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revision 22, Sat Mar 27 18:17:00 2004 UTC revision 848, Thu Aug 11 07:41:59 2005 UTC
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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>
125    
126            * R/dgTMatrix.R: add "[" method for triplet matrices
127            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
128    
129    2005-03-31  Douglas Bates  <bates@wisc.edu>
130    
131            * DESCRIPTION (Version): release 0.95-5 to CRAN
132    
133            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
134            * R/sparseMatrix.R: %*%, crossprod()
135            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
136            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
137            * src/lmer.c (lmer_fitted): fix thinko
138    
139    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/AllClass.R: add two virtual sparse classes ``on top''
142    
143    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
146                    correspondingly fix examples and tests/ since new()
147                    doesn't work for virtual classes.
148    
149    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Matrix.R (as.matrix): method and one for unname()
152            * tests/dpoMatrix.R: tests should now be less platform dependent;
153              also run for R 2.1.0; using as.matrix()
154    
155    2005-03-15  Douglas Bates  <bates@wisc.edu>
156    
157            * R/pMatrix.R: "pMatrix" class added
158            * ....
159    
160    2005-03-14  Douglas Bates  <bates@wisc.edu>
161    
162            * R/dtpMatrix.R: Add unpack method and an example.
163    
164            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
165            of general symmetric matrices and associated S4 methods.
166    
167    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
168            +
169    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/dgeMatrix.R (setAs): and many other files: more coercion,
172              crossprod() and "%*%" methods added; tests, too.
173            * tests/matprod.R: new, for testing these
174    
175    2005-03-03  Douglas Bates  <bates@wisc.edu>
176    
177            * src/lmer.c (lmer_fitted): Added.
178    
179    2005-03-02  Douglas Bates  <bates@wisc.edu>
180    
181            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
182    
183    2005-02-28  Douglas Bates  <bates@wisc.edu>
184    
185            * src/*.c,po/,inst/po: Internationalization and localization of
186            the package.
187    
188            * src/ldl.[ch]: Removed these as their contents are referenced in the
189            R_ldl.c file.
190    
191            * src/flame.[ch]: Removed these source files.
192    
193            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
194    
195            * src/LU.[ch],src/init.c: absorb in factorizations
196    
197            * src/Mutils.h: prepare for internationalization
198    
199            * src/cblas.h: move the enum definitions to Mutils.h and remove
200            this file
201    
202    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
205    
206            * R/dtrMatrix.R: fix t() method
207    
208            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
209            * NAMESPACE: export them (and import generics from "methods")
210            * tests/group-methods.R : and test them.
211    
212            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
213            border case
214    
215    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
216    
217            * DESCRIPTION (Version): 0.95-2  released to CRAN
218    
219            * src/dgBCMatrix.c:
220            * src/lmer.c: many changes
221            * ...
222    
223    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Matrix.R: add more sophisticated show() method.
226    
227    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * */* : almost complete reorganization of classes.
230    
231    2005-01-26  Douglas Bates  <bates@wisc.edu>
232    
233            * R/AllGeneric.R: Added matrix exponential generic expm and a method
234            for the geMatrix class.
235    
236    2005-01-24  Douglas Bates  <bates@wisc.edu>
237    
238            * src/Makefile (clean): Remove *.a and *.so
239    
240            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
241    
242    2005-01-23  Douglas Bates  <bates@wisc.edu>
243    
244            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
245            had an effect in cases with more than 2 grouping factors.
246    
247    2005-01-03  Douglas Bates  <bates@wisc.edu>
248    
249            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
250    
251    2004-12-23  Douglas Bates  <bates@wisc.edu>
252    
253            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
254            and R_useDynamicSymbols (suggested by B.D.Ripley).
255    
256    2004-12-14  Douglas Bates  <bates@wisc.edu>
257    
258            * R/sscMatrix.R: Add determinant methods
259    
260            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
261            for tripletMatrix to matrix.
262    
263    2004-12-13  Douglas Bates  <bates@wisc.edu>
264    
265            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
266            no longer used.
267    
268            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
269            with dynamic allocation of scratch arrays.
270    
271            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
272            for multivariate random effects with multiple grouping factors.
273            Fixes part but not all of #15.
274    
275    2004-12-03  Douglas Bates  <bates@wisc.edu>
276    
277            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
278            scalar grouping factors corrected.
279    
280    2004-11-29  Douglas Bates  <bates@wisc.edu>
281    
282            * src/bCrosstab.c: remove diag_update which is no longer used
283    
284    2004-11-16  Douglas Bates  <bates@wisc.edu>
285    
286            * src/Metis_utils.c: Move metis.h include to C sources so that the
287            .h file can be included.
288    
289    2004-11-12  Douglas Bates  <bates@wisc.edu>
290    
291            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
292            Complete allocation of slots in NEW_OBJECT.
293    
294            * src/Mutils.h: Moved list of symbols to an include file
295    
296    2004-11-11  Douglas Bates  <bates@wisc.edu>
297    
298            * src/geMutils.c (Matrix_init): remove unused function
299    
300    2004-11-10  Douglas Bates  <bates@wisc.edu>
301    
302            * src/cscMatrix.c (csc_to_imagemat): removed unused function
303    
304    2004-11-05  Douglas Bates  <bates@wisc.edu>
305    
306            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
307    
308    2004-10-27  Douglas Bates  <bates@wisc.edu>
309    
310            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
311    
312    2004-10-04  Douglas Bates  <bates@wisc.edu>
313    
314            * src/init.c: Created R_init_Matrix and added registration of C
315            routines.
316    
317    2004-10-02  Douglas Bates  <bates@wisc.edu>
318    
319            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
320    
321    2004-06-15  Douglas Bates  <bates@wisc.edu>
322    
323            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
324    
325    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
326    
327            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
328    
329    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * src/ssclme.c (ssclme_update_mm): fix logic error in
332            ssclme_update_mm
333    
334    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
337            in the order of unconstrained and constrained parameters.
338            (ssclme_gradient): Added the gradients (not yet correct for
339            multidimensional, unconstrained case).
340    
341    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
342    
343            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
344    
345            * src/Makefile.win: Remove unneeded ranlib call
346    
347    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
348    
349            * DESCRIPTION (Version): New release
350    
351            * src/Makefile.win: Update Makefile.win to umfpack removal.
352    
353    2004-04-05  Douglas Bates  <bates@bates2_home>
354    
355            * src/triplet_to_col.c: Create triplet_to_col as a native
356            function, not the version from umfpack.  There were problems with
357            the configuration of UMFPACK for 64-bit processors and there was
358            only one umfpack routine being used so I moved it here.
359    
360    2004-04-04  Douglas Bates  <bates@bates2_home>
361    
362            * src/ssclme.c (ssclme_variances): New function.
363    
364    2004-03-28  Douglas Bates  <bates@bates2_home>
365    
366            * src/ssclme.c (ssclme_fitted): Added function.
367    
368  2004-03-27  Douglas Bates  <bates@bates2_home>  2004-03-27  Douglas Bates  <bates@bates2_home>
369    
370          * src/ssclme.c (ssclme_transfer_dimnames): Add new function to          * src/ssclme.c (ssclme_transfer_dimnames): Add new function to

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