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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 848, Thu Aug 11 07:41:59 2005 UTC
# Line 1  Line 1 
1    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
58            mer object for the generalized model.  (Bug reported by Renaud
59            Lancelot).
60    
61    2005-07-03  Douglas Bates  <bates@wisc.edu>
62    
63            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
64            unidimensional case.
65    
66    2005-06-08  Douglas Bates  <bates@wisc.edu>
67    
68            * DESCRIPTION (Version): 0.96-1
69    
70            * moved  lmer-class' R and C code moved from lme4 to here
71    
72    2005-06-04  Douglas Bates  <bates@wisc.edu>
73    
74            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
75            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
76    
77    2005-06-02  Douglas Bates  <bates@wisc.edu>
78    
79            * src/Makefile.win: Forgot to update this when Makefile changed.
80    
81    2005-05-11  Douglas Bates  <bates@wisc.edu>
82    
83            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
84            bug reported by Kurt Hornik and Michael Hahsler.
85    
86    2005-05-10  Douglas Bates  <bates@wisc.edu>
87    
88            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
89            logical sparse matrices.  These will also be used in the symbolic
90            analysis for lmer objects.
91    
92            * 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
94    
95    2005-05-06  Douglas Bates  <bates@wisc.edu>
96    
97            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
98            colMeans, colSums, rowMeans and rowSums.
99    
100    2005-04-18  Douglas Bates  <bates@wisc.edu>
101    
102            * src/lgCMatrix.[ch]: code for _validate method and stub for
103            multiplication operation.
104    
105            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
106            to dgetrs.
107    
108            * src/init.c: Fix cut-and-paste error in definition of
109            dgeMatrix_matrix_solve
110    
111            * src/{many files}: Tighten code by using ALLOC_SLOT.
112    
113    2005-04-15  Douglas Bates  <bates@wisc.edu>
114    
115            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
116    
117            * DESCRIPTION: Eliminate import of stats.
118    
119    
120    2005-04-06  Douglas Bates  <bates@wisc.edu>
121    
122            * R/AllClass.R : add logical sparse matrix classes
123    
124  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
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 29  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 49  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 105  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 149  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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