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revision 109, Mon Apr 19 17:44:39 2004 UTC revision 871, Fri Aug 26 17:26:49 2005 UTC
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1    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R:  added first "[<-" methods; not yet functional
4            * R/denseMatrix.R: dito
5            * man/Subassign-methods.Rd: new help file for these
6    
7    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * DESCRIPTION (Version): 0.98-6
10    
11            * R/denseMatrix.R: new file for "[" fallback methods for all dense
12            matrices.
13    
14    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
17                    as( <logical>, "matrix")
18    
19            * R/pMatrix.R: coercion to "lgTMatrix"
20    
21            * R/gTMatrix.R: new virtual class to define "[" methods for.
22            * man/gTMatrix-class.Rd:
23            * General slight re-organization of where "[" methods are defined.
24              more to come.
25    
26    2005-08-18  Douglas Bates  <bates@wisc.edu>
27    
28            * DESCRIPTION (Version): 0.98-5  released to CRAN
29    
30            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
31            * .....
32    
33    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
34    
35            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
36            or glmer objects.
37    
38    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
41    
42    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
43    
44            * R/HBMM.R: finish re-writing R-only code.
45    
46    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
47    
48            * man/externalFormats.Rd: move documentation for writeHB and
49            writeMM here.
50    
51            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
52            (suggested by Paul Roecker).
53    
54            * tests/validObj.R (assertError): Comment out test that is failing
55            after recent changes in r-devel.
56    
57    
58    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/AllClass.R: intermediate virtual class "denseMatrix"
61            * man/denseMatrix-class.Rd
62            * NAMESPACE: export it, and also export
63            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
64    
65    2005-08-10  Douglas Bates  <bates@wisc.edu>
66    
67            * DESCRIPTION (Version): 0.98-3 to CRAN
68    
69            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
70            matrix_solve code (which was really, really wrong).
71    
72    2005-08-07  Douglas Bates  <bates@wisc.edu>
73    
74            * DESCRIPTION (Version): 0.98-2
75    
76            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
77    
78            * R/lmer.R (abbrvNms): new
79            * R/lmer.R (mcmcsamp): allow transformed parameters
80            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
81            for the Harwell-Boeing and the MatrixMarket formats.
82    
83    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * man/dtrMatrix-class.Rd: add examples
86            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
87    
88            * TODO: note the dtpMatrix (docu) bug
89    
90            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
91            in order to ensure that new as.matrix() is used by old functions,
92            e.g., svd(), qr(), eigen(), dist(),..;
93                  apply(), also matplot() or pairs().
94    
95    
96    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
99              add comments about 'control' / lmerControl() arguments
100    
101    2005-07-27  Douglas Bates  <bates@wisc.edu>
102    
103            * man/sleepstudy.Rd: Added the sleep data set.
104            * DESCRIPTION (Version): 0.98-1  released to CRAN
105    
106    2005-07-12  Douglas Bates  <bates@wisc.edu>
107            * man/sleepstudy.Rd: Added the sleep data set.
108    
109            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
110            .Call calls that were producing spurious output.
111    
112    2005-07-05  Douglas Bates  <bates@wisc.edu>
113    
114            * R/lmer.R (lmer): stored updated variance component estimates in
115            mer object for the generalized model.  (Bug reported by Renaud
116            Lancelot).
117    
118    2005-07-03  Douglas Bates  <bates@wisc.edu>
119    
120            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
121            unidimensional case.
122    
123    2005-06-08  Douglas Bates  <bates@wisc.edu>
124    
125            * DESCRIPTION (Version): 0.96-1
126    
127            * moved  lmer-class' R and C code moved from lme4 to here
128    
129    2005-06-04  Douglas Bates  <bates@wisc.edu>
130    
131            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
132            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
133    
134    2005-06-02  Douglas Bates  <bates@wisc.edu>
135    
136            * src/Makefile.win: Forgot to update this when Makefile changed.
137    
138    2005-05-11  Douglas Bates  <bates@wisc.edu>
139    
140            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
141            bug reported by Kurt Hornik and Michael Hahsler.
142    
143    2005-05-10  Douglas Bates  <bates@wisc.edu>
144    
145            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
146            logical sparse matrices.  These will also be used in the symbolic
147            analysis for lmer objects.
148    
149            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
150            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
151    
152    2005-05-06  Douglas Bates  <bates@wisc.edu>
153    
154            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
155            colMeans, colSums, rowMeans and rowSums.
156    
157    2005-04-18  Douglas Bates  <bates@wisc.edu>
158    
159            * src/lgCMatrix.[ch]: code for _validate method and stub for
160            multiplication operation.
161    
162            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
163            to dgetrs.
164    
165            * src/init.c: Fix cut-and-paste error in definition of
166            dgeMatrix_matrix_solve
167    
168            * src/{many files}: Tighten code by using ALLOC_SLOT.
169    
170    2005-04-15  Douglas Bates  <bates@wisc.edu>
171    
172            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
173    
174            * DESCRIPTION: Eliminate import of stats.
175    
176    
177    2005-04-06  Douglas Bates  <bates@wisc.edu>
178    
179            * R/AllClass.R : add logical sparse matrix classes
180    
181    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/dgTMatrix.R: add "[" method for triplet matrices
184            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
185    
186    2005-03-31  Douglas Bates  <bates@wisc.edu>
187    
188            * DESCRIPTION (Version): release 0.95-5 to CRAN
189    
190            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
191            * R/sparseMatrix.R: %*%, crossprod()
192            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
193            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
194            * src/lmer.c (lmer_fitted): fix thinko
195    
196    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/AllClass.R: add two virtual sparse classes ``on top''
199    
200    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
203                    correspondingly fix examples and tests/ since new()
204                    doesn't work for virtual classes.
205    
206    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Matrix.R (as.matrix): method and one for unname()
209            * tests/dpoMatrix.R: tests should now be less platform dependent;
210              also run for R 2.1.0; using as.matrix()
211    
212    2005-03-15  Douglas Bates  <bates@wisc.edu>
213    
214            * R/pMatrix.R: "pMatrix" class added
215            * ....
216    
217    2005-03-14  Douglas Bates  <bates@wisc.edu>
218    
219            * R/dtpMatrix.R: Add unpack method and an example.
220    
221            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
222            of general symmetric matrices and associated S4 methods.
223    
224    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
225            +
226    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/dgeMatrix.R (setAs): and many other files: more coercion,
229              crossprod() and "%*%" methods added; tests, too.
230            * tests/matprod.R: new, for testing these
231    
232    2005-03-03  Douglas Bates  <bates@wisc.edu>
233    
234            * src/lmer.c (lmer_fitted): Added.
235    
236    2005-03-02  Douglas Bates  <bates@wisc.edu>
237    
238            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
239    
240    2005-02-28  Douglas Bates  <bates@wisc.edu>
241    
242            * src/*.c,po/,inst/po: Internationalization and localization of
243            the package.
244    
245            * src/ldl.[ch]: Removed these as their contents are referenced in the
246            R_ldl.c file.
247    
248            * src/flame.[ch]: Removed these source files.
249    
250            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
251    
252            * src/LU.[ch],src/init.c: absorb in factorizations
253    
254            * src/Mutils.h: prepare for internationalization
255    
256            * src/cblas.h: move the enum definitions to Mutils.h and remove
257            this file
258    
259    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
262    
263            * R/dtrMatrix.R: fix t() method
264    
265            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
266            * NAMESPACE: export them (and import generics from "methods")
267            * tests/group-methods.R : and test them.
268    
269            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
270            border case
271    
272    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * DESCRIPTION (Version): 0.95-2  released to CRAN
275    
276            * src/dgBCMatrix.c:
277            * src/lmer.c: many changes
278            * ...
279    
280    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/Matrix.R: add more sophisticated show() method.
283    
284    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * */* : almost complete reorganization of classes.
287    
288    2005-01-26  Douglas Bates  <bates@wisc.edu>
289    
290            * R/AllGeneric.R: Added matrix exponential generic expm and a method
291            for the geMatrix class.
292    
293    2005-01-24  Douglas Bates  <bates@wisc.edu>
294    
295            * src/Makefile (clean): Remove *.a and *.so
296    
297            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
298    
299    2005-01-23  Douglas Bates  <bates@wisc.edu>
300    
301            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
302            had an effect in cases with more than 2 grouping factors.
303    
304    2005-01-03  Douglas Bates  <bates@wisc.edu>
305    
306            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
307    
308    2004-12-23  Douglas Bates  <bates@wisc.edu>
309    
310            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
311            and R_useDynamicSymbols (suggested by B.D.Ripley).
312    
313    2004-12-14  Douglas Bates  <bates@wisc.edu>
314    
315            * R/sscMatrix.R: Add determinant methods
316    
317            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
318            for tripletMatrix to matrix.
319    
320    2004-12-13  Douglas Bates  <bates@wisc.edu>
321    
322            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
323            no longer used.
324    
325            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
326            with dynamic allocation of scratch arrays.
327    
328            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
329            for multivariate random effects with multiple grouping factors.
330            Fixes part but not all of #15.
331    
332    2004-12-03  Douglas Bates  <bates@wisc.edu>
333    
334            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
335            scalar grouping factors corrected.
336    
337    2004-11-29  Douglas Bates  <bates@wisc.edu>
338    
339            * src/bCrosstab.c: remove diag_update which is no longer used
340    
341    2004-11-16  Douglas Bates  <bates@wisc.edu>
342    
343            * src/Metis_utils.c: Move metis.h include to C sources so that the
344            .h file can be included.
345    
346    2004-11-12  Douglas Bates  <bates@wisc.edu>
347    
348            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
349            Complete allocation of slots in NEW_OBJECT.
350    
351            * src/Mutils.h: Moved list of symbols to an include file
352    
353    2004-11-11  Douglas Bates  <bates@wisc.edu>
354    
355            * src/geMutils.c (Matrix_init): remove unused function
356    
357    2004-11-10  Douglas Bates  <bates@wisc.edu>
358    
359            * src/cscMatrix.c (csc_to_imagemat): removed unused function
360    
361    2004-11-05  Douglas Bates  <bates@wisc.edu>
362    
363            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
364    
365    2004-10-27  Douglas Bates  <bates@wisc.edu>
366    
367            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
368    
369    2004-10-04  Douglas Bates  <bates@wisc.edu>
370    
371            * src/init.c: Created R_init_Matrix and added registration of C
372            routines.
373    
374    2004-10-02  Douglas Bates  <bates@wisc.edu>
375    
376            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
377    
378    2004-06-15  Douglas Bates  <bates@wisc.edu>
379    
380            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
381    
382    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
383    
384            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
385    
386  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
387    
388          * src/ssclme.c (ssclme_update_mm): fix logic error in          * src/ssclme.c (ssclme_update_mm): fix logic error in

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