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revision 801, Wed Jul 6 16:24:33 2005 UTC revision 876, Sat Aug 27 22:50:57 2005 UTC
# Line 1  Line 1 
1  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-08-29  Douglas Bates  <bates@wisc.edu>
2    
3            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
4            indicator pos not being updated.  Also enforced upper triangular
5            for symmetric case.  Need to coerce edges component of elements of
6            edge list - grr! (Why don't they define their classes cleanly?)
7    
8    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Matrix.R:  added first "[<-" methods; not yet functional
11            * R/denseMatrix.R: dito
12            * man/Subassign-methods.Rd: new help file for these
13    
14    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * DESCRIPTION (Version): 0.98-6
17    
18            * R/denseMatrix.R: new file for "[" fallback methods for all dense
19            matrices.
20    
21    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
24                    as( <logical>, "matrix")
25    
26            * R/pMatrix.R: coercion to "lgTMatrix"
27    
28            * R/gTMatrix.R: new virtual class to define "[" methods for.
29            * man/gTMatrix-class.Rd:
30            * General slight re-organization of where "[" methods are defined.
31              more to come.
32    
33    2005-08-18  Douglas Bates  <bates@wisc.edu>
34    
35            * DESCRIPTION (Version): 0.98-5  released to CRAN
36    
37            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
38            * .....
39    
40    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
41    
42            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
43            or glmer objects.
44    
45    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
48    
49    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
50    
51            * R/HBMM.R: finish re-writing R-only code.
52    
53    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
54    
55            * man/externalFormats.Rd: move documentation for writeHB and
56            writeMM here.
57    
58            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
59            (suggested by Paul Roecker).
60    
61            * tests/validObj.R (assertError): Comment out test that is failing
62            after recent changes in r-devel.
63    
64    
65    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/AllClass.R: intermediate virtual class "denseMatrix"
68            * man/denseMatrix-class.Rd
69            * NAMESPACE: export it, and also export
70            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
71    
72    2005-08-10  Douglas Bates  <bates@wisc.edu>
73    
74            * DESCRIPTION (Version): 0.98-3 to CRAN
75    
76            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
77            matrix_solve code (which was really, really wrong).
78    
79    2005-08-07  Douglas Bates  <bates@wisc.edu>
80    
81            * DESCRIPTION (Version): 0.98-2
82    
83            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
84    
85            * R/lmer.R (abbrvNms): new
86            * R/lmer.R (mcmcsamp): allow transformed parameters
87            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
88            for the Harwell-Boeing and the MatrixMarket formats.
89    
90    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * man/dtrMatrix-class.Rd: add examples
93            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
94    
95            * TODO: note the dtpMatrix (docu) bug
96    
97            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
98            in order to ensure that new as.matrix() is used by old functions,
99            e.g., svd(), qr(), eigen(), dist(),..;
100                  apply(), also matplot() or pairs().
101    
102    
103    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
106              add comments about 'control' / lmerControl() arguments
107    
108    2005-07-27  Douglas Bates  <bates@wisc.edu>
109    
110            * man/sleepstudy.Rd: Added the sleep data set.
111            * DESCRIPTION (Version): 0.98-1  released to CRAN
112    
113    2005-07-12  Douglas Bates  <bates@wisc.edu>
114            * man/sleepstudy.Rd: Added the sleep data set.
115    
116            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
117            .Call calls that were producing spurious output.
118    
119    2005-07-05  Douglas Bates  <bates@wisc.edu>
120    
121          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
122          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
123          Lancelot).          Lancelot).
124    
125  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
126    
127          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
128          unidimensional case.          unidimensional case.
129    
130  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
131    
132          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
133    
134          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
135    
136  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
137    
138          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
139          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
140    
141  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
142    
143          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
144    
145  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
146    
147          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
148          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
149    
150  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
151    
152          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
153          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 156 
156          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
157          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
158    
159  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
160    
161          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
162          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
163    
164  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
165    
166          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
167          multiplication operation.          multiplication operation.
# Line 56  Line 174 
174    
175          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
176    
177  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
178    
179          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
180    
181          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
182    
183    
184  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
185    
186          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
187    
# Line 72  Line 190 
190          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
191          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
192    
193  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
194    
195          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
196    
# Line 98  Line 216 
216          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
217            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
218    
219  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
220    
221          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
222          * ....          * ....
223    
224  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
225    
226          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
227    
# Line 118  Line 236 
236            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
237          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
238    
239  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
240    
241          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
242    
243  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
244    
245          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
246    
247  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
248    
249          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
250          the package.          the package.
# Line 174  Line 292 
292    
293          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
294    
295  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
296    
297          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
298          for the geMatrix class.          for the geMatrix class.
299    
300  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
301    
302          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
303    
304          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
305    
306  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
307    
308          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
309          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
310    
311  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
312    
313          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
314    
315  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
316    
317          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
318          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
319    
320  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
321    
322          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
323    
324          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
325          for tripletMatrix to matrix.          for tripletMatrix to matrix.
326    
327  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
328    
329          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
330          no longer used.          no longer used.
# Line 218  Line 336 
336          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
337          Fixes part but not all of #15.          Fixes part but not all of #15.
338    
339  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
340    
341          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
342          scalar grouping factors corrected.          scalar grouping factors corrected.
343    
344  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
345    
346          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
347    
348  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
349    
350          * 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
351          .h file can be included.          .h file can be included.
352    
353  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
354    
355          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
356          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
357    
358          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
359    
360  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
361    
362          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
363    
364  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
365    
366          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
367    
368  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
369    
370          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
371    
372  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
373    
374          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
375    
376  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
377    
378          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
379          routines.          routines.
380    
381  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
382    
383          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
384    
385  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
386    
387          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
388    

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