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revision 45, Mon Apr 5 01:06:55 2004 UTC revision 868, Fri Aug 19 17:01:11 2005 UTC
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1    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
4                    as( <logical>, "matrix")
5    
6            * R/pMatrix.R: coercion to "lgTMatrix"
7    
8            * R/gTMatrix.R: new virtual class to define "[" methods for.
9            * man/gTMatrix-class.Rd:
10            * General slight re-organization of where "[" methods are defined.
11              more to come.
12    
13    
14    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
15    
16            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
17            or glmer objects.
18    
19    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
22    
23    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
24    
25            * R/HBMM.R: finish re-writing R-only code.
26    
27    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
28    
29            * man/externalFormats.Rd: move documentation for writeHB and
30            writeMM here.
31    
32            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
33            (suggested by Paul Roecker).
34    
35            * tests/validObj.R (assertError): Comment out test that is failing
36            after recent changes in r-devel.
37    
38    
39    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/AllClass.R: intermediate virtual class "denseMatrix"
42            * man/denseMatrix-class.Rd
43            * NAMESPACE: export it, and also export
44            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
45    
46    2005-08-10  Douglas Bates  <bates@wisc.edu>
47    
48            * DESCRIPTION (Version): 0.98-3 to CRAN
49    
50            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
51            matrix_solve code (which was really, really wrong).
52    
53    2005-08-07  Douglas Bates  <bates@wisc.edu>
54    
55            * DESCRIPTION (Version): 0.98-2
56    
57            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
58    
59            * R/lmer.R (abbrvNms): new
60            * R/lmer.R (mcmcsamp): allow transformed parameters
61            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
62            for the Harwell-Boeing and the MatrixMarket formats.
63    
64    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * man/dtrMatrix-class.Rd: add examples
67            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
68    
69            * TODO: note the dtpMatrix (docu) bug
70    
71            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
72            in order to ensure that new as.matrix() is used by old functions,
73            e.g., svd(), qr(), eigen(), dist(),..;
74                  apply(), also matplot() or pairs().
75    
76    
77    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
80              add comments about 'control' / lmerControl() arguments
81    
82    2005-07-27  Douglas Bates  <bates@wisc.edu>
83    
84            * man/sleepstudy.Rd: Added the sleep data set.
85            * DESCRIPTION (Version): 0.98-1  released to CRAN
86    
87    2005-07-12  Douglas Bates  <bates@wisc.edu>
88            * man/sleepstudy.Rd: Added the sleep data set.
89    
90            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
91            .Call calls that were producing spurious output.
92    
93    2005-07-05  Douglas Bates  <bates@wisc.edu>
94    
95            * R/lmer.R (lmer): stored updated variance component estimates in
96            mer object for the generalized model.  (Bug reported by Renaud
97            Lancelot).
98    
99    2005-07-03  Douglas Bates  <bates@wisc.edu>
100    
101            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
102            unidimensional case.
103    
104    2005-06-08  Douglas Bates  <bates@wisc.edu>
105    
106            * DESCRIPTION (Version): 0.96-1
107    
108            * moved  lmer-class' R and C code moved from lme4 to here
109    
110    2005-06-04  Douglas Bates  <bates@wisc.edu>
111    
112            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
113            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
114    
115    2005-06-02  Douglas Bates  <bates@wisc.edu>
116    
117            * src/Makefile.win: Forgot to update this when Makefile changed.
118    
119    2005-05-11  Douglas Bates  <bates@wisc.edu>
120    
121            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
122            bug reported by Kurt Hornik and Michael Hahsler.
123    
124    2005-05-10  Douglas Bates  <bates@wisc.edu>
125    
126            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
127            logical sparse matrices.  These will also be used in the symbolic
128            analysis for lmer objects.
129    
130            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
131            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
132    
133    2005-05-06  Douglas Bates  <bates@wisc.edu>
134    
135            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
136            colMeans, colSums, rowMeans and rowSums.
137    
138    2005-04-18  Douglas Bates  <bates@wisc.edu>
139    
140            * src/lgCMatrix.[ch]: code for _validate method and stub for
141            multiplication operation.
142    
143            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
144            to dgetrs.
145    
146            * src/init.c: Fix cut-and-paste error in definition of
147            dgeMatrix_matrix_solve
148    
149            * src/{many files}: Tighten code by using ALLOC_SLOT.
150    
151    2005-04-15  Douglas Bates  <bates@wisc.edu>
152    
153            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
154    
155            * DESCRIPTION: Eliminate import of stats.
156    
157    
158    2005-04-06  Douglas Bates  <bates@wisc.edu>
159    
160            * R/AllClass.R : add logical sparse matrix classes
161    
162    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/dgTMatrix.R: add "[" method for triplet matrices
165            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
166    
167    2005-03-31  Douglas Bates  <bates@wisc.edu>
168    
169            * DESCRIPTION (Version): release 0.95-5 to CRAN
170    
171            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
172            * R/sparseMatrix.R: %*%, crossprod()
173            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
174            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
175            * src/lmer.c (lmer_fitted): fix thinko
176    
177    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/AllClass.R: add two virtual sparse classes ``on top''
180    
181    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
184                    correspondingly fix examples and tests/ since new()
185                    doesn't work for virtual classes.
186    
187    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Matrix.R (as.matrix): method and one for unname()
190            * tests/dpoMatrix.R: tests should now be less platform dependent;
191              also run for R 2.1.0; using as.matrix()
192    
193    2005-03-15  Douglas Bates  <bates@wisc.edu>
194    
195            * R/pMatrix.R: "pMatrix" class added
196            * ....
197    
198    2005-03-14  Douglas Bates  <bates@wisc.edu>
199    
200            * R/dtpMatrix.R: Add unpack method and an example.
201    
202            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
203            of general symmetric matrices and associated S4 methods.
204    
205    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
206            +
207    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/dgeMatrix.R (setAs): and many other files: more coercion,
210              crossprod() and "%*%" methods added; tests, too.
211            * tests/matprod.R: new, for testing these
212    
213    2005-03-03  Douglas Bates  <bates@wisc.edu>
214    
215            * src/lmer.c (lmer_fitted): Added.
216    
217    2005-03-02  Douglas Bates  <bates@wisc.edu>
218    
219            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
220    
221    2005-02-28  Douglas Bates  <bates@wisc.edu>
222    
223            * src/*.c,po/,inst/po: Internationalization and localization of
224            the package.
225    
226            * src/ldl.[ch]: Removed these as their contents are referenced in the
227            R_ldl.c file.
228    
229            * src/flame.[ch]: Removed these source files.
230    
231            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
232    
233            * src/LU.[ch],src/init.c: absorb in factorizations
234    
235            * src/Mutils.h: prepare for internationalization
236    
237            * src/cblas.h: move the enum definitions to Mutils.h and remove
238            this file
239    
240    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
243    
244            * R/dtrMatrix.R: fix t() method
245    
246            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
247            * NAMESPACE: export them (and import generics from "methods")
248            * tests/group-methods.R : and test them.
249    
250            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
251            border case
252    
253    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
254    
255            * DESCRIPTION (Version): 0.95-2  released to CRAN
256    
257            * src/dgBCMatrix.c:
258            * src/lmer.c: many changes
259            * ...
260    
261    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/Matrix.R: add more sophisticated show() method.
264    
265    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
266    
267            * */* : almost complete reorganization of classes.
268    
269    2005-01-26  Douglas Bates  <bates@wisc.edu>
270    
271            * R/AllGeneric.R: Added matrix exponential generic expm and a method
272            for the geMatrix class.
273    
274    2005-01-24  Douglas Bates  <bates@wisc.edu>
275    
276            * src/Makefile (clean): Remove *.a and *.so
277    
278            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
279    
280    2005-01-23  Douglas Bates  <bates@wisc.edu>
281    
282            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
283            had an effect in cases with more than 2 grouping factors.
284    
285    2005-01-03  Douglas Bates  <bates@wisc.edu>
286    
287            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
288    
289    2004-12-23  Douglas Bates  <bates@wisc.edu>
290    
291            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
292            and R_useDynamicSymbols (suggested by B.D.Ripley).
293    
294    2004-12-14  Douglas Bates  <bates@wisc.edu>
295    
296            * R/sscMatrix.R: Add determinant methods
297    
298            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
299            for tripletMatrix to matrix.
300    
301    2004-12-13  Douglas Bates  <bates@wisc.edu>
302    
303            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
304            no longer used.
305    
306            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
307            with dynamic allocation of scratch arrays.
308    
309            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
310            for multivariate random effects with multiple grouping factors.
311            Fixes part but not all of #15.
312    
313    2004-12-03  Douglas Bates  <bates@wisc.edu>
314    
315            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
316            scalar grouping factors corrected.
317    
318    2004-11-29  Douglas Bates  <bates@wisc.edu>
319    
320            * src/bCrosstab.c: remove diag_update which is no longer used
321    
322    2004-11-16  Douglas Bates  <bates@wisc.edu>
323    
324            * src/Metis_utils.c: Move metis.h include to C sources so that the
325            .h file can be included.
326    
327    2004-11-12  Douglas Bates  <bates@wisc.edu>
328    
329            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
330            Complete allocation of slots in NEW_OBJECT.
331    
332            * src/Mutils.h: Moved list of symbols to an include file
333    
334    2004-11-11  Douglas Bates  <bates@wisc.edu>
335    
336            * src/geMutils.c (Matrix_init): remove unused function
337    
338    2004-11-10  Douglas Bates  <bates@wisc.edu>
339    
340            * src/cscMatrix.c (csc_to_imagemat): removed unused function
341    
342    2004-11-05  Douglas Bates  <bates@wisc.edu>
343    
344            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
345    
346    2004-10-27  Douglas Bates  <bates@wisc.edu>
347    
348            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
349    
350    2004-10-04  Douglas Bates  <bates@wisc.edu>
351    
352            * src/init.c: Created R_init_Matrix and added registration of C
353            routines.
354    
355    2004-10-02  Douglas Bates  <bates@wisc.edu>
356    
357            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
358    
359    2004-06-15  Douglas Bates  <bates@wisc.edu>
360    
361            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
362    
363    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
366    
367    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
368    
369            * src/ssclme.c (ssclme_update_mm): fix logic error in
370            ssclme_update_mm
371    
372    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
375            in the order of unconstrained and constrained parameters.
376            (ssclme_gradient): Added the gradients (not yet correct for
377            multidimensional, unconstrained case).
378    
379    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
380    
381            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
382    
383            * src/Makefile.win: Remove unneeded ranlib call
384    
385    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * DESCRIPTION (Version): New release
388    
389            * src/Makefile.win: Update Makefile.win to umfpack removal.
390    
391    2004-04-05  Douglas Bates  <bates@bates2_home>
392    
393            * src/triplet_to_col.c: Create triplet_to_col as a native
394            function, not the version from umfpack.  There were problems with
395            the configuration of UMFPACK for 64-bit processors and there was
396            only one umfpack routine being used so I moved it here.
397    
398  2004-04-04  Douglas Bates  <bates@bates2_home>  2004-04-04  Douglas Bates  <bates@bates2_home>
399    
400          * src/ssclme.c (ssclme_variances): New function.          * src/ssclme.c (ssclme_variances): New function.

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