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revision 809, Tue Jul 12 23:00:50 2005 UTC revision 868, Fri Aug 19 17:01:11 2005 UTC
# Line 1  Line 1 
1  2005-07-12  Douglas Bates  <bates@localhost.localdomain>  2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
4                    as( <logical>, "matrix")
5    
6            * R/pMatrix.R: coercion to "lgTMatrix"
7    
8            * R/gTMatrix.R: new virtual class to define "[" methods for.
9            * man/gTMatrix-class.Rd:
10            * General slight re-organization of where "[" methods are defined.
11              more to come.
12    
13    
14    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
15    
16            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
17            or glmer objects.
18    
19    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
22    
23    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
24    
25            * R/HBMM.R: finish re-writing R-only code.
26    
27    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
28    
29            * man/externalFormats.Rd: move documentation for writeHB and
30            writeMM here.
31    
32            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
33            (suggested by Paul Roecker).
34    
35            * tests/validObj.R (assertError): Comment out test that is failing
36            after recent changes in r-devel.
37    
38    
39    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/AllClass.R: intermediate virtual class "denseMatrix"
42            * man/denseMatrix-class.Rd
43            * NAMESPACE: export it, and also export
44            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
45    
46    2005-08-10  Douglas Bates  <bates@wisc.edu>
47    
48            * DESCRIPTION (Version): 0.98-3 to CRAN
49    
50            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
51            matrix_solve code (which was really, really wrong).
52    
53    2005-08-07  Douglas Bates  <bates@wisc.edu>
54    
55            * DESCRIPTION (Version): 0.98-2
56    
57            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
58    
59            * R/lmer.R (abbrvNms): new
60            * R/lmer.R (mcmcsamp): allow transformed parameters
61            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
62            for the Harwell-Boeing and the MatrixMarket formats.
63    
64    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * man/dtrMatrix-class.Rd: add examples
67            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
68    
69            * TODO: note the dtpMatrix (docu) bug
70    
71            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
72            in order to ensure that new as.matrix() is used by old functions,
73            e.g., svd(), qr(), eigen(), dist(),..;
74                  apply(), also matplot() or pairs().
75    
76    
77    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
80              add comments about 'control' / lmerControl() arguments
81    
82    2005-07-27  Douglas Bates  <bates@wisc.edu>
83    
84            * man/sleepstudy.Rd: Added the sleep data set.
85            * DESCRIPTION (Version): 0.98-1  released to CRAN
86    
87    2005-07-12  Douglas Bates  <bates@wisc.edu>
88            * man/sleepstudy.Rd: Added the sleep data set.
89    
90          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
91          .Call calls that were producing spurious output.          .Call calls that were producing spurious output.
92    
93  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-07-05  Douglas Bates  <bates@wisc.edu>
94    
95          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
96          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
97          Lancelot).          Lancelot).
98    
99  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
100    
101          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
102          unidimensional case.          unidimensional case.
103    
104  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
105    
106          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
107    
108          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
109    
110  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
111    
112          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
113          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
114    
115  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
116    
117          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
118    
119  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
120    
121          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
122          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
123    
124  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
125    
126          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
127          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 43  Line 130 
130          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
131          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
132    
133  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
134    
135          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
136          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
137    
138  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
139    
140          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
141          multiplication operation.          multiplication operation.
# Line 61  Line 148 
148    
149          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
150    
151  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
152    
153          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
154    
155          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
156    
157    
158  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
159    
160          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
161    
# Line 77  Line 164 
164          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
165          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
166    
167  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
168    
169          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
170    
# Line 103  Line 190 
190          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
191            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
192    
193  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
194    
195          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
196          * ....          * ....
197    
198  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
199    
200          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
201    
# Line 123  Line 210 
210            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
211          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
212    
213  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
214    
215          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
216    
217  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
218    
219          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
220    
221  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
222    
223          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
224          the package.          the package.
# Line 179  Line 266 
266    
267          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
268    
269  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
270    
271          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
272          for the geMatrix class.          for the geMatrix class.
273    
274  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
275    
276          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
277    
278          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
279    
280  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
281    
282          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
283          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
284    
285  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
286    
287          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
288    
289  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
290    
291          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
292          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
293    
294  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
295    
296          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
297    
298          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
299          for tripletMatrix to matrix.          for tripletMatrix to matrix.
300    
301  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
302    
303          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
304          no longer used.          no longer used.
# Line 223  Line 310 
310          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
311          Fixes part but not all of #15.          Fixes part but not all of #15.
312    
313  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
314    
315          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
316          scalar grouping factors corrected.          scalar grouping factors corrected.
317    
318  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
319    
320          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
321    
322  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
323    
324          * 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
325          .h file can be included.          .h file can be included.
326    
327  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
328    
329          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
330          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
331    
332          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
333    
334  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
335    
336          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
337    
338  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
339    
340          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
341    
342  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
343    
344          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
345    
346  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
347    
348          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
349    
350  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
351    
352          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
353          routines.          routines.
354    
355  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
356    
357          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
358    
359  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
360    
361          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
362    

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