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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1329, Fri Jul 21 06:47:06 2006 UTC
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1    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
4                    since that wrongly triggers also for M[ logi , ]
5    
6            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
7            a symmetric matrix that results in a non-symmetric one.
8            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
9    
10            * R/dMatrix.R: make round(M) work as round(M, 0)
11    
12            * R/dgTMatrix.R (image): coordinate system and axis now use
13            1-based indices, not 0-based ones.
14    
15            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
16            * tests/indexing.R: test it.
17    
18            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
19            * man/isSymmetric-methods.Rd: and document it.
20    
21            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
22            * man/SparseM-conv.Rd: docu them
23    
24            * tests/other-pkgs.R: renamed from tests/graph.R and add example
25                    for 'SparseM' conversions
26    
27    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
28    
29            * R/Matrix.R (head): added head() and tail() methods.
30    
31    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * DESCRIPTION (Version): 0.995-12 released to CRAN
34    
35    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * tests/simple.R: add check for correct dsT -> dgT coercion;
38                    add check for correct printing of symmetric sparse matrices.
39    
40            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
41            for sparse symmetric matrices.
42    
43            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
44            diagonal twice.
45    
46    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
47    
48            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
49            being applied to the x slot (detected by Brian Ripley).
50    
51    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
54    
55            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
56    
57    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * src/lgCMatrix.c (lgCMatrix_diag): new function
60            * R/lgCMatrix.R (diag): for new method
61    
62            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
63                 ==> construction of illegal "*gTMatrix" via new() should
64                 now be much less easy:
65            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
66    
67            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
68                    directly.
69            * man/Matrix.Rd: documents it.
70    
71    2006-07-06  Douglas Bates  <bates@R-project.org>
72    
73            * src/pedigree.c (pedigree_inbreeding): Correction in
74            initialization.  This function is not currently being used and is
75            not fully tested.
76    
77            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
78            Introduced the glmer class.  Added code for mcmcmsamp on glmer
79            objects.  Modified validity check on pedigree objects to account
80            for nonparallel patterns of missingness of parents.
81    
82            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
83            class.
84    
85    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/pMatrix.R: coercion pMatrix -> Tsparse
88    
89    2006-06-12  Douglas Bates  <bates@R-project.org>
90    
91            * DESCRIPTION (Version): 0.995-11 released to CRAN
92    
93            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
94            the output from mcmcsamp.
95    
96    2006-06-10  Douglas Bates  <bates@R-project.org>
97    
98            * R/lmer.R (simulestimate): added C code for calculating the trace
99            of the hat matrix.
100    
101    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
104            classes.
105            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
106    
107    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgTMatrix.R (colSums): etc. All four of
110            colSums(), rowSums(), colMeans(), rowMeans() now should work for
111            all "Matrices".
112    
113    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/lmer.R (panel.ci): Add a reference line at zero and a
116            background grid to the qqmath plot of ranef.lmer.
117    
118    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
121            grouping factors to be specified in the formula as (1|foo/bar).
122    
123    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/lmer.R (findbars and others): Change check of is.numeric to
126            !is.language to resolve the bug reported by Jacob Wegelin.
127    
128            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
129            code to evaluate inbreeding coefficients without calculating T,
130            based on code in Sargolzaei and Iwaisaki's paper.
131    
132    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
135            generic and mer methods for isNested and denomDF. This denomDF was
136            an attempt to emulate that in lme but I don't think that makes
137            sense.  Use the trace of the hat matrix instead.
138    
139    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
142            the C code depending on a slot structure that's no longer valid.
143            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
144    
145    
146    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
147    
148            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
149            of lowerTriMatrix generic and methods to tril (also upper to triu)
150            and added a general band extractor.
151    
152    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
153    
154            * R/pedigree.R (pedigree): Replace sire and dam values outside the
155            allowable range with NAs. Added a corresponding check in the
156            validity check for the pedigree class.
157    
158            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
159            crossprod methods now inherits from symmetricMatrix.
160    
161    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
162    
163            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
164            generics lowerTriMatrix and upperTriMatrix along with methods for
165            the Csparse virtual class.  Also added a C function Csparse_band
166            that implements these methods by calling cholmod_band.
167    
168    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
171            erased when it was NULL.  This led to invalid subselections!
172    
173    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
176            in method for "t" so as not to lose the unit diagonal property.
177    
178    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
179    
180            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
181            and methods.  This is now an option to the ranef method for the
182            mer class.
183    
184            * src/cs_utils.c: Ensure that the nz component is -1 for a
185            compressed column-oriented matrix.  Minor formatting cleanup.
186    
187            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
188            objects.
189    
190    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
193            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
194    
195    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
196    
197            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
198            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
199    
200            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
201            for the dtCMatrix class.
202    
203    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
206            and methods for it.
207    
208    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
211            arguments, such that M %*% 1:6 now works
212            * Tests/matprod.R: test the above
213    
214    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
215    
216            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
217            the ranef.lmer class.
218    
219            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
220            methods to extract the posterior variances from the bVar slot.
221    
222    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
225            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
226    
227            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
228            * tests/simple: (extended)
229    
230            * R/sparseMatrix.R (isTriangular): now using much improved
231            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
232    
233    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
234    
235            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
236            (problem report from Franklin Parlamis).  This should be done
237            generally.
238    
239    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
242            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
243            update the plot methods.
244    
245    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * R/lmer.R (resid and ranef methods):  Added methods for the
248            "residuals" and "resid" generic but only for linear mixed model
249            fits.  Changed the ranef method to return a list of data frames so
250            that the plot methods now work.
251    
252    2006-03-16  Douglas Bates  <bates@bates2>
253    
254            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
255            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
256    
257            * DESCRIPTION (Date): New release
258    
259    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
262    
263            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
264            * man/KNex.Rd: and other help files
265            * tests/*.R: several ones needed adaption
266            * inst/doc/Comparisons.Rnw: dito
267    
268    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
271    
272            * tests/indexing.R: tests for new [<- methods for sparse matrices.
273    
274    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
277    
278            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
279    
280    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/dMatrix.R: enable things like  M [ M < 10 ]
283            * R/dgeMatrix.R: implement it
284    
285    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/AllClass.R: define "summary.mer" and "*.lmer"
288            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
289            * R/lmer.R (show): now works with summary()
290    
291    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
294            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
295                    support the above
296    
297    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
298    
299            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
300            Use glmFit$prior.weights for weights in a glmm.
301            Allow an option usePQL = FALSE to skip the PQL steps for the
302            Laplace method (and, in time, the AGQ method).
303    
304            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
305            into a separate function internal_mer_Xfactor to be able to call
306            it from internal_bhat.
307    
308    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * tests/Class+Meth.R (tstMatrixClass): function for much better
311            testing; now again of all actual classes.
312    
313            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
314                    use macros and define make_d_matrix_* and make_i_matrix_*
315                    where _i_ is for the ldense routines:
316    
317            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
318            * src/ldense.c (lsyMatrix_as_lgeMatrix):
319    
320            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
321    
322    
323    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
326                    many different kinds of matrices.
327            * R/*.R: quite a few new methods were needed for R CMD check with
328                    new Matrix().  Very good for users playing around.
329    
330    
331    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * src/dgeMatrix.c (dMatrix_validate): new
334            * src/Mutils.c (dense_nonpacked_validate): new
335    
336            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
337    
338    
339    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
342    
343    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
344    
345            * DESCRIPTION (Version): 0.99-6 released to CRAN
346    
347            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
348            segfault in cases with multiple non-nested grouping factors.
349    
350    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
353                    (Depends): also on 'utils'
354    
355            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
356            * R/diagMatrix.R (Diagonal): constructor and methods for
357            diagonal matrices
358    
359            * R/ltTMatrix.R: new "minimal methods"
360    
361    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
364            all methods (and help files).
365    
366    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
369                    for case (dimn.  op  no_dimn.)
370    
371    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
372    
373            * DESCRIPTION (Version): 0.99-2  released to CRAN
374    
375    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
376    
377            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
378            by Julian Faraway.
379    
380    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Auxiliaries.R (try_as): new utility
383            * R/sparseMatrix.R: use try_as() in coercion to original class
384    
385    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
388    
389    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Auxiliaries.R (dimNamesCheck): added
392    
393            * R/Matrix.R (as.array), (as.vector): new
394    
395    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
398                    default.
399            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
400                    "pMatrix" now contains "sparseMatrix"
401    
402    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * tests/Class+Meth.R: new tests; t(t(m)) == m
405    
406            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
407    
408            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
409            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
410    
411            * R/dspMatrix.R: typo in "t" method
412    
413    2005-09-18  Douglas Bates  <bates@wisc.edu>
414    
415            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
416            * R/Tsparse.R: instead of R/gTMatrix.R
417            * R/Csparse.R: new
418            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
419            * src/Tsparse.c: new; many trivial methods calling cholmod_()
420            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
421                            via cholmod
422    
423    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/Auxiliaries.R (non0ind): new function using new C code
426            * src/dgCMatrix.c (compressed_non_0_ij): new utility
427    
428    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
429    
430            * src/chm_common.h: header file required by all C sources that
431            call CHOLMOD functions.  It defines a cholmod_common structure
432            called 'c' whose address is passed as the last argument to
433            (virtually) every CHOLMOD function.
434    
435            * src/Pattern.c: Simple example of the use of CHOLMOD.
436    
437            * src/init.c: initialize and finalize the cholmod_common structure.
438    
439            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
440            LDL and CCOLAMD from the U. of Florida sparse matrix library.
441    
442    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * inst/test-tools.R: new file collecting the utility functions used
445                    in ./tests/*.R
446    
447            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
448            * R/Matrix.R (cbind2): methods for NULL and missing
449    
450    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/AllClass.R: new "index" class for "[" and "[<-":
453                    First cut at "symmetricMatrix" and "triangularMatrix"
454            * R/gTMatrix.R (.ind.prep): new function;
455                    Logical and character indexing now work too.
456            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
457            * tests/indexing.R: new, including *.Rout.save
458            * tests/dgTMatrix.R: new
459    
460    2005-08-29  Douglas Bates  <bates@wisc.edu>
461    
462            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
463            indicator pos not being updated.  Also enforced upper triangular
464            for symmetric case.  Need to coerce edges component of elements of
465            edge list - grr! (Why don't they define their classes cleanly?)
466    
467    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/Matrix.R:  added first "[<-" methods; not yet functional
470            * R/denseMatrix.R: dito
471            * man/Subassign-methods.Rd: new help file for these
472    
473    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * DESCRIPTION (Version): 0.98-6
476    
477            * R/denseMatrix.R: new file for "[" fallback methods for all dense
478            matrices.
479    
480    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
483                    as( <logical>, "matrix")
484    
485            * R/pMatrix.R: coercion to "lgTMatrix"
486    
487            * R/gTMatrix.R: new virtual class to define "[" methods for.
488            * man/gTMatrix-class.Rd:
489            * General slight re-organization of where "[" methods are defined.
490              more to come.
491    
492    2005-08-18  Douglas Bates  <bates@wisc.edu>
493    
494            * DESCRIPTION (Version): 0.98-5  released to CRAN
495    
496            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
497            * .....
498    
499    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
500    
501            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
502            or glmer objects.
503    
504    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
507    
508    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
509    
510            * R/HBMM.R: finish re-writing R-only code.
511    
512    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
513    
514            * man/externalFormats.Rd: move documentation for writeHB and
515            writeMM here.
516    
517            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
518            (suggested by Paul Roecker).
519    
520            * tests/validObj.R (assertError): Comment out test that is failing
521            after recent changes in r-devel.
522    
523    
524    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/AllClass.R: intermediate virtual class "denseMatrix"
527            * man/denseMatrix-class.Rd
528            * NAMESPACE: export it, and also export
529            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
530    
531    2005-08-10  Douglas Bates  <bates@wisc.edu>
532    
533            * DESCRIPTION (Version): 0.98-3 to CRAN
534    
535            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
536            matrix_solve code (which was really, really wrong).
537    
538    2005-08-07  Douglas Bates  <bates@wisc.edu>
539    
540            * DESCRIPTION (Version): 0.98-2
541    
542            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
543    
544            * R/lmer.R (abbrvNms): new
545            * R/lmer.R (mcmcsamp): allow transformed parameters
546            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
547            for the Harwell-Boeing and the MatrixMarket formats.
548    
549    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * man/dtrMatrix-class.Rd: add examples
552            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
553    
554            * TODO: note the dtpMatrix (docu) bug
555    
556            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
557            in order to ensure that new as.matrix() is used by old functions,
558            e.g., svd(), qr(), eigen(), dist(),..;
559                  apply(), also matplot() or pairs().
560    
561    
562    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
565              add comments about 'control' / lmerControl() arguments
566    
567    2005-07-27  Douglas Bates  <bates@wisc.edu>
568    
569            * man/sleepstudy.Rd: Added the sleep data set.
570            * DESCRIPTION (Version): 0.98-1  released to CRAN
571    
572    2005-07-12  Douglas Bates  <bates@wisc.edu>
573            * man/sleepstudy.Rd: Added the sleep data set.
574    
575            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
576            .Call calls that were producing spurious output.
577    
578    2005-07-05  Douglas Bates  <bates@wisc.edu>
579    
580            * R/lmer.R (lmer): stored updated variance component estimates in
581            mer object for the generalized model.  (Bug reported by Renaud
582            Lancelot).
583    
584    2005-07-03  Douglas Bates  <bates@wisc.edu>
585    
586            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
587            unidimensional case.
588    
589    2005-06-08  Douglas Bates  <bates@wisc.edu>
590    
591            * DESCRIPTION (Version): 0.96-1
592    
593            * moved  lmer-class' R and C code moved from lme4 to here
594    
595    2005-06-04  Douglas Bates  <bates@wisc.edu>
596    
597            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
598            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
599    
600    2005-06-02  Douglas Bates  <bates@wisc.edu>
601    
602            * src/Makefile.win: Forgot to update this when Makefile changed.
603    
604    2005-05-11  Douglas Bates  <bates@wisc.edu>
605    
606            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
607            bug reported by Kurt Hornik and Michael Hahsler.
608    
609    2005-05-10  Douglas Bates  <bates@wisc.edu>
610    
611            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
612            logical sparse matrices.  These will also be used in the symbolic
613            analysis for lmer objects.
614    
615            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
616            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
617    
618    2005-05-06  Douglas Bates  <bates@wisc.edu>
619    
620            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
621            colMeans, colSums, rowMeans and rowSums.
622    
623    2005-04-18  Douglas Bates  <bates@wisc.edu>
624    
625            * src/lgCMatrix.[ch]: code for _validate method and stub for
626            multiplication operation.
627    
628            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
629            to dgetrs.
630    
631            * src/init.c: Fix cut-and-paste error in definition of
632            dgeMatrix_matrix_solve
633    
634            * src/{many files}: Tighten code by using ALLOC_SLOT.
635    
636    2005-04-15  Douglas Bates  <bates@wisc.edu>
637    
638            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
639    
640            * DESCRIPTION: Eliminate import of stats.
641    
642    
643    2005-04-06  Douglas Bates  <bates@wisc.edu>
644    
645            * R/AllClass.R : add logical sparse matrix classes
646    
647  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
650          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
651    
652  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
653    
654          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
655    
# Line 29  Line 675 
675          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
676            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
677    
678  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
679    
680          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
681          * ....          * ....
682    
683  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
684    
685          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
686    
# Line 49  Line 695 
695            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
696          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
697    
698  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
699    
700          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
701    
702  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
703    
704          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
705    
706  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
707    
708          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
709          the package.          the package.
# Line 105  Line 751 
751    
752          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
753    
754  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
755    
756          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
757          for the geMatrix class.          for the geMatrix class.
758    
759  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
760    
761          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
762    
763          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
764    
765  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
766    
767          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
768          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
769    
770  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
771    
772          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
773    
774  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
775    
776          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
777          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
778    
779  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
780    
781          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
782    
783          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
784          for tripletMatrix to matrix.          for tripletMatrix to matrix.
785    
786  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
787    
788          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
789          no longer used.          no longer used.
# Line 149  Line 795 
795          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
796          Fixes part but not all of #15.          Fixes part but not all of #15.
797    
798  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
799    
800          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
801          scalar grouping factors corrected.          scalar grouping factors corrected.
802    
803  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
804    
805          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
806    
807  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
808    
809          * 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
810          .h file can be included.          .h file can be included.
811    
812  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
813    
814          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
815          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
816    
817          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
818    
819  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
820    
821          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
822    
823  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
824    
825          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
826    
827  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
828    
829          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
830    
831  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
832    
833          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
834    
835  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
836    
837          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
838          routines.          routines.
839    
840  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
841    
842          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
843    
844  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
845    
846          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
847    

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