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revision 726, Thu May 12 14:59:04 2005 UTC revision 1319, Mon Jul 17 13:08:04 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/simple.R: add check for correct dsT -> dgT coercion;
4                    add check for correct printing of symmetric sparse matrices.
5    
6            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
7            for sparse symmetric matrices.
8    
9            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
10            diagonal twice.
11    
12    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
13    
14            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
15            being applied to the x slot (detected by Brian Ripley).
16    
17    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
20    
21            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
22    
23    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * src/lgCMatrix.c (lgCMatrix_diag): new function
26            * R/lgCMatrix.R (diag): for new method
27    
28            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
29                 ==> construction of illegal "*gTMatrix" via new() should
30                 now be much less easy:
31            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
32    
33            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
34                    directly.
35            * man/Matrix.Rd: documents it.
36    
37    2006-07-06  Douglas Bates  <bates@R-project.org>
38    
39            * src/pedigree.c (pedigree_inbreeding): Correction in
40            initialization.  This function is not currently being used and is
41            not fully tested.
42    
43            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
44            Introduced the glmer class.  Added code for mcmcmsamp on glmer
45            objects.  Modified validity check on pedigree objects to account
46            for nonparallel patterns of missingness of parents.
47    
48            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
49            class.
50    
51    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/pMatrix.R: coercion pMatrix -> Tsparse
54    
55    2006-06-12  Douglas Bates  <bates@R-project.org>
56    
57            * DESCRIPTION (Version): 0.995-11 released to CRAN
58    
59            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
60            the output from mcmcsamp.
61    
62    2006-06-10  Douglas Bates  <bates@R-project.org>
63    
64            * R/lmer.R (simulestimate): added C code for calculating the trace
65            of the hat matrix.
66    
67    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
70            classes.
71            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
72    
73    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/dgTMatrix.R (colSums): etc. All four of
76            colSums(), rowSums(), colMeans(), rowMeans() now should work for
77            all "Matrices".
78    
79    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * R/lmer.R (panel.ci): Add a reference line at zero and a
82            background grid to the qqmath plot of ranef.lmer.
83    
84    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
85    
86            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
87            grouping factors to be specified in the formula as (1|foo/bar).
88    
89    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
90    
91            * R/lmer.R (findbars and others): Change check of is.numeric to
92            !is.language to resolve the bug reported by Jacob Wegelin.
93    
94            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
95            code to evaluate inbreeding coefficients without calculating T,
96            based on code in Sargolzaei and Iwaisaki's paper.
97    
98    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
101            generic and mer methods for isNested and denomDF. This denomDF was
102            an attempt to emulate that in lme but I don't think that makes
103            sense.  Use the trace of the hat matrix instead.
104    
105    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
108            the C code depending on a slot structure that's no longer valid.
109            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
110    
111    
112    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
113    
114            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
115            of lowerTriMatrix generic and methods to tril (also upper to triu)
116            and added a general band extractor.
117    
118    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/pedigree.R (pedigree): Replace sire and dam values outside the
121            allowable range with NAs. Added a corresponding check in the
122            validity check for the pedigree class.
123    
124            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
125            crossprod methods now inherits from symmetricMatrix.
126    
127    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
130            generics lowerTriMatrix and upperTriMatrix along with methods for
131            the Csparse virtual class.  Also added a C function Csparse_band
132            that implements these methods by calling cholmod_band.
133    
134    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
137            erased when it was NULL.  This led to invalid subselections!
138    
139    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
140    
141            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
142            in method for "t" so as not to lose the unit diagonal property.
143    
144    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
145    
146            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
147            and methods.  This is now an option to the ranef method for the
148            mer class.
149    
150            * src/cs_utils.c: Ensure that the nz component is -1 for a
151            compressed column-oriented matrix.  Minor formatting cleanup.
152    
153            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
154            objects.
155    
156    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
159            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
160    
161    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
162    
163            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
164            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
165    
166            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
167            for the dtCMatrix class.
168    
169    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
170    
171            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
172            and methods for it.
173    
174    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
177            arguments, such that M %*% 1:6 now works
178            * Tests/matprod.R: test the above
179    
180    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
181    
182            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
183            the ranef.lmer class.
184    
185            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
186            methods to extract the posterior variances from the bVar slot.
187    
188    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
191            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
192    
193            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
194            * tests/simple: (extended)
195    
196            * R/sparseMatrix.R (isTriangular): now using much improved
197            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
198    
199    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
202            (problem report from Franklin Parlamis).  This should be done
203            generally.
204    
205    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
206    
207            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
208            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
209            update the plot methods.
210    
211    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
212    
213            * R/lmer.R (resid and ranef methods):  Added methods for the
214            "residuals" and "resid" generic but only for linear mixed model
215            fits.  Changed the ranef method to return a list of data frames so
216            that the plot methods now work.
217    
218    2006-03-16  Douglas Bates  <bates@bates2>
219    
220            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
221            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
222    
223            * DESCRIPTION (Date): New release
224    
225    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
228    
229            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
230            * man/KNex.Rd: and other help files
231            * tests/*.R: several ones needed adaption
232            * inst/doc/Comparisons.Rnw: dito
233    
234    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
237    
238            * tests/indexing.R: tests for new [<- methods for sparse matrices.
239    
240    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
243    
244            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
245    
246    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dMatrix.R: enable things like  M [ M < 10 ]
249            * R/dgeMatrix.R: implement it
250    
251    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/AllClass.R: define "summary.mer" and "*.lmer"
254            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
255            * R/lmer.R (show): now works with summary()
256    
257    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
260            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
261                    support the above
262    
263    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
266            Use glmFit$prior.weights for weights in a glmm.
267            Allow an option usePQL = FALSE to skip the PQL steps for the
268            Laplace method (and, in time, the AGQ method).
269    
270            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
271            into a separate function internal_mer_Xfactor to be able to call
272            it from internal_bhat.
273    
274    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * tests/Class+Meth.R (tstMatrixClass): function for much better
277            testing; now again of all actual classes.
278    
279            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
280                    use macros and define make_d_matrix_* and make_i_matrix_*
281                    where _i_ is for the ldense routines:
282    
283            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
284            * src/ldense.c (lsyMatrix_as_lgeMatrix):
285    
286            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
287    
288    
289    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
292                    many different kinds of matrices.
293            * R/*.R: quite a few new methods were needed for R CMD check with
294                    new Matrix().  Very good for users playing around.
295    
296    
297    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * src/dgeMatrix.c (dMatrix_validate): new
300            * src/Mutils.c (dense_nonpacked_validate): new
301    
302            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
303    
304    
305    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
308    
309    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
310    
311            * DESCRIPTION (Version): 0.99-6 released to CRAN
312    
313            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
314            segfault in cases with multiple non-nested grouping factors.
315    
316    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
319                    (Depends): also on 'utils'
320    
321            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
322            * R/diagMatrix.R (Diagonal): constructor and methods for
323            diagonal matrices
324    
325            * R/ltTMatrix.R: new "minimal methods"
326    
327    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
330            all methods (and help files).
331    
332    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
335                    for case (dimn.  op  no_dimn.)
336    
337    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
338    
339            * DESCRIPTION (Version): 0.99-2  released to CRAN
340    
341    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
342    
343            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
344            by Julian Faraway.
345    
346    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Auxiliaries.R (try_as): new utility
349            * R/sparseMatrix.R: use try_as() in coercion to original class
350    
351    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
354    
355    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Auxiliaries.R (dimNamesCheck): added
358    
359            * R/Matrix.R (as.array), (as.vector): new
360    
361    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
364                    default.
365            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
366                    "pMatrix" now contains "sparseMatrix"
367    
368    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * tests/Class+Meth.R: new tests; t(t(m)) == m
371    
372            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
373    
374            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
375            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
376    
377            * R/dspMatrix.R: typo in "t" method
378    
379    2005-09-18  Douglas Bates  <bates@wisc.edu>
380    
381            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
382            * R/Tsparse.R: instead of R/gTMatrix.R
383            * R/Csparse.R: new
384            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
385            * src/Tsparse.c: new; many trivial methods calling cholmod_()
386            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
387                            via cholmod
388    
389    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Auxiliaries.R (non0ind): new function using new C code
392            * src/dgCMatrix.c (compressed_non_0_ij): new utility
393    
394    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
395    
396            * src/chm_common.h: header file required by all C sources that
397            call CHOLMOD functions.  It defines a cholmod_common structure
398            called 'c' whose address is passed as the last argument to
399            (virtually) every CHOLMOD function.
400    
401            * src/Pattern.c: Simple example of the use of CHOLMOD.
402    
403            * src/init.c: initialize and finalize the cholmod_common structure.
404    
405            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
406            LDL and CCOLAMD from the U. of Florida sparse matrix library.
407    
408    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * inst/test-tools.R: new file collecting the utility functions used
411                    in ./tests/*.R
412    
413            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
414            * R/Matrix.R (cbind2): methods for NULL and missing
415    
416    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/AllClass.R: new "index" class for "[" and "[<-":
419                    First cut at "symmetricMatrix" and "triangularMatrix"
420            * R/gTMatrix.R (.ind.prep): new function;
421                    Logical and character indexing now work too.
422            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
423            * tests/indexing.R: new, including *.Rout.save
424            * tests/dgTMatrix.R: new
425    
426    2005-08-29  Douglas Bates  <bates@wisc.edu>
427    
428            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
429            indicator pos not being updated.  Also enforced upper triangular
430            for symmetric case.  Need to coerce edges component of elements of
431            edge list - grr! (Why don't they define their classes cleanly?)
432    
433    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Matrix.R:  added first "[<-" methods; not yet functional
436            * R/denseMatrix.R: dito
437            * man/Subassign-methods.Rd: new help file for these
438    
439    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * DESCRIPTION (Version): 0.98-6
442    
443            * R/denseMatrix.R: new file for "[" fallback methods for all dense
444            matrices.
445    
446    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
449                    as( <logical>, "matrix")
450    
451            * R/pMatrix.R: coercion to "lgTMatrix"
452    
453            * R/gTMatrix.R: new virtual class to define "[" methods for.
454            * man/gTMatrix-class.Rd:
455            * General slight re-organization of where "[" methods are defined.
456              more to come.
457    
458    2005-08-18  Douglas Bates  <bates@wisc.edu>
459    
460            * DESCRIPTION (Version): 0.98-5  released to CRAN
461    
462            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
463            * .....
464    
465    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
466    
467            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
468            or glmer objects.
469    
470    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
473    
474    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
475    
476            * R/HBMM.R: finish re-writing R-only code.
477    
478    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
479    
480            * man/externalFormats.Rd: move documentation for writeHB and
481            writeMM here.
482    
483            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
484            (suggested by Paul Roecker).
485    
486            * tests/validObj.R (assertError): Comment out test that is failing
487            after recent changes in r-devel.
488    
489    
490    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/AllClass.R: intermediate virtual class "denseMatrix"
493            * man/denseMatrix-class.Rd
494            * NAMESPACE: export it, and also export
495            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
496    
497    2005-08-10  Douglas Bates  <bates@wisc.edu>
498    
499            * DESCRIPTION (Version): 0.98-3 to CRAN
500    
501            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
502            matrix_solve code (which was really, really wrong).
503    
504    2005-08-07  Douglas Bates  <bates@wisc.edu>
505    
506            * DESCRIPTION (Version): 0.98-2
507    
508            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
509    
510            * R/lmer.R (abbrvNms): new
511            * R/lmer.R (mcmcsamp): allow transformed parameters
512            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
513            for the Harwell-Boeing and the MatrixMarket formats.
514    
515    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * man/dtrMatrix-class.Rd: add examples
518            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
519    
520            * TODO: note the dtpMatrix (docu) bug
521    
522            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
523            in order to ensure that new as.matrix() is used by old functions,
524            e.g., svd(), qr(), eigen(), dist(),..;
525                  apply(), also matplot() or pairs().
526    
527    
528    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
531              add comments about 'control' / lmerControl() arguments
532    
533    2005-07-27  Douglas Bates  <bates@wisc.edu>
534    
535            * man/sleepstudy.Rd: Added the sleep data set.
536            * DESCRIPTION (Version): 0.98-1  released to CRAN
537    
538    2005-07-12  Douglas Bates  <bates@wisc.edu>
539            * man/sleepstudy.Rd: Added the sleep data set.
540    
541            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
542            .Call calls that were producing spurious output.
543    
544    2005-07-05  Douglas Bates  <bates@wisc.edu>
545    
546            * R/lmer.R (lmer): stored updated variance component estimates in
547            mer object for the generalized model.  (Bug reported by Renaud
548            Lancelot).
549    
550    2005-07-03  Douglas Bates  <bates@wisc.edu>
551    
552            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
553            unidimensional case.
554    
555    2005-06-08  Douglas Bates  <bates@wisc.edu>
556    
557            * DESCRIPTION (Version): 0.96-1
558    
559            * moved  lmer-class' R and C code moved from lme4 to here
560    
561    2005-06-04  Douglas Bates  <bates@wisc.edu>
562    
563            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
564            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
565    
566    2005-06-02  Douglas Bates  <bates@wisc.edu>
567    
568            * src/Makefile.win: Forgot to update this when Makefile changed.
569    
570    2005-05-11  Douglas Bates  <bates@wisc.edu>
571    
572          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
573          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
574    
575  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
576    
577          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
578          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 581 
581          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
582          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
583    
584  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
585    
586          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
587          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
588    
589  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
590    
591          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
592          multiplication operation.          multiplication operation.
# Line 30  Line 599 
599    
600          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
601    
602  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
603    
604          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
605    
606          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
607    
608    
609  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
610    
611          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
612    
# Line 46  Line 615 
615          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
616          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
617    
618  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
619    
620          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
621    
# Line 72  Line 641 
641          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
642            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
643    
644  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
645    
646          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
647          * ....          * ....
648    
649  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
650    
651          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
652    
# Line 92  Line 661 
661            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
662          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
663    
664  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
665    
666          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
667    
668  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
669    
670          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
671    
672  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
673    
674          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
675          the package.          the package.
# Line 148  Line 717 
717    
718          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
719    
720  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
721    
722          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
723          for the geMatrix class.          for the geMatrix class.
724    
725  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
726    
727          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
728    
729          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
730    
731  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
732    
733          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
734          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
735    
736  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
737    
738          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
739    
740  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
741    
742          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
743          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
744    
745  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
746    
747          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
748    
749          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
750          for tripletMatrix to matrix.          for tripletMatrix to matrix.
751    
752  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
753    
754          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
755          no longer used.          no longer used.
# Line 192  Line 761 
761          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
762          Fixes part but not all of #15.          Fixes part but not all of #15.
763    
764  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
765    
766          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
767          scalar grouping factors corrected.          scalar grouping factors corrected.
768    
769  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
770    
771          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
772    
773  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
774    
775          * 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
776          .h file can be included.          .h file can be included.
777    
778  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
779    
780          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
781          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
782    
783          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
784    
785  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
786    
787          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
788    
789  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
790    
791          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
792    
793  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
794    
795          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
796    
797  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
798    
799          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
800    
801  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
802    
803          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
804          routines.          routines.
805    
806  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
807    
808          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
809    
810  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
811    
812          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
813    

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