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revision 10, Mon Mar 22 20:20:05 2004 UTC revision 794, Mon Jul 4 14:54:33 2005 UTC
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1    2005-07-03  Douglas Bates  <bates@bates1-home>
2    
3            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
4            unidimensional case.
5    
6    2005-06-08  Douglas Bates  <bates@bates1-home>
7    
8            * DESCRIPTION (Version): 0.96-1
9    
10            * moved  lmer-class' R and C code moved from lme4 to here
11    
12    2005-06-04  Douglas Bates  <bates@bates1-home>
13    
14            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
15            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
16    
17    2005-06-02  Douglas Bates  <bates@bates1-home>
18    
19            * src/Makefile.win: Forgot to update this when Makefile changed.
20    
21    2005-05-11  Douglas Bates  <bates@bates1-home>
22    
23            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
24            bug reported by Kurt Hornik and Michael Hahsler.
25    
26    2005-05-10  Douglas Bates  <bates@bates1-home>
27    
28            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
29            logical sparse matrices.  These will also be used in the symbolic
30            analysis for lmer objects.
31    
32            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
33            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
34    
35    2005-05-06  Douglas Bates  <bates@bates1-home>
36    
37            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
38            colMeans, colSums, rowMeans and rowSums.
39    
40    2005-04-18  Douglas Bates  <bates@bates1-home>
41    
42            * src/lgCMatrix.[ch]: code for _validate method and stub for
43            multiplication operation.
44    
45            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
46            to dgetrs.
47    
48            * src/init.c: Fix cut-and-paste error in definition of
49            dgeMatrix_matrix_solve
50    
51            * src/{many files}: Tighten code by using ALLOC_SLOT.
52    
53    2005-04-15  Douglas Bates  <bates@bates1-home>
54    
55            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
56    
57            * DESCRIPTION: Eliminate import of stats.
58    
59    
60    2005-04-06  Douglas Bates  <bates@bates1-home>
61    
62            * R/AllClass.R : add logical sparse matrix classes
63    
64    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/dgTMatrix.R: add "[" method for triplet matrices
67            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
68    
69    2005-03-31  Douglas Bates  <bates@bates1-home>
70    
71            * DESCRIPTION (Version): release 0.95-5 to CRAN
72    
73            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
74            * R/sparseMatrix.R: %*%, crossprod()
75            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
76            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
77            * src/lmer.c (lmer_fitted): fix thinko
78    
79    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/AllClass.R: add two virtual sparse classes ``on top''
82    
83    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
86                    correspondingly fix examples and tests/ since new()
87                    doesn't work for virtual classes.
88    
89    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/Matrix.R (as.matrix): method and one for unname()
92            * tests/dpoMatrix.R: tests should now be less platform dependent;
93              also run for R 2.1.0; using as.matrix()
94    
95    2005-03-15  Douglas Bates  <bates@bates1-home>
96    
97            * R/pMatrix.R: "pMatrix" class added
98            * ....
99    
100    2005-03-14  Douglas Bates  <bates@bates1-home>
101    
102            * R/dtpMatrix.R: Add unpack method and an example.
103    
104            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
105            of general symmetric matrices and associated S4 methods.
106    
107    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
108            +
109    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/dgeMatrix.R (setAs): and many other files: more coercion,
112              crossprod() and "%*%" methods added; tests, too.
113            * tests/matprod.R: new, for testing these
114    
115    2005-03-03  Douglas Bates  <bates@bates1-home>
116    
117            * src/lmer.c (lmer_fitted): Added.
118    
119    2005-03-02  Douglas Bates  <bates@bates1-home>
120    
121            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
122    
123    2005-02-28  Douglas Bates  <bates@bates1-home>
124    
125            * src/*.c,po/,inst/po: Internationalization and localization of
126            the package.
127    
128            * src/ldl.[ch]: Removed these as their contents are referenced in the
129            R_ldl.c file.
130    
131            * src/flame.[ch]: Removed these source files.
132    
133            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
134    
135            * src/LU.[ch],src/init.c: absorb in factorizations
136    
137            * src/Mutils.h: prepare for internationalization
138    
139            * src/cblas.h: move the enum definitions to Mutils.h and remove
140            this file
141    
142    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
145    
146            * R/dtrMatrix.R: fix t() method
147    
148            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
149            * NAMESPACE: export them (and import generics from "methods")
150            * tests/group-methods.R : and test them.
151    
152            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
153            border case
154    
155    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
156    
157            * DESCRIPTION (Version): 0.95-2  released to CRAN
158    
159            * src/dgBCMatrix.c:
160            * src/lmer.c: many changes
161            * ...
162    
163    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/Matrix.R: add more sophisticated show() method.
166    
167    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
168    
169            * */* : almost complete reorganization of classes.
170    
171    2005-01-26  Douglas Bates  <bates@bates7>
172    
173            * R/AllGeneric.R: Added matrix exponential generic expm and a method
174            for the geMatrix class.
175    
176    2005-01-24  Douglas Bates  <bates@bates7>
177    
178            * src/Makefile (clean): Remove *.a and *.so
179    
180            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
181    
182    2005-01-23  Douglas Bates  <bates@bates7>
183    
184            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
185            had an effect in cases with more than 2 grouping factors.
186    
187    2005-01-03  Douglas Bates  <bates@bates1-home>
188    
189            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
190    
191    2004-12-23  Douglas Bates  <bates@bates1-home>
192    
193            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
194            and R_useDynamicSymbols (suggested by B.D.Ripley).
195    
196    2004-12-14  Douglas Bates  <bates@bates1-home>
197    
198            * R/sscMatrix.R: Add determinant methods
199    
200            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
201            for tripletMatrix to matrix.
202    
203    2004-12-13  Douglas Bates  <bates@bates1-home>
204    
205            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
206            no longer used.
207    
208            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
209            with dynamic allocation of scratch arrays.
210    
211            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
212            for multivariate random effects with multiple grouping factors.
213            Fixes part but not all of #15.
214    
215    2004-12-03  Douglas Bates  <bates@bates1-home>
216    
217            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
218            scalar grouping factors corrected.
219    
220    2004-11-29  Douglas Bates  <bates@bates1-home>
221    
222            * src/bCrosstab.c: remove diag_update which is no longer used
223    
224    2004-11-16  Douglas Bates  <bates@bates1-home>
225    
226            * src/Metis_utils.c: Move metis.h include to C sources so that the
227            .h file can be included.
228    
229    2004-11-12  Douglas Bates  <bates@bates1-home>
230    
231            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
232            Complete allocation of slots in NEW_OBJECT.
233    
234            * src/Mutils.h: Moved list of symbols to an include file
235    
236    2004-11-11  Douglas Bates  <bates@bates1-home>
237    
238            * src/geMutils.c (Matrix_init): remove unused function
239    
240    2004-11-10  Douglas Bates  <bates@bates1-home>
241    
242            * src/cscMatrix.c (csc_to_imagemat): removed unused function
243    
244    2004-11-05  Douglas Bates  <bates@bates1-home>
245    
246            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
247    
248    2004-10-27  Douglas Bates  <bates@bates1-home>
249    
250            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
251    
252    2004-10-04  Douglas Bates  <bates@bates1-home>
253    
254            * src/init.c: Created R_init_Matrix and added registration of C
255            routines.
256    
257    2004-10-02  Douglas Bates  <bates@bates1-home>
258    
259            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
260    
261    2004-06-15  Douglas Bates  <bates@bates7>
262    
263            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
264    
265    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
266    
267            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
268    
269    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
270    
271            * src/ssclme.c (ssclme_update_mm): fix logic error in
272            ssclme_update_mm
273    
274    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
277            in the order of unconstrained and constrained parameters.
278            (ssclme_gradient): Added the gradients (not yet correct for
279            multidimensional, unconstrained case).
280    
281    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
282    
283            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
284    
285            * src/Makefile.win: Remove unneeded ranlib call
286    
287    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
288    
289            * DESCRIPTION (Version): New release
290    
291            * src/Makefile.win: Update Makefile.win to umfpack removal.
292    
293    2004-04-05  Douglas Bates  <bates@bates2_home>
294    
295            * src/triplet_to_col.c: Create triplet_to_col as a native
296            function, not the version from umfpack.  There were problems with
297            the configuration of UMFPACK for 64-bit processors and there was
298            only one umfpack routine being used so I moved it here.
299    
300    2004-04-04  Douglas Bates  <bates@bates2_home>
301    
302            * src/ssclme.c (ssclme_variances): New function.
303    
304    2004-03-28  Douglas Bates  <bates@bates2_home>
305    
306            * src/ssclme.c (ssclme_fitted): Added function.
307    
308    2004-03-27  Douglas Bates  <bates@bates2_home>
309    
310            * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
311            store the dimnames in the XtX and bVar slots
312            (ssclme_update_mm): Change the dimensions of the bVar slot
313            components and the returned value from ssclme_ranef.
314    
315  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>
316    
317          * 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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