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revision 801, Wed Jul 6 16:24:33 2005 UTC revision 848, Thu Aug 11 07:41:59 2005 UTC
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1  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R: intermediate virtual class "denseMatrix"
4            * man/denseMatrix-class.Rd
5            * NAMESPACE: export it, and also export
6            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
7    
8    2005-08-10  Douglas Bates  <bates@wisc.edu>
9    
10            * DESCRIPTION (Version): 0.98-3 to CRAN
11    
12            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
13            matrix_solve code (which was really, really wrong).
14    
15    2005-08-07  Douglas Bates  <bates@wisc.edu>
16    
17            * DESCRIPTION (Version): 0.98-2
18    
19            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
20    
21            * R/lmer.R (abbrvNms): new
22            * R/lmer.R (mcmcsamp): allow transformed parameters
23            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
24            for the Harwell-Boeing and the MatrixMarket formats.
25    
26    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * man/dtrMatrix-class.Rd: add examples
29            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
30    
31            * TODO: note the dtpMatrix (docu) bug
32    
33            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
34            in order to ensure that new as.matrix() is used by old functions,
35            e.g., svd(), qr(), eigen(), dist(),..;
36                  apply(), also matplot() or pairs().
37    
38    
39    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
42              add comments about 'control' / lmerControl() arguments
43    
44    2005-07-27  Douglas Bates  <bates@wisc.edu>
45    
46            * man/sleepstudy.Rd: Added the sleep data set.
47            * DESCRIPTION (Version): 0.98-1  released to CRAN
48    
49    2005-07-12  Douglas Bates  <bates@wisc.edu>
50            * man/sleepstudy.Rd: Added the sleep data set.
51    
52            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
53            .Call calls that were producing spurious output.
54    
55    2005-07-05  Douglas Bates  <bates@wisc.edu>
56    
57          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
58          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
59          Lancelot).          Lancelot).
60    
61  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
62    
63          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
64          unidimensional case.          unidimensional case.
65    
66  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
67    
68          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
69    
70          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
71    
72  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
73    
74          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
75          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
76    
77  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
78    
79          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
80    
81  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
82    
83          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
84          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
85    
86  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
87    
88          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
89          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 38  Line 92 
92          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
93          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
94    
95  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
96    
97          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
98          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
99    
100  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
101    
102          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
103          multiplication operation.          multiplication operation.
# Line 56  Line 110 
110    
111          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
112    
113  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
114    
115          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
116    
117          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
118    
119    
120  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
121    
122          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
123    
# Line 72  Line 126 
126          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
127          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
128    
129  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
130    
131          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
132    
# Line 98  Line 152 
152          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
153            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
154    
155  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
156    
157          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
158          * ....          * ....
159    
160  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
161    
162          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
163    
# Line 118  Line 172 
172            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
173          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
174    
175  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
176    
177          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
178    
179  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
180    
181          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
182    
183  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
184    
185          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
186          the package.          the package.
# Line 174  Line 228 
228    
229          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
230    
231  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
232    
233          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
234          for the geMatrix class.          for the geMatrix class.
235    
236  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
237    
238          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
239    
240          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
241    
242  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
243    
244          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
245          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
246    
247  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
248    
249          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
250    
251  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
252    
253          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
254          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
255    
256  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
257    
258          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
259    
260          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
261          for tripletMatrix to matrix.          for tripletMatrix to matrix.
262    
263  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
264    
265          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
266          no longer used.          no longer used.
# Line 218  Line 272 
272          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
273          Fixes part but not all of #15.          Fixes part but not all of #15.
274    
275  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
276    
277          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
278          scalar grouping factors corrected.          scalar grouping factors corrected.
279    
280  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
281    
282          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
283    
284  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
285    
286          * 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
287          .h file can be included.          .h file can be included.
288    
289  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
290    
291          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
292          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
293    
294          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
295    
296  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
297    
298          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
299    
300  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
301    
302          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
303    
304  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
305    
306          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
307    
308  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
309    
310          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
311    
312  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
313    
314          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
315          routines.          routines.
316    
317  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
318    
319          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
320    
321  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
322    
323          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
324    

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