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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 908, Thu Sep 8 15:30:08 2005 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * inst/test-tools.R: new file collecting the utility functions used
4                    in ./tests/*.R
5    
6            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
7            * R/Matrix.R (cbind2): methods for NULL and missing
8    
9    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R: new "index" class for "[" and "[<-":
12                    First cut at "symmetricMatrix" and "triangularMatrix"
13            * R/gTMatrix.R (.ind.prep): new function;
14                    Logical and character indexing now work too.
15            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
16            * tests/indexing.R: new, including *.Rout.save
17            * tests/dgTMatrix.R: new
18    
19    2005-08-29  Douglas Bates  <bates@wisc.edu>
20    
21            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
22            indicator pos not being updated.  Also enforced upper triangular
23            for symmetric case.  Need to coerce edges component of elements of
24            edge list - grr! (Why don't they define their classes cleanly?)
25    
26    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Matrix.R:  added first "[<-" methods; not yet functional
29            * R/denseMatrix.R: dito
30            * man/Subassign-methods.Rd: new help file for these
31    
32    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * DESCRIPTION (Version): 0.98-6
35    
36            * R/denseMatrix.R: new file for "[" fallback methods for all dense
37            matrices.
38    
39    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
42                    as( <logical>, "matrix")
43    
44            * R/pMatrix.R: coercion to "lgTMatrix"
45    
46            * R/gTMatrix.R: new virtual class to define "[" methods for.
47            * man/gTMatrix-class.Rd:
48            * General slight re-organization of where "[" methods are defined.
49              more to come.
50    
51    2005-08-18  Douglas Bates  <bates@wisc.edu>
52    
53            * DESCRIPTION (Version): 0.98-5  released to CRAN
54    
55            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
56            * .....
57    
58    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
59    
60            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
61            or glmer objects.
62    
63    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
66    
67    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
68    
69            * R/HBMM.R: finish re-writing R-only code.
70    
71    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
72    
73            * man/externalFormats.Rd: move documentation for writeHB and
74            writeMM here.
75    
76            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
77            (suggested by Paul Roecker).
78    
79            * tests/validObj.R (assertError): Comment out test that is failing
80            after recent changes in r-devel.
81    
82    
83    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/AllClass.R: intermediate virtual class "denseMatrix"
86            * man/denseMatrix-class.Rd
87            * NAMESPACE: export it, and also export
88            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
89    
90    2005-08-10  Douglas Bates  <bates@wisc.edu>
91    
92            * DESCRIPTION (Version): 0.98-3 to CRAN
93    
94            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
95            matrix_solve code (which was really, really wrong).
96    
97    2005-08-07  Douglas Bates  <bates@wisc.edu>
98    
99            * DESCRIPTION (Version): 0.98-2
100    
101            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
102    
103            * R/lmer.R (abbrvNms): new
104            * R/lmer.R (mcmcsamp): allow transformed parameters
105            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
106            for the Harwell-Boeing and the MatrixMarket formats.
107    
108    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * man/dtrMatrix-class.Rd: add examples
111            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
112    
113            * TODO: note the dtpMatrix (docu) bug
114    
115            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
116            in order to ensure that new as.matrix() is used by old functions,
117            e.g., svd(), qr(), eigen(), dist(),..;
118                  apply(), also matplot() or pairs().
119    
120    
121    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
124              add comments about 'control' / lmerControl() arguments
125    
126    2005-07-27  Douglas Bates  <bates@wisc.edu>
127    
128            * man/sleepstudy.Rd: Added the sleep data set.
129            * DESCRIPTION (Version): 0.98-1  released to CRAN
130    
131    2005-07-12  Douglas Bates  <bates@wisc.edu>
132            * man/sleepstudy.Rd: Added the sleep data set.
133    
134            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
135            .Call calls that were producing spurious output.
136    
137    2005-07-05  Douglas Bates  <bates@wisc.edu>
138    
139            * R/lmer.R (lmer): stored updated variance component estimates in
140            mer object for the generalized model.  (Bug reported by Renaud
141            Lancelot).
142    
143    2005-07-03  Douglas Bates  <bates@wisc.edu>
144    
145            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
146            unidimensional case.
147    
148    2005-06-08  Douglas Bates  <bates@wisc.edu>
149    
150            * DESCRIPTION (Version): 0.96-1
151    
152            * moved  lmer-class' R and C code moved from lme4 to here
153    
154    2005-06-04  Douglas Bates  <bates@wisc.edu>
155    
156            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
157            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
158    
159    2005-06-02  Douglas Bates  <bates@wisc.edu>
160    
161            * src/Makefile.win: Forgot to update this when Makefile changed.
162    
163    2005-05-11  Douglas Bates  <bates@wisc.edu>
164    
165            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
166            bug reported by Kurt Hornik and Michael Hahsler.
167    
168    2005-05-10  Douglas Bates  <bates@wisc.edu>
169    
170            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
171            logical sparse matrices.  These will also be used in the symbolic
172            analysis for lmer objects.
173    
174            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
175            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
176    
177    2005-05-06  Douglas Bates  <bates@wisc.edu>
178    
179            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
180            colMeans, colSums, rowMeans and rowSums.
181    
182    2005-04-18  Douglas Bates  <bates@wisc.edu>
183    
184            * src/lgCMatrix.[ch]: code for _validate method and stub for
185            multiplication operation.
186    
187            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
188            to dgetrs.
189    
190            * src/init.c: Fix cut-and-paste error in definition of
191            dgeMatrix_matrix_solve
192    
193            * src/{many files}: Tighten code by using ALLOC_SLOT.
194    
195    2005-04-15  Douglas Bates  <bates@wisc.edu>
196    
197            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
198    
199            * DESCRIPTION: Eliminate import of stats.
200    
201    
202    2005-04-06  Douglas Bates  <bates@wisc.edu>
203    
204            * R/AllClass.R : add logical sparse matrix classes
205    
206    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/dgTMatrix.R: add "[" method for triplet matrices
209            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
210    
211    2005-03-31  Douglas Bates  <bates@wisc.edu>
212    
213            * DESCRIPTION (Version): release 0.95-5 to CRAN
214    
215            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
216            * R/sparseMatrix.R: %*%, crossprod()
217            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
218            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
219            * src/lmer.c (lmer_fitted): fix thinko
220    
221    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/AllClass.R: add two virtual sparse classes ``on top''
224    
225    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
228                    correspondingly fix examples and tests/ since new()
229                    doesn't work for virtual classes.
230    
231    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/Matrix.R (as.matrix): method and one for unname()
234            * tests/dpoMatrix.R: tests should now be less platform dependent;
235              also run for R 2.1.0; using as.matrix()
236    
237    2005-03-15  Douglas Bates  <bates@wisc.edu>
238    
239            * R/pMatrix.R: "pMatrix" class added
240            * ....
241    
242    2005-03-14  Douglas Bates  <bates@wisc.edu>
243    
244            * R/dtpMatrix.R: Add unpack method and an example.
245    
246            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
247            of general symmetric matrices and associated S4 methods.
248    
249    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
250            +
251    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/dgeMatrix.R (setAs): and many other files: more coercion,
254              crossprod() and "%*%" methods added; tests, too.
255            * tests/matprod.R: new, for testing these
256    
257    2005-03-03  Douglas Bates  <bates@wisc.edu>
258    
259            * src/lmer.c (lmer_fitted): Added.
260    
261    2005-03-02  Douglas Bates  <bates@wisc.edu>
262    
263            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
264    
265    2005-02-28  Douglas Bates  <bates@wisc.edu>
266    
267            * src/*.c,po/,inst/po: Internationalization and localization of
268            the package.
269    
270            * src/ldl.[ch]: Removed these as their contents are referenced in the
271            R_ldl.c file.
272    
273            * src/flame.[ch]: Removed these source files.
274    
275            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
276    
277            * src/LU.[ch],src/init.c: absorb in factorizations
278    
279            * src/Mutils.h: prepare for internationalization
280    
281            * src/cblas.h: move the enum definitions to Mutils.h and remove
282            this file
283    
284    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
287    
288            * R/dtrMatrix.R: fix t() method
289    
290            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
291            * NAMESPACE: export them (and import generics from "methods")
292            * tests/group-methods.R : and test them.
293    
294            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
295            border case
296    
297    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
298    
299            * DESCRIPTION (Version): 0.95-2  released to CRAN
300    
301            * src/dgBCMatrix.c:
302            * src/lmer.c: many changes
303            * ...
304    
305    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Matrix.R: add more sophisticated show() method.
308    
309    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
310    
311            * */* : almost complete reorganization of classes.
312    
313    2005-01-26  Douglas Bates  <bates@wisc.edu>
314    
315            * R/AllGeneric.R: Added matrix exponential generic expm and a method
316            for the geMatrix class.
317    
318    2005-01-24  Douglas Bates  <bates@wisc.edu>
319    
320            * src/Makefile (clean): Remove *.a and *.so
321    
322            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
323    
324    2005-01-23  Douglas Bates  <bates@wisc.edu>
325    
326            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
327            had an effect in cases with more than 2 grouping factors.
328    
329    2005-01-03  Douglas Bates  <bates@wisc.edu>
330    
331            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
332    
333    2004-12-23  Douglas Bates  <bates@wisc.edu>
334    
335            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
336            and R_useDynamicSymbols (suggested by B.D.Ripley).
337    
338    2004-12-14  Douglas Bates  <bates@wisc.edu>
339    
340            * R/sscMatrix.R: Add determinant methods
341    
342            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
343            for tripletMatrix to matrix.
344    
345    2004-12-13  Douglas Bates  <bates@wisc.edu>
346    
347            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
348            no longer used.
349    
350            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
351            with dynamic allocation of scratch arrays.
352    
353            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
354            for multivariate random effects with multiple grouping factors.
355            Fixes part but not all of #15.
356    
357    2004-12-03  Douglas Bates  <bates@wisc.edu>
358    
359            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
360            scalar grouping factors corrected.
361    
362    2004-11-29  Douglas Bates  <bates@wisc.edu>
363    
364            * src/bCrosstab.c: remove diag_update which is no longer used
365    
366    2004-11-16  Douglas Bates  <bates@wisc.edu>
367    
368          * 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
369          .h file can be included.          .h file can be included.
370    
371  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
372    
373          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
374          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
375    
376          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
377    
378  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
379    
380          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
381    
382  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
383    
384          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
385    
386  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
387    
388          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
389    
390  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
391    
392          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
393    
394  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
395    
396          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
397          routines.          routines.
398    
399  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
400    
401          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
402    
403  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
404    
405          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
406    

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