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revision 109, Mon Apr 19 17:44:39 2004 UTC revision 846, Wed Aug 10 22:08:35 2005 UTC
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1    2005-08-10  Douglas Bates  <bates@wisc.edu>
2    
3            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
4            matrix_solve code (which was really, really wrong).
5    
6    2005-08-07  Douglas Bates  <bates@wisc.edu>
7    
8            * DESCRIPTION (Version): 0.98-2
9    
10            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
11    
12            * R/lmer.R (abbrvNms): new
13            * R/lmer.R (mcmcsamp): allow transformed parameters
14            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
15            for the Harwell-Boeing and the MatrixMarket formats.
16    
17    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * man/dtrMatrix-class.Rd: add examples
20            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
21    
22            * TODO: note the dtpMatrix (docu) bug
23    
24            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
25            in order to ensure that new as.matrix() is used by old functions,
26            e.g., svd(), qr(), eigen(), dist(),..;
27                  apply(), also matplot() or pairs().
28    
29    
30    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
33              add comments about 'control' / lmerControl() arguments
34    
35    2005-07-27  Douglas Bates  <bates@wisc.edu>
36    
37            * man/sleepstudy.Rd: Added the sleep data set.
38            * DESCRIPTION (Version): 0.98-1  released to CRAN
39    
40    2005-07-12  Douglas Bates  <bates@wisc.edu>
41            * man/sleepstudy.Rd: Added the sleep data set.
42    
43            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
44            .Call calls that were producing spurious output.
45    
46    2005-07-05  Douglas Bates  <bates@wisc.edu>
47    
48            * R/lmer.R (lmer): stored updated variance component estimates in
49            mer object for the generalized model.  (Bug reported by Renaud
50            Lancelot).
51    
52    2005-07-03  Douglas Bates  <bates@wisc.edu>
53    
54            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
55            unidimensional case.
56    
57    2005-06-08  Douglas Bates  <bates@wisc.edu>
58    
59            * DESCRIPTION (Version): 0.96-1
60    
61            * moved  lmer-class' R and C code moved from lme4 to here
62    
63    2005-06-04  Douglas Bates  <bates@wisc.edu>
64    
65            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
66            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
67    
68    2005-06-02  Douglas Bates  <bates@wisc.edu>
69    
70            * src/Makefile.win: Forgot to update this when Makefile changed.
71    
72    2005-05-11  Douglas Bates  <bates@wisc.edu>
73    
74            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
75            bug reported by Kurt Hornik and Michael Hahsler.
76    
77    2005-05-10  Douglas Bates  <bates@wisc.edu>
78    
79            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
80            logical sparse matrices.  These will also be used in the symbolic
81            analysis for lmer objects.
82    
83            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
84            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
85    
86    2005-05-06  Douglas Bates  <bates@wisc.edu>
87    
88            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
89            colMeans, colSums, rowMeans and rowSums.
90    
91    2005-04-18  Douglas Bates  <bates@wisc.edu>
92    
93            * src/lgCMatrix.[ch]: code for _validate method and stub for
94            multiplication operation.
95    
96            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
97            to dgetrs.
98    
99            * src/init.c: Fix cut-and-paste error in definition of
100            dgeMatrix_matrix_solve
101    
102            * src/{many files}: Tighten code by using ALLOC_SLOT.
103    
104    2005-04-15  Douglas Bates  <bates@wisc.edu>
105    
106            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
107    
108            * DESCRIPTION: Eliminate import of stats.
109    
110    
111    2005-04-06  Douglas Bates  <bates@wisc.edu>
112    
113            * R/AllClass.R : add logical sparse matrix classes
114    
115    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/dgTMatrix.R: add "[" method for triplet matrices
118            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
119    
120    2005-03-31  Douglas Bates  <bates@wisc.edu>
121    
122            * DESCRIPTION (Version): release 0.95-5 to CRAN
123    
124            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
125            * R/sparseMatrix.R: %*%, crossprod()
126            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
127            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
128            * src/lmer.c (lmer_fitted): fix thinko
129    
130    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/AllClass.R: add two virtual sparse classes ``on top''
133    
134    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
137                    correspondingly fix examples and tests/ since new()
138                    doesn't work for virtual classes.
139    
140    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Matrix.R (as.matrix): method and one for unname()
143            * tests/dpoMatrix.R: tests should now be less platform dependent;
144              also run for R 2.1.0; using as.matrix()
145    
146    2005-03-15  Douglas Bates  <bates@wisc.edu>
147    
148            * R/pMatrix.R: "pMatrix" class added
149            * ....
150    
151    2005-03-14  Douglas Bates  <bates@wisc.edu>
152    
153            * R/dtpMatrix.R: Add unpack method and an example.
154    
155            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
156            of general symmetric matrices and associated S4 methods.
157    
158    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
159            +
160    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/dgeMatrix.R (setAs): and many other files: more coercion,
163              crossprod() and "%*%" methods added; tests, too.
164            * tests/matprod.R: new, for testing these
165    
166    2005-03-03  Douglas Bates  <bates@wisc.edu>
167    
168            * src/lmer.c (lmer_fitted): Added.
169    
170    2005-03-02  Douglas Bates  <bates@wisc.edu>
171    
172            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
173    
174    2005-02-28  Douglas Bates  <bates@wisc.edu>
175    
176            * src/*.c,po/,inst/po: Internationalization and localization of
177            the package.
178    
179            * src/ldl.[ch]: Removed these as their contents are referenced in the
180            R_ldl.c file.
181    
182            * src/flame.[ch]: Removed these source files.
183    
184            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
185    
186            * src/LU.[ch],src/init.c: absorb in factorizations
187    
188            * src/Mutils.h: prepare for internationalization
189    
190            * src/cblas.h: move the enum definitions to Mutils.h and remove
191            this file
192    
193    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
196    
197            * R/dtrMatrix.R: fix t() method
198    
199            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
200            * NAMESPACE: export them (and import generics from "methods")
201            * tests/group-methods.R : and test them.
202    
203            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
204            border case
205    
206    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * DESCRIPTION (Version): 0.95-2  released to CRAN
209    
210            * src/dgBCMatrix.c:
211            * src/lmer.c: many changes
212            * ...
213    
214    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/Matrix.R: add more sophisticated show() method.
217    
218    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
219    
220            * */* : almost complete reorganization of classes.
221    
222    2005-01-26  Douglas Bates  <bates@wisc.edu>
223    
224            * R/AllGeneric.R: Added matrix exponential generic expm and a method
225            for the geMatrix class.
226    
227    2005-01-24  Douglas Bates  <bates@wisc.edu>
228    
229            * src/Makefile (clean): Remove *.a and *.so
230    
231            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
232    
233    2005-01-23  Douglas Bates  <bates@wisc.edu>
234    
235            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
236            had an effect in cases with more than 2 grouping factors.
237    
238    2005-01-03  Douglas Bates  <bates@wisc.edu>
239    
240            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
241    
242    2004-12-23  Douglas Bates  <bates@wisc.edu>
243    
244            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
245            and R_useDynamicSymbols (suggested by B.D.Ripley).
246    
247    2004-12-14  Douglas Bates  <bates@wisc.edu>
248    
249            * R/sscMatrix.R: Add determinant methods
250    
251            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
252            for tripletMatrix to matrix.
253    
254    2004-12-13  Douglas Bates  <bates@wisc.edu>
255    
256            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
257            no longer used.
258    
259            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
260            with dynamic allocation of scratch arrays.
261    
262            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
263            for multivariate random effects with multiple grouping factors.
264            Fixes part but not all of #15.
265    
266    2004-12-03  Douglas Bates  <bates@wisc.edu>
267    
268            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
269            scalar grouping factors corrected.
270    
271    2004-11-29  Douglas Bates  <bates@wisc.edu>
272    
273            * src/bCrosstab.c: remove diag_update which is no longer used
274    
275    2004-11-16  Douglas Bates  <bates@wisc.edu>
276    
277            * src/Metis_utils.c: Move metis.h include to C sources so that the
278            .h file can be included.
279    
280    2004-11-12  Douglas Bates  <bates@wisc.edu>
281    
282            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
283            Complete allocation of slots in NEW_OBJECT.
284    
285            * src/Mutils.h: Moved list of symbols to an include file
286    
287    2004-11-11  Douglas Bates  <bates@wisc.edu>
288    
289            * src/geMutils.c (Matrix_init): remove unused function
290    
291    2004-11-10  Douglas Bates  <bates@wisc.edu>
292    
293            * src/cscMatrix.c (csc_to_imagemat): removed unused function
294    
295    2004-11-05  Douglas Bates  <bates@wisc.edu>
296    
297            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
298    
299    2004-10-27  Douglas Bates  <bates@wisc.edu>
300    
301            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
302    
303    2004-10-04  Douglas Bates  <bates@wisc.edu>
304    
305            * src/init.c: Created R_init_Matrix and added registration of C
306            routines.
307    
308    2004-10-02  Douglas Bates  <bates@wisc.edu>
309    
310            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
311    
312    2004-06-15  Douglas Bates  <bates@wisc.edu>
313    
314            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
315    
316    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
317    
318            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
319    
320  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
321    
322          * src/ssclme.c (ssclme_update_mm): fix logic error in          * src/ssclme.c (ssclme_update_mm): fix logic error in

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