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revision 10, Mon Mar 22 20:20:05 2004 UTC revision 835, Mon Aug 8 13:33:18 2005 UTC
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1    2005-08-07  Douglas Bates  <bates@wisc.edu>
2    
3            * DESCRIPTION (Version): 0.98-2
4    
5            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
6    
7            * R/lmer.R (abbrvNms): new
8            * R/lmer.R (mcmcsamp): allow transformed parameters
9            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
10            for the Harwell-Boeing and the MatrixMarket formats.
11    
12    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * man/dtrMatrix-class.Rd: add examples
15            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
16    
17            * TODO: note the dtpMatrix (docu) bug
18    
19            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
20            in order to ensure that new as.matrix() is used by old functions,
21            e.g., svd(), qr(), eigen(), dist(),..;
22                  apply(), also matplot() or pairs().
23    
24    
25    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
28              add comments about 'control' / lmerControl() arguments
29    
30    2005-07-27  Douglas Bates  <bates@wisc.edu>
31    
32            * man/sleepstudy.Rd: Added the sleep data set.
33            * DESCRIPTION (Version): 0.98-1  released to CRAN
34    
35    2005-07-12  Douglas Bates  <bates@wisc.edu>
36            * man/sleepstudy.Rd: Added the sleep data set.
37    
38            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
39            .Call calls that were producing spurious output.
40    
41    2005-07-05  Douglas Bates  <bates@wisc.edu>
42    
43            * R/lmer.R (lmer): stored updated variance component estimates in
44            mer object for the generalized model.  (Bug reported by Renaud
45            Lancelot).
46    
47    2005-07-03  Douglas Bates  <bates@wisc.edu>
48    
49            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
50            unidimensional case.
51    
52    2005-06-08  Douglas Bates  <bates@wisc.edu>
53    
54            * DESCRIPTION (Version): 0.96-1
55    
56            * moved  lmer-class' R and C code moved from lme4 to here
57    
58    2005-06-04  Douglas Bates  <bates@wisc.edu>
59    
60            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
61            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
62    
63    2005-06-02  Douglas Bates  <bates@wisc.edu>
64    
65            * src/Makefile.win: Forgot to update this when Makefile changed.
66    
67    2005-05-11  Douglas Bates  <bates@wisc.edu>
68    
69            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
70            bug reported by Kurt Hornik and Michael Hahsler.
71    
72    2005-05-10  Douglas Bates  <bates@wisc.edu>
73    
74            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
75            logical sparse matrices.  These will also be used in the symbolic
76            analysis for lmer objects.
77    
78            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
79            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
80    
81    2005-05-06  Douglas Bates  <bates@wisc.edu>
82    
83            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
84            colMeans, colSums, rowMeans and rowSums.
85    
86    2005-04-18  Douglas Bates  <bates@wisc.edu>
87    
88            * src/lgCMatrix.[ch]: code for _validate method and stub for
89            multiplication operation.
90    
91            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
92            to dgetrs.
93    
94            * src/init.c: Fix cut-and-paste error in definition of
95            dgeMatrix_matrix_solve
96    
97            * src/{many files}: Tighten code by using ALLOC_SLOT.
98    
99    2005-04-15  Douglas Bates  <bates@wisc.edu>
100    
101            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
102    
103            * DESCRIPTION: Eliminate import of stats.
104    
105    
106    2005-04-06  Douglas Bates  <bates@wisc.edu>
107    
108            * R/AllClass.R : add logical sparse matrix classes
109    
110    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dgTMatrix.R: add "[" method for triplet matrices
113            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
114    
115    2005-03-31  Douglas Bates  <bates@wisc.edu>
116    
117            * DESCRIPTION (Version): release 0.95-5 to CRAN
118    
119            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
120            * R/sparseMatrix.R: %*%, crossprod()
121            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
122            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
123            * src/lmer.c (lmer_fitted): fix thinko
124    
125    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R: add two virtual sparse classes ``on top''
128    
129    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
132                    correspondingly fix examples and tests/ since new()
133                    doesn't work for virtual classes.
134    
135    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Matrix.R (as.matrix): method and one for unname()
138            * tests/dpoMatrix.R: tests should now be less platform dependent;
139              also run for R 2.1.0; using as.matrix()
140    
141    2005-03-15  Douglas Bates  <bates@wisc.edu>
142    
143            * R/pMatrix.R: "pMatrix" class added
144            * ....
145    
146    2005-03-14  Douglas Bates  <bates@wisc.edu>
147    
148            * R/dtpMatrix.R: Add unpack method and an example.
149    
150            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
151            of general symmetric matrices and associated S4 methods.
152    
153    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
154            +
155    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/dgeMatrix.R (setAs): and many other files: more coercion,
158              crossprod() and "%*%" methods added; tests, too.
159            * tests/matprod.R: new, for testing these
160    
161    2005-03-03  Douglas Bates  <bates@wisc.edu>
162    
163            * src/lmer.c (lmer_fitted): Added.
164    
165    2005-03-02  Douglas Bates  <bates@wisc.edu>
166    
167            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
168    
169    2005-02-28  Douglas Bates  <bates@wisc.edu>
170    
171            * src/*.c,po/,inst/po: Internationalization and localization of
172            the package.
173    
174            * src/ldl.[ch]: Removed these as their contents are referenced in the
175            R_ldl.c file.
176    
177            * src/flame.[ch]: Removed these source files.
178    
179            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
180    
181            * src/LU.[ch],src/init.c: absorb in factorizations
182    
183            * src/Mutils.h: prepare for internationalization
184    
185            * src/cblas.h: move the enum definitions to Mutils.h and remove
186            this file
187    
188    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
191    
192            * R/dtrMatrix.R: fix t() method
193    
194            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
195            * NAMESPACE: export them (and import generics from "methods")
196            * tests/group-methods.R : and test them.
197    
198            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
199            border case
200    
201    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
202    
203            * DESCRIPTION (Version): 0.95-2  released to CRAN
204    
205            * src/dgBCMatrix.c:
206            * src/lmer.c: many changes
207            * ...
208    
209    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/Matrix.R: add more sophisticated show() method.
212    
213    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * */* : almost complete reorganization of classes.
216    
217    2005-01-26  Douglas Bates  <bates@wisc.edu>
218    
219            * R/AllGeneric.R: Added matrix exponential generic expm and a method
220            for the geMatrix class.
221    
222    2005-01-24  Douglas Bates  <bates@wisc.edu>
223    
224            * src/Makefile (clean): Remove *.a and *.so
225    
226            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
227    
228    2005-01-23  Douglas Bates  <bates@wisc.edu>
229    
230            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
231            had an effect in cases with more than 2 grouping factors.
232    
233    2005-01-03  Douglas Bates  <bates@wisc.edu>
234    
235            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
236    
237    2004-12-23  Douglas Bates  <bates@wisc.edu>
238    
239            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
240            and R_useDynamicSymbols (suggested by B.D.Ripley).
241    
242    2004-12-14  Douglas Bates  <bates@wisc.edu>
243    
244            * R/sscMatrix.R: Add determinant methods
245    
246            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
247            for tripletMatrix to matrix.
248    
249    2004-12-13  Douglas Bates  <bates@wisc.edu>
250    
251            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
252            no longer used.
253    
254            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
255            with dynamic allocation of scratch arrays.
256    
257            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
258            for multivariate random effects with multiple grouping factors.
259            Fixes part but not all of #15.
260    
261    2004-12-03  Douglas Bates  <bates@wisc.edu>
262    
263            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
264            scalar grouping factors corrected.
265    
266    2004-11-29  Douglas Bates  <bates@wisc.edu>
267    
268            * src/bCrosstab.c: remove diag_update which is no longer used
269    
270    2004-11-16  Douglas Bates  <bates@wisc.edu>
271    
272            * src/Metis_utils.c: Move metis.h include to C sources so that the
273            .h file can be included.
274    
275    2004-11-12  Douglas Bates  <bates@wisc.edu>
276    
277            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
278            Complete allocation of slots in NEW_OBJECT.
279    
280            * src/Mutils.h: Moved list of symbols to an include file
281    
282    2004-11-11  Douglas Bates  <bates@wisc.edu>
283    
284            * src/geMutils.c (Matrix_init): remove unused function
285    
286    2004-11-10  Douglas Bates  <bates@wisc.edu>
287    
288            * src/cscMatrix.c (csc_to_imagemat): removed unused function
289    
290    2004-11-05  Douglas Bates  <bates@wisc.edu>
291    
292            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
293    
294    2004-10-27  Douglas Bates  <bates@wisc.edu>
295    
296            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
297    
298    2004-10-04  Douglas Bates  <bates@wisc.edu>
299    
300            * src/init.c: Created R_init_Matrix and added registration of C
301            routines.
302    
303    2004-10-02  Douglas Bates  <bates@wisc.edu>
304    
305            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
306    
307    2004-06-15  Douglas Bates  <bates@wisc.edu>
308    
309            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
310    
311    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
314    
315    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
316    
317            * src/ssclme.c (ssclme_update_mm): fix logic error in
318            ssclme_update_mm
319    
320    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
321    
322            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
323            in the order of unconstrained and constrained parameters.
324            (ssclme_gradient): Added the gradients (not yet correct for
325            multidimensional, unconstrained case).
326    
327    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
330    
331            * src/Makefile.win: Remove unneeded ranlib call
332    
333    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
334    
335            * DESCRIPTION (Version): New release
336    
337            * src/Makefile.win: Update Makefile.win to umfpack removal.
338    
339    2004-04-05  Douglas Bates  <bates@bates2_home>
340    
341            * src/triplet_to_col.c: Create triplet_to_col as a native
342            function, not the version from umfpack.  There were problems with
343            the configuration of UMFPACK for 64-bit processors and there was
344            only one umfpack routine being used so I moved it here.
345    
346    2004-04-04  Douglas Bates  <bates@bates2_home>
347    
348            * src/ssclme.c (ssclme_variances): New function.
349    
350    2004-03-28  Douglas Bates  <bates@bates2_home>
351    
352            * src/ssclme.c (ssclme_fitted): Added function.
353    
354    2004-03-27  Douglas Bates  <bates@bates2_home>
355    
356            * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
357            store the dimnames in the XtX and bVar slots
358            (ssclme_update_mm): Change the dimensions of the bVar slot
359            components and the returned value from ssclme_ranef.
360    
361  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>
362    
363          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},

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