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revision 714, Fri May 6 23:52:34 2005 UTC revision 876, Sat Aug 27 22:50:57 2005 UTC
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1  2005-05-06  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
122            mer object for the generalized model.  (Bug reported by Renaud
123            Lancelot).
124    
125    2005-07-03  Douglas Bates  <bates@wisc.edu>
126    
127            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
128            unidimensional case.
129    
130    2005-06-08  Douglas Bates  <bates@wisc.edu>
131    
132            * DESCRIPTION (Version): 0.96-1
133    
134            * moved  lmer-class' R and C code moved from lme4 to here
135    
136    2005-06-04  Douglas Bates  <bates@wisc.edu>
137    
138            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
139            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
140    
141    2005-06-02  Douglas Bates  <bates@wisc.edu>
142    
143            * src/Makefile.win: Forgot to update this when Makefile changed.
144    
145    2005-05-11  Douglas Bates  <bates@wisc.edu>
146    
147            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
148            bug reported by Kurt Hornik and Michael Hahsler.
149    
150    2005-05-10  Douglas Bates  <bates@wisc.edu>
151    
152            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
153            logical sparse matrices.  These will also be used in the symbolic
154            analysis for lmer objects.
155    
156            * 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
158    
159    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 16  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 32  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 58  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 78  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 134  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 178  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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