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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 860, Wed Aug 17 05:50:50 2005 UTC
# Line 1  Line 1 
1  2004-12-14  Douglas Bates  <bates@bates1-home>  2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
4    
5    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
6    
7            * R/HBMM.R: finish re-writing R-only code.
8    
9    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
10    
11            * man/externalFormats.Rd: move documentation for writeHB and
12            writeMM here.
13    
14            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
15            (suggested by Paul Roecker).
16    
17            * tests/validObj.R (assertError): Comment out test that is failing
18            after recent changes in r-devel.
19    
20    
21    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/AllClass.R: intermediate virtual class "denseMatrix"
24            * man/denseMatrix-class.Rd
25            * NAMESPACE: export it, and also export
26            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
27    
28    2005-08-10  Douglas Bates  <bates@wisc.edu>
29    
30            * DESCRIPTION (Version): 0.98-3 to CRAN
31    
32            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
33            matrix_solve code (which was really, really wrong).
34    
35    2005-08-07  Douglas Bates  <bates@wisc.edu>
36    
37            * DESCRIPTION (Version): 0.98-2
38    
39            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
40    
41            * R/lmer.R (abbrvNms): new
42            * R/lmer.R (mcmcsamp): allow transformed parameters
43            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
44            for the Harwell-Boeing and the MatrixMarket formats.
45    
46    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * man/dtrMatrix-class.Rd: add examples
49            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
50    
51            * TODO: note the dtpMatrix (docu) bug
52    
53            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
54            in order to ensure that new as.matrix() is used by old functions,
55            e.g., svd(), qr(), eigen(), dist(),..;
56                  apply(), also matplot() or pairs().
57    
58    
59    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
62              add comments about 'control' / lmerControl() arguments
63    
64    2005-07-27  Douglas Bates  <bates@wisc.edu>
65    
66            * man/sleepstudy.Rd: Added the sleep data set.
67            * DESCRIPTION (Version): 0.98-1  released to CRAN
68    
69    2005-07-12  Douglas Bates  <bates@wisc.edu>
70            * man/sleepstudy.Rd: Added the sleep data set.
71    
72            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
73            .Call calls that were producing spurious output.
74    
75    2005-07-05  Douglas Bates  <bates@wisc.edu>
76    
77            * R/lmer.R (lmer): stored updated variance component estimates in
78            mer object for the generalized model.  (Bug reported by Renaud
79            Lancelot).
80    
81    2005-07-03  Douglas Bates  <bates@wisc.edu>
82    
83            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
84            unidimensional case.
85    
86    2005-06-08  Douglas Bates  <bates@wisc.edu>
87    
88            * DESCRIPTION (Version): 0.96-1
89    
90            * moved  lmer-class' R and C code moved from lme4 to here
91    
92    2005-06-04  Douglas Bates  <bates@wisc.edu>
93    
94            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
95            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
96    
97    2005-06-02  Douglas Bates  <bates@wisc.edu>
98    
99            * src/Makefile.win: Forgot to update this when Makefile changed.
100    
101    2005-05-11  Douglas Bates  <bates@wisc.edu>
102    
103            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
104            bug reported by Kurt Hornik and Michael Hahsler.
105    
106    2005-05-10  Douglas Bates  <bates@wisc.edu>
107    
108            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
109            logical sparse matrices.  These will also be used in the symbolic
110            analysis for lmer objects.
111    
112            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
113            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
114    
115    2005-05-06  Douglas Bates  <bates@wisc.edu>
116    
117            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
118            colMeans, colSums, rowMeans and rowSums.
119    
120    2005-04-18  Douglas Bates  <bates@wisc.edu>
121    
122            * src/lgCMatrix.[ch]: code for _validate method and stub for
123            multiplication operation.
124    
125            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
126            to dgetrs.
127    
128            * src/init.c: Fix cut-and-paste error in definition of
129            dgeMatrix_matrix_solve
130    
131            * src/{many files}: Tighten code by using ALLOC_SLOT.
132    
133    2005-04-15  Douglas Bates  <bates@wisc.edu>
134    
135            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
136    
137            * DESCRIPTION: Eliminate import of stats.
138    
139    
140    2005-04-06  Douglas Bates  <bates@wisc.edu>
141    
142            * R/AllClass.R : add logical sparse matrix classes
143    
144    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/dgTMatrix.R: add "[" method for triplet matrices
147            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
148    
149    2005-03-31  Douglas Bates  <bates@wisc.edu>
150    
151            * DESCRIPTION (Version): release 0.95-5 to CRAN
152    
153            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
154            * R/sparseMatrix.R: %*%, crossprod()
155            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
156            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
157            * src/lmer.c (lmer_fitted): fix thinko
158    
159    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/AllClass.R: add two virtual sparse classes ``on top''
162    
163    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
166                    correspondingly fix examples and tests/ since new()
167                    doesn't work for virtual classes.
168    
169    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Matrix.R (as.matrix): method and one for unname()
172            * tests/dpoMatrix.R: tests should now be less platform dependent;
173              also run for R 2.1.0; using as.matrix()
174    
175    2005-03-15  Douglas Bates  <bates@wisc.edu>
176    
177            * R/pMatrix.R: "pMatrix" class added
178            * ....
179    
180    2005-03-14  Douglas Bates  <bates@wisc.edu>
181    
182            * R/dtpMatrix.R: Add unpack method and an example.
183    
184            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
185            of general symmetric matrices and associated S4 methods.
186    
187    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
188            +
189    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/dgeMatrix.R (setAs): and many other files: more coercion,
192              crossprod() and "%*%" methods added; tests, too.
193            * tests/matprod.R: new, for testing these
194    
195    2005-03-03  Douglas Bates  <bates@wisc.edu>
196    
197            * src/lmer.c (lmer_fitted): Added.
198    
199    2005-03-02  Douglas Bates  <bates@wisc.edu>
200    
201            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
202    
203    2005-02-28  Douglas Bates  <bates@wisc.edu>
204    
205            * src/*.c,po/,inst/po: Internationalization and localization of
206            the package.
207    
208            * src/ldl.[ch]: Removed these as their contents are referenced in the
209            R_ldl.c file.
210    
211            * src/flame.[ch]: Removed these source files.
212    
213            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
214    
215            * src/LU.[ch],src/init.c: absorb in factorizations
216    
217            * src/Mutils.h: prepare for internationalization
218    
219            * src/cblas.h: move the enum definitions to Mutils.h and remove
220            this file
221    
222    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
225    
226            * R/dtrMatrix.R: fix t() method
227    
228            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
229            * NAMESPACE: export them (and import generics from "methods")
230            * tests/group-methods.R : and test them.
231    
232            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
233            border case
234    
235    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
236    
237            * DESCRIPTION (Version): 0.95-2  released to CRAN
238    
239            * src/dgBCMatrix.c:
240            * src/lmer.c: many changes
241            * ...
242    
243    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Matrix.R: add more sophisticated show() method.
246    
247    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
248    
249            * */* : almost complete reorganization of classes.
250    
251    2005-01-26  Douglas Bates  <bates@wisc.edu>
252    
253            * R/AllGeneric.R: Added matrix exponential generic expm and a method
254            for the geMatrix class.
255    
256    2005-01-24  Douglas Bates  <bates@wisc.edu>
257    
258            * src/Makefile (clean): Remove *.a and *.so
259    
260            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
261    
262    2005-01-23  Douglas Bates  <bates@wisc.edu>
263    
264            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
265            had an effect in cases with more than 2 grouping factors.
266    
267    2005-01-03  Douglas Bates  <bates@wisc.edu>
268    
269            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
270    
271    2004-12-23  Douglas Bates  <bates@wisc.edu>
272    
273            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
274            and R_useDynamicSymbols (suggested by B.D.Ripley).
275    
276    2004-12-14  Douglas Bates  <bates@wisc.edu>
277    
278          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
279    
280          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
281          for tripletMatrix to matrix.          for tripletMatrix to matrix.
282    
283  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
284    
285          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
286          no longer used.          no longer used.
# Line 17  Line 292 
292          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
293          Fixes part but not all of #15.          Fixes part but not all of #15.
294    
295  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
296    
297          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
298          scalar grouping factors corrected.          scalar grouping factors corrected.
299    
300  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
301    
302          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
303    
304  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
305    
306          * 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
307          .h file can be included.          .h file can be included.
308    
309  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
310    
311          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
312          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
313    
314          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
315    
316  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
317    
318          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
319    
320  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
321    
322          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
323    
324  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
325    
326          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
327    
328  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
329    
330          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
331    
332  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
333    
334          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
335          routines.          routines.
336    
337  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
338    
339          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
340    
341  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
342    
343          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
344    

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