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revision 834, Mon Aug 8 08:36:34 2005 UTC revision 1312, Thu Jul 6 15:29:56 2006 UTC
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1  2005-08-07  Douglas Bates <bates@localhost.localdomain>  2006-07-06  Douglas Bates  <bates@R-project.org>
2    
3            * src/pedigree.c (pedigree_inbreeding): Correction in
4            initialization.  This function is not currently being used and is
5            not fully tested.
6    
7            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
8            Introduced the glmer class.  Added code for mcmcmsamp on glmer
9            objects.  Modified validity check on pedigree objects to account
10            for nonparallel patterns of missingness of parents.
11    
12    2006-06-12  Douglas Bates  <bates@R-project.org>
13    
14            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
15            the output from mcmcsamp.
16    
17    2006-06-10  Douglas Bates  <bates@R-project.org>
18    
19            * R/lmer.R (simulestimate): added C code for calculating the trace
20            of the hat matrix.
21    
22    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
25            classes.
26    
27    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/dgTMatrix.R (colSums): etc. All four of
30            colSums(), rowSums(), colMeans(), rowMeans() now should work for
31            all "Matrices".
32    
33    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/lmer.R (panel.ci): Add a reference line at zero and a
36            background grid to the qqmath plot of ranef.lmer.
37    
38    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
41            grouping factors to be specified in the formula as (1|foo/bar).
42    
43    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/lmer.R (findbars and others): Change check of is.numeric to
46            !is.language to resolve the bug reported by Jacob Wegelin.
47    
48            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
49            code to evaluate inbreeding coefficients without calculating T,
50            based on code in Sargolzaei and Iwaisaki's paper.
51    
52    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
55            generic and mer methods for isNested and denomDF. This denomDF was
56            an attempt to emulate that in lme but I don't think that makes
57            sense.  Use the trace of the hat matrix instead.
58    
59    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
62            the C code depending on a slot structure that's no longer valid.
63            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
64    
65    
66    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
67    
68            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
69            of lowerTriMatrix generic and methods to tril (also upper to triu)
70            and added a general band extractor.
71    
72    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/pedigree.R (pedigree): Replace sire and dam values outside the
75            allowable range with NAs. Added a corresponding check in the
76            validity check for the pedigree class.
77    
78            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
79            crossprod methods now inherits from symmetricMatrix.
80    
81    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
84            generics lowerTriMatrix and upperTriMatrix along with methods for
85            the Csparse virtual class.  Also added a C function Csparse_band
86            that implements these methods by calling cholmod_band.
87    
88    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
91            erased when it was NULL.  This led to invalid subselections!
92    
93    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
94    
95            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
96            in method for "t" so as not to lose the unit diagonal property.
97    
98    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
101            and methods.  This is now an option to the ranef method for the
102            mer class.
103    
104            * src/cs_utils.c: Ensure that the nz component is -1 for a
105            compressed column-oriented matrix.  Minor formatting cleanup.
106    
107            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
108            objects.
109    
110    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
113            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
114    
115    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
118            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
119    
120            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
121            for the dtCMatrix class.
122    
123    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
126            and methods for it.
127    
128    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
131            arguments, such that M %*% 1:6 now works
132            * Tests/matprod.R: test the above
133    
134    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
135    
136            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
137            the ranef.lmer class.
138    
139            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
140            methods to extract the posterior variances from the bVar slot.
141    
142    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
145            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
146    
147            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
148            * tests/simple: (extended)
149    
150            * R/sparseMatrix.R (isTriangular): now using much improved
151            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
152    
153    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
156            (problem report from Franklin Parlamis).  This should be done
157            generally.
158    
159    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
162            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
163            update the plot methods.
164    
165    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
166    
167            * R/lmer.R (resid and ranef methods):  Added methods for the
168            "residuals" and "resid" generic but only for linear mixed model
169            fits.  Changed the ranef method to return a list of data frames so
170            that the plot methods now work.
171    
172    2006-03-16  Douglas Bates  <bates@bates2>
173    
174            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
175            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
176    
177            * DESCRIPTION (Date): New release
178    
179    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
182    
183            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
184            * man/KNex.Rd: and other help files
185            * tests/*.R: several ones needed adaption
186            * inst/doc/Comparisons.Rnw: dito
187    
188    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
191    
192            * tests/indexing.R: tests for new [<- methods for sparse matrices.
193    
194    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
197    
198            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
199    
200    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/dMatrix.R: enable things like  M [ M < 10 ]
203            * R/dgeMatrix.R: implement it
204    
205    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/AllClass.R: define "summary.mer" and "*.lmer"
208            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
209            * R/lmer.R (show): now works with summary()
210    
211    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
214            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
215                    support the above
216    
217    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
218    
219            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
220            Use glmFit$prior.weights for weights in a glmm.
221            Allow an option usePQL = FALSE to skip the PQL steps for the
222            Laplace method (and, in time, the AGQ method).
223    
224            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
225            into a separate function internal_mer_Xfactor to be able to call
226            it from internal_bhat.
227    
228    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * tests/Class+Meth.R (tstMatrixClass): function for much better
231            testing; now again of all actual classes.
232    
233            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
234                    use macros and define make_d_matrix_* and make_i_matrix_*
235                    where _i_ is for the ldense routines:
236    
237            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
238            * src/ldense.c (lsyMatrix_as_lgeMatrix):
239    
240            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
241    
242    
243    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
246                    many different kinds of matrices.
247            * R/*.R: quite a few new methods were needed for R CMD check with
248                    new Matrix().  Very good for users playing around.
249    
250    
251    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * src/dgeMatrix.c (dMatrix_validate): new
254            * src/Mutils.c (dense_nonpacked_validate): new
255    
256            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
257    
258    
259    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
262    
263    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * DESCRIPTION (Version): 0.99-6 released to CRAN
266    
267            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
268            segfault in cases with multiple non-nested grouping factors.
269    
270    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
273                    (Depends): also on 'utils'
274    
275            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
276            * R/diagMatrix.R (Diagonal): constructor and methods for
277            diagonal matrices
278    
279            * R/ltTMatrix.R: new "minimal methods"
280    
281    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
284            all methods (and help files).
285    
286    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
289                    for case (dimn.  op  no_dimn.)
290    
291    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
292    
293            * DESCRIPTION (Version): 0.99-2  released to CRAN
294    
295    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
298            by Julian Faraway.
299    
300    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Auxiliaries.R (try_as): new utility
303            * R/sparseMatrix.R: use try_as() in coercion to original class
304    
305    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
308    
309    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Auxiliaries.R (dimNamesCheck): added
312    
313            * R/Matrix.R (as.array), (as.vector): new
314    
315    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
318                    default.
319            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
320                    "pMatrix" now contains "sparseMatrix"
321    
322    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * tests/Class+Meth.R: new tests; t(t(m)) == m
325    
326            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
327    
328            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
329            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
330    
331            * R/dspMatrix.R: typo in "t" method
332    
333    2005-09-18  Douglas Bates  <bates@wisc.edu>
334    
335            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
336            * R/Tsparse.R: instead of R/gTMatrix.R
337            * R/Csparse.R: new
338            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
339            * src/Tsparse.c: new; many trivial methods calling cholmod_()
340            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
341                            via cholmod
342    
343    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Auxiliaries.R (non0ind): new function using new C code
346            * src/dgCMatrix.c (compressed_non_0_ij): new utility
347    
348    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
349    
350            * src/chm_common.h: header file required by all C sources that
351            call CHOLMOD functions.  It defines a cholmod_common structure
352            called 'c' whose address is passed as the last argument to
353            (virtually) every CHOLMOD function.
354    
355            * src/Pattern.c: Simple example of the use of CHOLMOD.
356    
357            * src/init.c: initialize and finalize the cholmod_common structure.
358    
359            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
360            LDL and CCOLAMD from the U. of Florida sparse matrix library.
361    
362    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * inst/test-tools.R: new file collecting the utility functions used
365                    in ./tests/*.R
366    
367            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
368            * R/Matrix.R (cbind2): methods for NULL and missing
369    
370    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/AllClass.R: new "index" class for "[" and "[<-":
373                    First cut at "symmetricMatrix" and "triangularMatrix"
374            * R/gTMatrix.R (.ind.prep): new function;
375                    Logical and character indexing now work too.
376            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
377            * tests/indexing.R: new, including *.Rout.save
378            * tests/dgTMatrix.R: new
379    
380    2005-08-29  Douglas Bates  <bates@wisc.edu>
381    
382            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
383            indicator pos not being updated.  Also enforced upper triangular
384            for symmetric case.  Need to coerce edges component of elements of
385            edge list - grr! (Why don't they define their classes cleanly?)
386    
387    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/Matrix.R:  added first "[<-" methods; not yet functional
390            * R/denseMatrix.R: dito
391            * man/Subassign-methods.Rd: new help file for these
392    
393    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * DESCRIPTION (Version): 0.98-6
396    
397            * R/denseMatrix.R: new file for "[" fallback methods for all dense
398            matrices.
399    
400    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
403                    as( <logical>, "matrix")
404    
405            * R/pMatrix.R: coercion to "lgTMatrix"
406    
407            * R/gTMatrix.R: new virtual class to define "[" methods for.
408            * man/gTMatrix-class.Rd:
409            * General slight re-organization of where "[" methods are defined.
410              more to come.
411    
412    2005-08-18  Douglas Bates  <bates@wisc.edu>
413    
414            * DESCRIPTION (Version): 0.98-5  released to CRAN
415    
416            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
417            * .....
418    
419    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
420    
421            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
422            or glmer objects.
423    
424    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
427    
428    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
429    
430            * R/HBMM.R: finish re-writing R-only code.
431    
432    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
433    
434            * man/externalFormats.Rd: move documentation for writeHB and
435            writeMM here.
436    
437            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
438            (suggested by Paul Roecker).
439    
440            * tests/validObj.R (assertError): Comment out test that is failing
441            after recent changes in r-devel.
442    
443    
444    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/AllClass.R: intermediate virtual class "denseMatrix"
447            * man/denseMatrix-class.Rd
448            * NAMESPACE: export it, and also export
449            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
450    
451    2005-08-10  Douglas Bates  <bates@wisc.edu>
452    
453            * DESCRIPTION (Version): 0.98-3 to CRAN
454    
455            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
456            matrix_solve code (which was really, really wrong).
457    
458    2005-08-07  Douglas Bates  <bates@wisc.edu>
459    
460          * DESCRIPTION (Version): 0.98-2          * DESCRIPTION (Version): 0.98-2
461    
# Line 6  Line 463 
463    
464          * R/lmer.R (abbrvNms): new          * R/lmer.R (abbrvNms): new
465          * R/lmer.R (mcmcsamp): allow transformed parameters          * R/lmer.R (mcmcsamp): allow transformed parameters
466            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
467            for the Harwell-Boeing and the MatrixMarket formats.
468    
469  2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471          * man/dtrMatrix-class.Rd: add examples          * man/dtrMatrix-class.Rd: add examples
472          * man/dtpMatrix-class.Rd: dito; plus note about PROBLEM          * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
473    
474          * TODO: note the dtpMatrix (docu) bug          * TODO: note the dtpMatrix (docu) bug
475    
# Line 25  Line 484 
484          * R/lmer.R: add 'fixme' comments and move the linear vs glm check;          * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
485            add comments about 'control' / lmerControl() arguments            add comments about 'control' / lmerControl() arguments
486    
487  2005-07-27  Douglas Bates  <bates@localhost.localdomain>  2005-07-27  Douglas Bates  <bates@wisc.edu>
488    
489            * man/sleepstudy.Rd: Added the sleep data set.
490          * DESCRIPTION (Version): 0.98-1  released to CRAN          * DESCRIPTION (Version): 0.98-1  released to CRAN
491    
492    2005-07-12  Douglas Bates  <bates@wisc.edu>
493          * man/sleepstudy.Rd: Added the sleep data set.          * man/sleepstudy.Rd: Added the sleep data set.
494    
 2005-07-12  Douglas Bates  <bates@localhost.localdomain>  
   
495          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
496          .Call calls that were producing spurious output.          .Call calls that were producing spurious output.
497    
498  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-07-05  Douglas Bates  <bates@wisc.edu>
499    
500          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
501          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
502          Lancelot).          Lancelot).
503    
504  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
505    
506          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
507          unidimensional case.          unidimensional case.
508    
509  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
510    
511          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
512    
513          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
514    
515  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
516    
517          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
518          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
519    
520  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
521    
522          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
523    
524  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
525    
526          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
527          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
528    
529  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
530    
531          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
532          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 76  Line 535 
535          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
536          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
537    
538  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
539    
540          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
541          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
542    
543  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
544    
545          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
546          multiplication operation.          multiplication operation.
# Line 94  Line 553 
553    
554          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
555    
556  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
557    
558          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
559    
560          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
561    
562    
563  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
564    
565          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
566    
# Line 110  Line 569 
569          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
570          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
571    
572  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
573    
574          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
575    
# Line 136  Line 595 
595          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
596            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
597    
598  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
599    
600          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
601          * ....          * ....
602    
603  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
604    
605          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
606    
# Line 156  Line 615 
615            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
616          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
617    
618  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
619    
620          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
621    
622  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
623    
624          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
625    
626  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
627    
628          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
629          the package.          the package.
# Line 212  Line 671 
671    
672          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
673    
674  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
675    
676          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
677          for the geMatrix class.          for the geMatrix class.
678    
679  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
680    
681          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
682    
683          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
684    
685  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
686    
687          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
688          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
689    
690  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
691    
692          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
693    
694  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
695    
696          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
697          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
698    
699  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
700    
701          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
702    
703          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
704          for tripletMatrix to matrix.          for tripletMatrix to matrix.
705    
706  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
707    
708          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
709          no longer used.          no longer used.
# Line 256  Line 715 
715          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
716          Fixes part but not all of #15.          Fixes part but not all of #15.
717    
718  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
719    
720          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
721          scalar grouping factors corrected.          scalar grouping factors corrected.
722    
723  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
724    
725          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
726    
727  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
728    
729          * 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
730          .h file can be included.          .h file can be included.
731    
732  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
733    
734          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
735          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
736    
737          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
738    
739  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
740    
741          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
742    
743  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
744    
745          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
746    
747  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
748    
749          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
750    
751  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
752    
753          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
754    
755  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
756    
757          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
758          routines.          routines.
759    
760  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
761    
762          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
763    
764  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
765    
766          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
767    

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