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revision 834, Mon Aug 8 08:36:34 2005 UTC revision 835, Mon Aug 8 13:33:18 2005 UTC
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1  2005-08-07  Douglas Bates <bates@localhost.localdomain>  2005-08-07  Douglas Bates  <bates@wisc.edu>
2    
3          * DESCRIPTION (Version): 0.98-2          * DESCRIPTION (Version): 0.98-2
4    
# Line 6  Line 6 
6    
7          * R/lmer.R (abbrvNms): new          * R/lmer.R (abbrvNms): new
8          * R/lmer.R (mcmcsamp): allow transformed parameters          * R/lmer.R (mcmcsamp): allow transformed parameters
9            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
10            for the Harwell-Boeing and the MatrixMarket formats.
11    
12  2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14          * man/dtrMatrix-class.Rd: add examples          * man/dtrMatrix-class.Rd: add examples
15          * man/dtpMatrix-class.Rd: dito; plus note about PROBLEM          * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
16    
17          * TODO: note the dtpMatrix (docu) bug          * TODO: note the dtpMatrix (docu) bug
18    
# Line 25  Line 27 
27          * R/lmer.R: add 'fixme' comments and move the linear vs glm check;          * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
28            add comments about 'control' / lmerControl() arguments            add comments about 'control' / lmerControl() arguments
29    
30  2005-07-27  Douglas Bates  <bates@localhost.localdomain>  2005-07-27  Douglas Bates  <bates@wisc.edu>
31    
32            * man/sleepstudy.Rd: Added the sleep data set.
33          * DESCRIPTION (Version): 0.98-1  released to CRAN          * DESCRIPTION (Version): 0.98-1  released to CRAN
34    
35    2005-07-12  Douglas Bates  <bates@wisc.edu>
36          * man/sleepstudy.Rd: Added the sleep data set.          * man/sleepstudy.Rd: Added the sleep data set.
37    
 2005-07-12  Douglas Bates  <bates@localhost.localdomain>  
   
38          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
39          .Call calls that were producing spurious output.          .Call calls that were producing spurious output.
40    
41  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-07-05  Douglas Bates  <bates@wisc.edu>
42    
43          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
44          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
45          Lancelot).          Lancelot).
46    
47  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
48    
49          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
50          unidimensional case.          unidimensional case.
51    
52  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
53    
54          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
55    
56          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
57    
58  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
59    
60          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
61          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
62    
63  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
64    
65          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
66    
67  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
68    
69          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
70          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
71    
72  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
73    
74          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
75          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 76  Line 78 
78          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
79          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
80    
81  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
82    
83          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
84          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
85    
86  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
87    
88          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
89          multiplication operation.          multiplication operation.
# Line 94  Line 96 
96    
97          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
98    
99  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
100    
101          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
102    
103          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
104    
105    
106  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
107    
108          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
109    
# Line 110  Line 112 
112          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
113          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
114    
115  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
116    
117          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
118    
# Line 136  Line 138 
138          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
139            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
140    
141  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
142    
143          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
144          * ....          * ....
145    
146  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
147    
148          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
149    
# Line 156  Line 158 
158            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
159          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
160    
161  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
162    
163          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
164    
165  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
166    
167          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
168    
169  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
170    
171          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
172          the package.          the package.
# Line 212  Line 214 
214    
215          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
216    
217  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
218    
219          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
220          for the geMatrix class.          for the geMatrix class.
221    
222  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
223    
224          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
225    
226          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
227    
228  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
229    
230          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
231          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
232    
233  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
234    
235          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
236    
237  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
238    
239          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
240          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
241    
242  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
243    
244          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
245    
246          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
247          for tripletMatrix to matrix.          for tripletMatrix to matrix.
248    
249  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
250    
251          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
252          no longer used.          no longer used.
# Line 256  Line 258 
258          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
259          Fixes part but not all of #15.          Fixes part but not all of #15.
260    
261  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
262    
263          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
264          scalar grouping factors corrected.          scalar grouping factors corrected.
265    
266  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
267    
268          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
269    
270  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
271    
272          * 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
273          .h file can be included.          .h file can be included.
274    
275  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
276    
277          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
278          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
279    
280          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
281    
282  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
283    
284          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
285    
286  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
287    
288          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
289    
290  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
291    
292          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
293    
294  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
295    
296          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
297    
298  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
299    
300          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
301          routines.          routines.
302    
303  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
304    
305          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
306    
307  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
308    
309          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
310    

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