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revision 109, Mon Apr 19 17:44:39 2004 UTC revision 801, Wed Jul 6 16:24:33 2005 UTC
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1    2005-07-05  Douglas Bates  <bates@bates1-home>
2    
3            * R/lmer.R (lmer): stored updated variance component estimates in
4            mer object for the generalized model.  (Bug reported by Renaud
5            Lancelot).
6    
7    2005-07-03  Douglas Bates  <bates@bates1-home>
8    
9            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
10            unidimensional case.
11    
12    2005-06-08  Douglas Bates  <bates@bates1-home>
13    
14            * DESCRIPTION (Version): 0.96-1
15    
16            * moved  lmer-class' R and C code moved from lme4 to here
17    
18    2005-06-04  Douglas Bates  <bates@bates1-home>
19    
20            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
21            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
22    
23    2005-06-02  Douglas Bates  <bates@bates1-home>
24    
25            * src/Makefile.win: Forgot to update this when Makefile changed.
26    
27    2005-05-11  Douglas Bates  <bates@bates1-home>
28    
29            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
30            bug reported by Kurt Hornik and Michael Hahsler.
31    
32    2005-05-10  Douglas Bates  <bates@bates1-home>
33    
34            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
35            logical sparse matrices.  These will also be used in the symbolic
36            analysis for lmer objects.
37    
38            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
39            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
40    
41    2005-05-06  Douglas Bates  <bates@bates1-home>
42    
43            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
44            colMeans, colSums, rowMeans and rowSums.
45    
46    2005-04-18  Douglas Bates  <bates@bates1-home>
47    
48            * src/lgCMatrix.[ch]: code for _validate method and stub for
49            multiplication operation.
50    
51            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
52            to dgetrs.
53    
54            * src/init.c: Fix cut-and-paste error in definition of
55            dgeMatrix_matrix_solve
56    
57            * src/{many files}: Tighten code by using ALLOC_SLOT.
58    
59    2005-04-15  Douglas Bates  <bates@bates1-home>
60    
61            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
62    
63            * DESCRIPTION: Eliminate import of stats.
64    
65    
66    2005-04-06  Douglas Bates  <bates@bates1-home>
67    
68            * R/AllClass.R : add logical sparse matrix classes
69    
70    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dgTMatrix.R: add "[" method for triplet matrices
73            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
74    
75    2005-03-31  Douglas Bates  <bates@bates1-home>
76    
77            * DESCRIPTION (Version): release 0.95-5 to CRAN
78    
79            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
80            * R/sparseMatrix.R: %*%, crossprod()
81            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
82            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
83            * src/lmer.c (lmer_fitted): fix thinko
84    
85    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/AllClass.R: add two virtual sparse classes ``on top''
88    
89    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
92                    correspondingly fix examples and tests/ since new()
93                    doesn't work for virtual classes.
94    
95    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R (as.matrix): method and one for unname()
98            * tests/dpoMatrix.R: tests should now be less platform dependent;
99              also run for R 2.1.0; using as.matrix()
100    
101    2005-03-15  Douglas Bates  <bates@bates1-home>
102    
103            * R/pMatrix.R: "pMatrix" class added
104            * ....
105    
106    2005-03-14  Douglas Bates  <bates@bates1-home>
107    
108            * R/dtpMatrix.R: Add unpack method and an example.
109    
110            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
111            of general symmetric matrices and associated S4 methods.
112    
113    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
114            +
115    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/dgeMatrix.R (setAs): and many other files: more coercion,
118              crossprod() and "%*%" methods added; tests, too.
119            * tests/matprod.R: new, for testing these
120    
121    2005-03-03  Douglas Bates  <bates@bates1-home>
122    
123            * src/lmer.c (lmer_fitted): Added.
124    
125    2005-03-02  Douglas Bates  <bates@bates1-home>
126    
127            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
128    
129    2005-02-28  Douglas Bates  <bates@bates1-home>
130    
131            * src/*.c,po/,inst/po: Internationalization and localization of
132            the package.
133    
134            * src/ldl.[ch]: Removed these as their contents are referenced in the
135            R_ldl.c file.
136    
137            * src/flame.[ch]: Removed these source files.
138    
139            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
140    
141            * src/LU.[ch],src/init.c: absorb in factorizations
142    
143            * src/Mutils.h: prepare for internationalization
144    
145            * src/cblas.h: move the enum definitions to Mutils.h and remove
146            this file
147    
148    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
151    
152            * R/dtrMatrix.R: fix t() method
153    
154            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
155            * NAMESPACE: export them (and import generics from "methods")
156            * tests/group-methods.R : and test them.
157    
158            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
159            border case
160    
161    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
162    
163            * DESCRIPTION (Version): 0.95-2  released to CRAN
164    
165            * src/dgBCMatrix.c:
166            * src/lmer.c: many changes
167            * ...
168    
169    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Matrix.R: add more sophisticated show() method.
172    
173    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * */* : almost complete reorganization of classes.
176    
177    2005-01-26  Douglas Bates  <bates@bates7>
178    
179            * R/AllGeneric.R: Added matrix exponential generic expm and a method
180            for the geMatrix class.
181    
182    2005-01-24  Douglas Bates  <bates@bates7>
183    
184            * src/Makefile (clean): Remove *.a and *.so
185    
186            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
187    
188    2005-01-23  Douglas Bates  <bates@bates7>
189    
190            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
191            had an effect in cases with more than 2 grouping factors.
192    
193    2005-01-03  Douglas Bates  <bates@bates1-home>
194    
195            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
196    
197    2004-12-23  Douglas Bates  <bates@bates1-home>
198    
199            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
200            and R_useDynamicSymbols (suggested by B.D.Ripley).
201    
202    2004-12-14  Douglas Bates  <bates@bates1-home>
203    
204            * R/sscMatrix.R: Add determinant methods
205    
206            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
207            for tripletMatrix to matrix.
208    
209    2004-12-13  Douglas Bates  <bates@bates1-home>
210    
211            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
212            no longer used.
213    
214            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
215            with dynamic allocation of scratch arrays.
216    
217            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
218            for multivariate random effects with multiple grouping factors.
219            Fixes part but not all of #15.
220    
221    2004-12-03  Douglas Bates  <bates@bates1-home>
222    
223            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
224            scalar grouping factors corrected.
225    
226    2004-11-29  Douglas Bates  <bates@bates1-home>
227    
228            * src/bCrosstab.c: remove diag_update which is no longer used
229    
230    2004-11-16  Douglas Bates  <bates@bates1-home>
231    
232            * src/Metis_utils.c: Move metis.h include to C sources so that the
233            .h file can be included.
234    
235    2004-11-12  Douglas Bates  <bates@bates1-home>
236    
237            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
238            Complete allocation of slots in NEW_OBJECT.
239    
240            * src/Mutils.h: Moved list of symbols to an include file
241    
242    2004-11-11  Douglas Bates  <bates@bates1-home>
243    
244            * src/geMutils.c (Matrix_init): remove unused function
245    
246    2004-11-10  Douglas Bates  <bates@bates1-home>
247    
248            * src/cscMatrix.c (csc_to_imagemat): removed unused function
249    
250    2004-11-05  Douglas Bates  <bates@bates1-home>
251    
252            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
253    
254    2004-10-27  Douglas Bates  <bates@bates1-home>
255    
256            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
257    
258    2004-10-04  Douglas Bates  <bates@bates1-home>
259    
260            * src/init.c: Created R_init_Matrix and added registration of C
261            routines.
262    
263    2004-10-02  Douglas Bates  <bates@bates1-home>
264    
265            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
266    
267    2004-06-15  Douglas Bates  <bates@bates7>
268    
269            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
270    
271    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
272    
273            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
274    
275  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>  2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
276    
277          * src/ssclme.c (ssclme_update_mm): fix logic error in          * src/ssclme.c (ssclme_update_mm): fix logic error in

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