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revision 109, Mon Apr 19 17:44:39 2004 UTC revision 863, Thu Aug 18 21:31:31 2005 UTC
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1    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
2    
3            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
4            or glmer objects.
5    
6    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
9    
10    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
11    
12            * R/HBMM.R: finish re-writing R-only code.
13    
14    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
15    
16            * man/externalFormats.Rd: move documentation for writeHB and
17            writeMM here.
18    
19            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
20            (suggested by Paul Roecker).
21    
22            * tests/validObj.R (assertError): Comment out test that is failing
23            after recent changes in r-devel.
24    
25    
26    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/AllClass.R: intermediate virtual class "denseMatrix"
29            * man/denseMatrix-class.Rd
30            * NAMESPACE: export it, and also export
31            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
32    
33    2005-08-10  Douglas Bates  <bates@wisc.edu>
34    
35            * DESCRIPTION (Version): 0.98-3 to CRAN
36    
37            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
38            matrix_solve code (which was really, really wrong).
39    
40    2005-08-07  Douglas Bates  <bates@wisc.edu>
41    
42            * DESCRIPTION (Version): 0.98-2
43    
44            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
45    
46            * R/lmer.R (abbrvNms): new
47            * R/lmer.R (mcmcsamp): allow transformed parameters
48            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
49            for the Harwell-Boeing and the MatrixMarket formats.
50    
51    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * man/dtrMatrix-class.Rd: add examples
54            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
55    
56            * TODO: note the dtpMatrix (docu) bug
57    
58            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
59            in order to ensure that new as.matrix() is used by old functions,
60            e.g., svd(), qr(), eigen(), dist(),..;
61                  apply(), also matplot() or pairs().
62    
63    
64    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
67              add comments about 'control' / lmerControl() arguments
68    
69    2005-07-27  Douglas Bates  <bates@wisc.edu>
70    
71            * man/sleepstudy.Rd: Added the sleep data set.
72            * DESCRIPTION (Version): 0.98-1  released to CRAN
73    
74    2005-07-12  Douglas Bates  <bates@wisc.edu>
75            * man/sleepstudy.Rd: Added the sleep data set.
76    
77            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
78            .Call calls that were producing spurious output.
79    
80    2005-07-05  Douglas Bates  <bates@wisc.edu>
81    
82            * R/lmer.R (lmer): stored updated variance component estimates in
83            mer object for the generalized model.  (Bug reported by Renaud
84            Lancelot).
85    
86    2005-07-03  Douglas Bates  <bates@wisc.edu>
87    
88            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
89            unidimensional case.
90    
91    2005-06-08  Douglas Bates  <bates@wisc.edu>
92    
93            * DESCRIPTION (Version): 0.96-1
94    
95            * moved  lmer-class' R and C code moved from lme4 to here
96    
97    2005-06-04  Douglas Bates  <bates@wisc.edu>
98    
99            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
100            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
101    
102    2005-06-02  Douglas Bates  <bates@wisc.edu>
103    
104            * src/Makefile.win: Forgot to update this when Makefile changed.
105    
106    2005-05-11  Douglas Bates  <bates@wisc.edu>
107    
108            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
109            bug reported by Kurt Hornik and Michael Hahsler.
110    
111    2005-05-10  Douglas Bates  <bates@wisc.edu>
112    
113            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
114            logical sparse matrices.  These will also be used in the symbolic
115            analysis for lmer objects.
116    
117            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
118            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
119    
120    2005-05-06  Douglas Bates  <bates@wisc.edu>
121    
122            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
123            colMeans, colSums, rowMeans and rowSums.
124    
125    2005-04-18  Douglas Bates  <bates@wisc.edu>
126    
127            * src/lgCMatrix.[ch]: code for _validate method and stub for
128            multiplication operation.
129    
130            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
131            to dgetrs.
132    
133            * src/init.c: Fix cut-and-paste error in definition of
134            dgeMatrix_matrix_solve
135    
136            * src/{many files}: Tighten code by using ALLOC_SLOT.
137    
138    2005-04-15  Douglas Bates  <bates@wisc.edu>
139    
140            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
141    
142            * DESCRIPTION: Eliminate import of stats.
143    
144    
145    2005-04-06  Douglas Bates  <bates@wisc.edu>
146    
147            * R/AllClass.R : add logical sparse matrix classes
148    
149    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dgTMatrix.R: add "[" method for triplet matrices
152            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
153    
154    2005-03-31  Douglas Bates  <bates@wisc.edu>
155    
156            * DESCRIPTION (Version): release 0.95-5 to CRAN
157    
158            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
159            * R/sparseMatrix.R: %*%, crossprod()
160            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
161            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
162            * src/lmer.c (lmer_fitted): fix thinko
163    
164    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllClass.R: add two virtual sparse classes ``on top''
167    
168    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
171                    correspondingly fix examples and tests/ since new()
172                    doesn't work for virtual classes.
173    
174    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/Matrix.R (as.matrix): method and one for unname()
177            * tests/dpoMatrix.R: tests should now be less platform dependent;
178              also run for R 2.1.0; using as.matrix()
179    
180    2005-03-15  Douglas Bates  <bates@wisc.edu>
181    
182            * R/pMatrix.R: "pMatrix" class added
183            * ....
184    
185    2005-03-14  Douglas Bates  <bates@wisc.edu>
186    
187            * R/dtpMatrix.R: Add unpack method and an example.
188    
189            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
190            of general symmetric matrices and associated S4 methods.
191    
192    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
193            +
194    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgeMatrix.R (setAs): and many other files: more coercion,
197              crossprod() and "%*%" methods added; tests, too.
198            * tests/matprod.R: new, for testing these
199    
200    2005-03-03  Douglas Bates  <bates@wisc.edu>
201    
202            * src/lmer.c (lmer_fitted): Added.
203    
204    2005-03-02  Douglas Bates  <bates@wisc.edu>
205    
206            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
207    
208    2005-02-28  Douglas Bates  <bates@wisc.edu>
209    
210            * src/*.c,po/,inst/po: Internationalization and localization of
211            the package.
212    
213            * src/ldl.[ch]: Removed these as their contents are referenced in the
214            R_ldl.c file.
215    
216            * src/flame.[ch]: Removed these source files.
217    
218            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
219    
220            * src/LU.[ch],src/init.c: absorb in factorizations
221    
222            * src/Mutils.h: prepare for internationalization
223    
224            * src/cblas.h: move the enum definitions to Mutils.h and remove
225            this file
226    
227    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
230    
231            * R/dtrMatrix.R: fix t() method
232    
233            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
234            * NAMESPACE: export them (and import generics from "methods")
235            * tests/group-methods.R : and test them.
236    
237            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
238            border case
239    
240    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
241    
242            * DESCRIPTION (Version): 0.95-2  released to CRAN
243    
244            * src/dgBCMatrix.c:
245            * src/lmer.c: many changes
246            * ...
247    
248    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Matrix.R: add more sophisticated show() method.
251    
252    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
253    
254            * */* : almost complete reorganization of classes.
255    
256    2005-01-26  Douglas Bates  <bates@wisc.edu>
257    
258            * R/AllGeneric.R: Added matrix exponential generic expm and a method
259            for the geMatrix class.
260    
261    2005-01-24  Douglas Bates  <bates@wisc.edu>
262    
263            * src/Makefile (clean): Remove *.a and *.so
264    
265            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
266    
267    2005-01-23  Douglas Bates  <bates@wisc.edu>
268    
269            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
270            had an effect in cases with more than 2 grouping factors.
271    
272    2005-01-03  Douglas Bates  <bates@wisc.edu>
273    
274            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
275    
276    2004-12-23  Douglas Bates  <bates@wisc.edu>
277    
278            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
279            and R_useDynamicSymbols (suggested by B.D.Ripley).
280    
281    2004-12-14  Douglas Bates  <bates@wisc.edu>
282    
283            * R/sscMatrix.R: Add determinant methods
284    
285            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
286            for tripletMatrix to matrix.
287    
288    2004-12-13  Douglas Bates  <bates@wisc.edu>
289    
290            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
291            no longer used.
292    
293            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
294            with dynamic allocation of scratch arrays.
295    
296            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
297            for multivariate random effects with multiple grouping factors.
298            Fixes part but not all of #15.
299    
300    2004-12-03  Douglas Bates  <bates@wisc.edu>
301    
302            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
303            scalar grouping factors corrected.
304    
305    2004-11-29  Douglas Bates  <bates@wisc.edu>
306    
307            * src/bCrosstab.c: remove diag_update which is no longer used
308    
309    2004-11-16  Douglas Bates  <bates@wisc.edu>
310    
311            * src/Metis_utils.c: Move metis.h include to C sources so that the
312            .h file can be included.
313    
314    2004-11-12  Douglas Bates  <bates@wisc.edu>
315    
316            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
317            Complete allocation of slots in NEW_OBJECT.
318    
319            * src/Mutils.h: Moved list of symbols to an include file
320    
321    2004-11-11  Douglas Bates  <bates@wisc.edu>
322    
323            * src/geMutils.c (Matrix_init): remove unused function
324    
325    2004-11-10  Douglas Bates  <bates@wisc.edu>
326    
327            * src/cscMatrix.c (csc_to_imagemat): removed unused function
328    
329    2004-11-05  Douglas Bates  <bates@wisc.edu>
330    
331            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
332    
333    2004-10-27  Douglas Bates  <bates@wisc.edu>
334    
335            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
336    
337    2004-10-04  Douglas Bates  <bates@wisc.edu>
338    
339            * src/init.c: Created R_init_Matrix and added registration of C
340            routines.
341    
342    2004-10-02  Douglas Bates  <bates@wisc.edu>
343    
344            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
345    
346    2004-06-15  Douglas Bates  <bates@wisc.edu>
347    
348            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
349    
350    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
353    
354  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
355    
356          * src/ssclme.c (ssclme_update_mm): fix logic error in          * src/ssclme.c (ssclme_update_mm): fix logic error in

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