
134    
135            * R/lmer.R (resid and ranef methods):  Added methods for the
136            "residuals" and "resid" generic but only for linear mixed model
137            fits.  Changed the ranef method to return a list of data frames so
138            that the plot methods now work.
139    
140    2006-03-16  Douglas Bates  <bates@bates2>
141    
142            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
143            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
144    
145            * DESCRIPTION (Date): New release
146    
147    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
150    
151            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
152            * man/KNex.Rd: and other help files
153            * tests/*.R: several ones needed adaption
154            * inst/doc/Comparisons.Rnw: dito
155    
156    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
159    
160            * tests/indexing.R: tests for new [<- methods for sparse matrices.
161    
162    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
165    
166            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
167    
168    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/dMatrix.R: enable things like  M [ M < 10 ]
171            * R/dgeMatrix.R: implement it
172    
173    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/AllClass.R: define "summary.mer" and "*.lmer"
176            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
177            * R/lmer.R (show): now works with summary()
178    
179    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
182            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
183                    support the above
184    
185    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
186    
187            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
188            Use glmFit$prior.weights for weights in a glmm.
189            Allow an option usePQL = FALSE to skip the PQL steps for the
190            Laplace method (and, in time, the AGQ method).
191    
192            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
193            into a separate function internal_mer_Xfactor to be able to call
194            it from internal_bhat.
195    
196    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * tests/Class+Meth.R (tstMatrixClass): function for much better
199            testing; now again of all actual classes.
200    
201            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
202                    use macros and define make_d_matrix_* and make_i_matrix_*
203                    where _i_ is for the ldense routines:
204    
205            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
206            * src/ldense.c (lsyMatrix_as_lgeMatrix):
207    
208            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
209    
210    
211    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
214                    many different kinds of matrices.
215            * R/*.R: quite a few new methods were needed for R CMD check with
216                    new Matrix().  Very good for users playing around.
217    
218    
219    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * src/dgeMatrix.c (dMatrix_validate): new
222            * src/Mutils.c (dense_nonpacked_validate): new
223    
224            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
225    
226    
227    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
230    
231    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
232    
233            * DESCRIPTION (Version): 0.99-6 released to CRAN
234    
235            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
236            segfault in cases with multiple non-nested grouping factors.
237    
238    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
241                    (Depends): also on 'utils'
242    
243            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
244            * R/diagMatrix.R (Diagonal): constructor and methods for
245            diagonal matrices
246    
247            * R/ltTMatrix.R: new "minimal methods"
248    
249    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
252            all methods (and help files).
253    
254    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
257                    for case (dimn.  op  no_dimn.)
258    
259    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * DESCRIPTION (Version): 0.99-2  released to CRAN
262    
263    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
266            by Julian Faraway.
267    
268    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Auxiliaries.R (try_as): new utility
271            * R/sparseMatrix.R: use try_as() in coercion to original class
272    
273    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
276    
277    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Auxiliaries.R (dimNamesCheck): added
280    
281            * R/Matrix.R (as.array), (as.vector): new
282    
283    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
286                    default.
287            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
288                    "pMatrix" now contains "sparseMatrix"
289    
290    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * tests/Class+Meth.R: new tests; t(t(m)) == m
293    
294            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
295    
296            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
297            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
298    
299            * R/dspMatrix.R: typo in "t" method
300    
301    2005-09-18  Douglas Bates  <bates@wisc.edu>
302    
303            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
304            * R/Tsparse.R: instead of R/gTMatrix.R
305            * R/Csparse.R: new
306            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
307            * src/Tsparse.c: new; many trivial methods calling cholmod_()
308            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
309                            via cholmod
310    
311    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Auxiliaries.R (non0ind): new function using new C code
314            * src/dgCMatrix.c (compressed_non_0_ij): new utility
315    
316    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
317    
318            * src/chm_common.h: header file required by all C sources that
319            call CHOLMOD functions.  It defines a cholmod_common structure
320            called 'c' whose address is passed as the last argument to
321            (virtually) every CHOLMOD function.
322    
323            * src/Pattern.c: Simple example of the use of CHOLMOD.
324    
325            * src/init.c: initialize and finalize the cholmod_common structure.
326    
327            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
328            LDL and CCOLAMD from the U. of Florida sparse matrix library.
329    
330    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * inst/test-tools.R: new file collecting the utility functions used
333                    in ./tests/*.R
334    
335            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
336            * R/Matrix.R (cbind2): methods for NULL and missing
337    
338    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/AllClass.R: new "index" class for "[" and "[<-":
341                    First cut at "symmetricMatrix" and "triangularMatrix"
342            * R/gTMatrix.R (.ind.prep): new function;
343                    Logical and character indexing now work too.
344            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
345            * tests/indexing.R: new, including *.Rout.save
346            * tests/dgTMatrix.R: new
347    
348    2005-08-29  Douglas Bates  <bates@wisc.edu>
349    
350            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
351            indicator pos not being updated.  Also enforced upper triangular
352            for symmetric case.  Need to coerce edges component of elements of
353            edge list - grr! (Why don't they define their classes cleanly?)
354    
355    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Matrix.R:  added first "[<-" methods; not yet functional
358            * R/denseMatrix.R: dito
359            * man/Subassign-methods.Rd: new help file for these
360    
361    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * DESCRIPTION (Version): 0.98-6
364    
365            * R/denseMatrix.R: new file for "[" fallback methods for all dense
366            matrices.
367    
368    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
371                    as( <logical>, "matrix")
372    
373            * R/pMatrix.R: coercion to "lgTMatrix"
374    
375            * R/gTMatrix.R: new virtual class to define "[" methods for.
376            * man/gTMatrix-class.Rd:
377            * General slight re-organization of where "[" methods are defined.
378              more to come.
379    
380    2005-08-18  Douglas Bates  <bates@wisc.edu>
381    
382            * DESCRIPTION (Version): 0.98-5  released to CRAN
383    
384            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
385            * .....
386    
387    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
388    
389            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
390            or glmer objects.
391    
392    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
395    
396    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
397    
398            * R/HBMM.R: finish re-writing R-only code.
399    
400    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
401    
402            * man/externalFormats.Rd: move documentation for writeHB and
403            writeMM here.
404    
405            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
406            (suggested by Paul Roecker).
407    
408            * tests/validObj.R (assertError): Comment out test that is failing
409            after recent changes in r-devel.
410    
411    
412    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/AllClass.R: intermediate virtual class "denseMatrix"
415            * man/denseMatrix-class.Rd
416            * NAMESPACE: export it, and also export
417            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
418    
419    2005-08-10  Douglas Bates  <bates@wisc.edu>
420    
421            * DESCRIPTION (Version): 0.98-3 to CRAN
422    
423            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
424            matrix_solve code (which was really, really wrong).
425    
426    2005-08-07  Douglas Bates  <bates@wisc.edu>
427    
428            * DESCRIPTION (Version): 0.98-2
429    
430            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
431    
432            * R/lmer.R (abbrvNms): new
433            * R/lmer.R (mcmcsamp): allow transformed parameters
434            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
435            for the Harwell-Boeing and the MatrixMarket formats.
436    
437    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * man/dtrMatrix-class.Rd: add examples
440            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
441    
442            * TODO: note the dtpMatrix (docu) bug
443    
444            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
445            in order to ensure that new as.matrix() is used by old functions,
446            e.g., svd(), qr(), eigen(), dist(),..;
447                  apply(), also matplot() or pairs().
448    
449    
450    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
453              add comments about 'control' / lmerControl() arguments
454    
455    2005-07-27  Douglas Bates  <bates@wisc.edu>
456    
457            * man/sleepstudy.Rd: Added the sleep data set.
458            * DESCRIPTION (Version): 0.98-1  released to CRAN
459    
460    2005-07-12  Douglas Bates  <bates@wisc.edu>
461            * man/sleepstudy.Rd: Added the sleep data set.
462    
463          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
464          .Call calls that were producing spurious output.          .Call calls that were producing spurious output.
465    
466  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-07-05  Douglas Bates  <bates@wisc.edu>
467    
468          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
469          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
470          Lancelot).          Lancelot).
471    
472  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
473    
474          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
475          unidimensional case.          unidimensional case.
476    
477  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
478    
479          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
480    
481          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
482    
483  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
484    
485          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
486          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
487    
488  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
489    
490          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
491    
492  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
493    
494          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
495          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
496    
497  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
498    
499          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
500          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 503 
503          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
504          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
505    
506  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
507    
508          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
509          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
510    
511  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
512    
513          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
514          multiplication operation.          multiplication operation.
# Line 65  Line 521 
521    
522          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
523    
524  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
525    
526          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
527    
528          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
529    
530    
531  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
532    
533          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
534    
# Line 81  Line 537 
537          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
538          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
539    
540  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
541    
542          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
543    
# Line 107  Line 563 
563          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
564            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
565    
566  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
567    
568          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
569          * ....          * ....
570    
571  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
572    
573          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
574    
# Line 127  Line 583 
583            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
584          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
585    
586  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
587    
588          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
589    
590  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
591    
592          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
593    
594  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
595    
596          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
597          the package.          the package.
# Line 183  Line 639 
639    
640          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
641    
642  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
643    
644          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
645          for the geMatrix class.          for the geMatrix class.
646    
647  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
648    
649          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
650    
651          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
652    
653  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
654    
655          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
656          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
657    
658  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
659    
660          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
661    
662  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
663    
664          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
665          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
666    
667  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
668    
669          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
670    
671          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
672          for tripletMatrix to matrix.          for tripletMatrix to matrix.
673    
674  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
675    
676          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
677          no longer used.          no longer used.
# Line 227  Line 683 
683          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
684          Fixes part but not all of #15.          Fixes part but not all of #15.
685    
686  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
687    
688          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
689          scalar grouping factors corrected.          scalar grouping factors corrected.
690    
691  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
692    
693          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
694    
695  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
696    
697          * 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
698          .h file can be included.          .h file can be included.
699    
700  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
701    
702          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
703          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
704    
705          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
706    
707  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
708    
709          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
710    
711  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
712    
713          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
714    
715  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
716    
717          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
718    
719  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
720    
721          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
722    
723  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
724    
725          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
726          routines.          routines.
727    
728  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
729    
730          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
731    
732  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
733    
734          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
735    

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