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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1264, Mon May 15 21:05:20 2006 UTC
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1    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
4            erased when it was NULL.  This led to invalid subselections!
5    
6    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
9            in method for "t" so as not to lose the unit diagonal property.
10    
11    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
14            and methods.  This is now an option to the ranef method for the
15            mer class.
16    
17            * src/cs_utils.c: Ensure that the nz component is -1 for a
18            compressed column-oriented matrix.  Minor formatting cleanup.
19    
20            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
21            objects.
22    
23    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
26            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
27    
28    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
31            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
32    
33            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
34            for the dtCMatrix class.
35    
36    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
37    
38            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
39            and methods for it.
40    
41    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
44            arguments, such that M %*% 1:6 now works
45            * Tests/matprod.R: test the above
46    
47    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
50            the ranef.lmer class.
51    
52            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
53            methods to extract the posterior variances from the bVar slot.
54    
55    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
58            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
59    
60            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
61            * tests/simple: (extended)
62    
63            * R/sparseMatrix.R (isTriangular): now using much improved
64            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
65    
66    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
69            (problem report from Franklin Parlamis).  This should be done
70            generally.
71    
72    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
75            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
76            update the plot methods.
77    
78    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * R/lmer.R (resid and ranef methods):  Added methods for the
81            "residuals" and "resid" generic but only for linear mixed model
82            fits.  Changed the ranef method to return a list of data frames so
83            that the plot methods now work.
84    
85    2006-03-16  Douglas Bates  <bates@bates2>
86    
87            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
88            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
89    
90            * DESCRIPTION (Date): New release
91    
92    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
95    
96            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
97            * man/KNex.Rd: and other help files
98            * tests/*.R: several ones needed adaption
99            * inst/doc/Comparisons.Rnw: dito
100    
101    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
104    
105            * tests/indexing.R: tests for new [<- methods for sparse matrices.
106    
107    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
110    
111            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
112    
113    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/dMatrix.R: enable things like  M [ M < 10 ]
116            * R/dgeMatrix.R: implement it
117    
118    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/AllClass.R: define "summary.mer" and "*.lmer"
121            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
122            * R/lmer.R (show): now works with summary()
123    
124    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
127            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
128                    support the above
129    
130    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
131    
132            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
133            Use glmFit$prior.weights for weights in a glmm.
134            Allow an option usePQL = FALSE to skip the PQL steps for the
135            Laplace method (and, in time, the AGQ method).
136    
137            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
138            into a separate function internal_mer_Xfactor to be able to call
139            it from internal_bhat.
140    
141    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * tests/Class+Meth.R (tstMatrixClass): function for much better
144            testing; now again of all actual classes.
145    
146            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
147                    use macros and define make_d_matrix_* and make_i_matrix_*
148                    where _i_ is for the ldense routines:
149    
150            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
151            * src/ldense.c (lsyMatrix_as_lgeMatrix):
152    
153            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
154    
155    
156    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
159                    many different kinds of matrices.
160            * R/*.R: quite a few new methods were needed for R CMD check with
161                    new Matrix().  Very good for users playing around.
162    
163    
164    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * src/dgeMatrix.c (dMatrix_validate): new
167            * src/Mutils.c (dense_nonpacked_validate): new
168    
169            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
170    
171    
172    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
173    
174            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
175    
176    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
177    
178            * DESCRIPTION (Version): 0.99-6 released to CRAN
179    
180            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
181            segfault in cases with multiple non-nested grouping factors.
182    
183    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
186                    (Depends): also on 'utils'
187    
188            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
189            * R/diagMatrix.R (Diagonal): constructor and methods for
190            diagonal matrices
191    
192            * R/ltTMatrix.R: new "minimal methods"
193    
194    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
197            all methods (and help files).
198    
199    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
202                    for case (dimn.  op  no_dimn.)
203    
204    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
205    
206            * DESCRIPTION (Version): 0.99-2  released to CRAN
207    
208    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
211            by Julian Faraway.
212    
213    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Auxiliaries.R (try_as): new utility
216            * R/sparseMatrix.R: use try_as() in coercion to original class
217    
218    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
221    
222    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Auxiliaries.R (dimNamesCheck): added
225    
226            * R/Matrix.R (as.array), (as.vector): new
227    
228    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
231                    default.
232            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
233                    "pMatrix" now contains "sparseMatrix"
234    
235    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * tests/Class+Meth.R: new tests; t(t(m)) == m
238    
239            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
240    
241            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
242            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
243    
244            * R/dspMatrix.R: typo in "t" method
245    
246    2005-09-18  Douglas Bates  <bates@wisc.edu>
247    
248            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
249            * R/Tsparse.R: instead of R/gTMatrix.R
250            * R/Csparse.R: new
251            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
252            * src/Tsparse.c: new; many trivial methods calling cholmod_()
253            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
254                            via cholmod
255    
256    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Auxiliaries.R (non0ind): new function using new C code
259            * src/dgCMatrix.c (compressed_non_0_ij): new utility
260    
261    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
262    
263            * src/chm_common.h: header file required by all C sources that
264            call CHOLMOD functions.  It defines a cholmod_common structure
265            called 'c' whose address is passed as the last argument to
266            (virtually) every CHOLMOD function.
267    
268            * src/Pattern.c: Simple example of the use of CHOLMOD.
269    
270            * src/init.c: initialize and finalize the cholmod_common structure.
271    
272            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
273            LDL and CCOLAMD from the U. of Florida sparse matrix library.
274    
275    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * inst/test-tools.R: new file collecting the utility functions used
278                    in ./tests/*.R
279    
280            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
281            * R/Matrix.R (cbind2): methods for NULL and missing
282    
283    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/AllClass.R: new "index" class for "[" and "[<-":
286                    First cut at "symmetricMatrix" and "triangularMatrix"
287            * R/gTMatrix.R (.ind.prep): new function;
288                    Logical and character indexing now work too.
289            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
290            * tests/indexing.R: new, including *.Rout.save
291            * tests/dgTMatrix.R: new
292    
293    2005-08-29  Douglas Bates  <bates@wisc.edu>
294    
295            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
296            indicator pos not being updated.  Also enforced upper triangular
297            for symmetric case.  Need to coerce edges component of elements of
298            edge list - grr! (Why don't they define their classes cleanly?)
299    
300    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Matrix.R:  added first "[<-" methods; not yet functional
303            * R/denseMatrix.R: dito
304            * man/Subassign-methods.Rd: new help file for these
305    
306    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * DESCRIPTION (Version): 0.98-6
309    
310            * R/denseMatrix.R: new file for "[" fallback methods for all dense
311            matrices.
312    
313    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
316                    as( <logical>, "matrix")
317    
318            * R/pMatrix.R: coercion to "lgTMatrix"
319    
320            * R/gTMatrix.R: new virtual class to define "[" methods for.
321            * man/gTMatrix-class.Rd:
322            * General slight re-organization of where "[" methods are defined.
323              more to come.
324    
325    2005-08-18  Douglas Bates  <bates@wisc.edu>
326    
327            * DESCRIPTION (Version): 0.98-5  released to CRAN
328    
329            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
330            * .....
331    
332    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
333    
334            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
335            or glmer objects.
336    
337    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
340    
341    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
342    
343            * R/HBMM.R: finish re-writing R-only code.
344    
345    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
346    
347            * man/externalFormats.Rd: move documentation for writeHB and
348            writeMM here.
349    
350            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
351            (suggested by Paul Roecker).
352    
353            * tests/validObj.R (assertError): Comment out test that is failing
354            after recent changes in r-devel.
355    
356    
357    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/AllClass.R: intermediate virtual class "denseMatrix"
360            * man/denseMatrix-class.Rd
361            * NAMESPACE: export it, and also export
362            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
363    
364    2005-08-10  Douglas Bates  <bates@wisc.edu>
365    
366            * DESCRIPTION (Version): 0.98-3 to CRAN
367    
368            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
369            matrix_solve code (which was really, really wrong).
370    
371    2005-08-07  Douglas Bates  <bates@wisc.edu>
372    
373            * DESCRIPTION (Version): 0.98-2
374    
375            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
376    
377            * R/lmer.R (abbrvNms): new
378            * R/lmer.R (mcmcsamp): allow transformed parameters
379            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
380            for the Harwell-Boeing and the MatrixMarket formats.
381    
382    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * man/dtrMatrix-class.Rd: add examples
385            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
386    
387            * TODO: note the dtpMatrix (docu) bug
388    
389            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
390            in order to ensure that new as.matrix() is used by old functions,
391            e.g., svd(), qr(), eigen(), dist(),..;
392                  apply(), also matplot() or pairs().
393    
394    
395    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
398              add comments about 'control' / lmerControl() arguments
399    
400    2005-07-27  Douglas Bates  <bates@wisc.edu>
401    
402            * man/sleepstudy.Rd: Added the sleep data set.
403            * DESCRIPTION (Version): 0.98-1  released to CRAN
404    
405    2005-07-12  Douglas Bates  <bates@wisc.edu>
406            * man/sleepstudy.Rd: Added the sleep data set.
407    
408            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
409            .Call calls that were producing spurious output.
410    
411    2005-07-05  Douglas Bates  <bates@wisc.edu>
412    
413            * R/lmer.R (lmer): stored updated variance component estimates in
414            mer object for the generalized model.  (Bug reported by Renaud
415            Lancelot).
416    
417    2005-07-03  Douglas Bates  <bates@wisc.edu>
418    
419            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
420            unidimensional case.
421    
422    2005-06-08  Douglas Bates  <bates@wisc.edu>
423    
424            * DESCRIPTION (Version): 0.96-1
425    
426            * moved  lmer-class' R and C code moved from lme4 to here
427    
428    2005-06-04  Douglas Bates  <bates@wisc.edu>
429    
430            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
431            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
432    
433    2005-06-02  Douglas Bates  <bates@wisc.edu>
434    
435            * src/Makefile.win: Forgot to update this when Makefile changed.
436    
437    2005-05-11  Douglas Bates  <bates@wisc.edu>
438    
439            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
440            bug reported by Kurt Hornik and Michael Hahsler.
441    
442    2005-05-10  Douglas Bates  <bates@wisc.edu>
443    
444            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
445            logical sparse matrices.  These will also be used in the symbolic
446            analysis for lmer objects.
447    
448            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
449            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
450    
451    2005-05-06  Douglas Bates  <bates@wisc.edu>
452    
453            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
454            colMeans, colSums, rowMeans and rowSums.
455    
456    2005-04-18  Douglas Bates  <bates@wisc.edu>
457    
458            * src/lgCMatrix.[ch]: code for _validate method and stub for
459            multiplication operation.
460    
461            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
462            to dgetrs.
463    
464            * src/init.c: Fix cut-and-paste error in definition of
465            dgeMatrix_matrix_solve
466    
467            * src/{many files}: Tighten code by using ALLOC_SLOT.
468    
469    2005-04-15  Douglas Bates  <bates@wisc.edu>
470    
471            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
472    
473            * DESCRIPTION: Eliminate import of stats.
474    
475    
476    2005-04-06  Douglas Bates  <bates@wisc.edu>
477    
478            * R/AllClass.R : add logical sparse matrix classes
479    
480  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
483          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
484    
485  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
486    
487          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
488    
# Line 29  Line 508 
508          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
509            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
510    
511  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
512    
513          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
514          * ....          * ....
515    
516  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
517    
518          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
519    
# Line 49  Line 528 
528            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
529          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
530    
531  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
532    
533          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
534    
535  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
536    
537          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
538    
539  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
540    
541          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
542          the package.          the package.
# Line 105  Line 584 
584    
585          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
586    
587  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
588    
589          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
590          for the geMatrix class.          for the geMatrix class.
591    
592  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
593    
594          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
595    
596          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
597    
598  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
599    
600          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
601          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
602    
603  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
604    
605          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
606    
607  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
608    
609          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
610          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
611    
612  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
613    
614          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
615    
616          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
617          for tripletMatrix to matrix.          for tripletMatrix to matrix.
618    
619  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
620    
621          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
622          no longer used.          no longer used.
# Line 149  Line 628 
628          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
629          Fixes part but not all of #15.          Fixes part but not all of #15.
630    
631  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
632    
633          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
634          scalar grouping factors corrected.          scalar grouping factors corrected.
635    
636  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
637    
638          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
639    
640  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
641    
642          * 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
643          .h file can be included.          .h file can be included.
644    
645  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
646    
647          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
648          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
649    
650          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
651    
652  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
653    
654          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
655    
656  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
657    
658          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
659    
660  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
661    
662          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
663    
664  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
665    
666          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
667    
668  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
669    
670          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
671          routines.          routines.
672    
673  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
674    
675          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
676    
677  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
678    
679          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
680    

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