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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 834, Mon Aug 8 08:36:34 2005 UTC
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1    2005-08-07  Douglas Bates <bates@localhost.localdomain>
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    
10    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * man/dtrMatrix-class.Rd: add examples
13            * man/dtpMatrix-class.Rd: dito; plus note about PROBLEM
14    
15            * TODO: note the dtpMatrix (docu) bug
16    
17            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
18            in order to ensure that new as.matrix() is used by old functions,
19            e.g., svd(), qr(), eigen(), dist(),..;
20                  apply(), also matplot() or pairs().
21    
22    
23    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
26              add comments about 'control' / lmerControl() arguments
27    
28    2005-07-27  Douglas Bates  <bates@localhost.localdomain>
29    
30            * DESCRIPTION (Version): 0.98-1  released to CRAN
31    
32            * man/sleepstudy.Rd: Added the sleep data set.
33    
34    2005-07-12  Douglas Bates  <bates@localhost.localdomain>
35    
36            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
37            .Call calls that were producing spurious output.
38    
39    2005-07-05  Douglas Bates  <bates@bates1-home>
40    
41            * R/lmer.R (lmer): stored updated variance component estimates in
42            mer object for the generalized model.  (Bug reported by Renaud
43            Lancelot).
44    
45    2005-07-03  Douglas Bates  <bates@bates1-home>
46    
47            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
48            unidimensional case.
49    
50    2005-06-08  Douglas Bates  <bates@bates1-home>
51    
52            * DESCRIPTION (Version): 0.96-1
53    
54            * moved  lmer-class' R and C code moved from lme4 to here
55    
56    2005-06-04  Douglas Bates  <bates@bates1-home>
57    
58            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
59            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
60    
61    2005-06-02  Douglas Bates  <bates@bates1-home>
62    
63            * src/Makefile.win: Forgot to update this when Makefile changed.
64    
65    2005-05-11  Douglas Bates  <bates@bates1-home>
66    
67            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
68            bug reported by Kurt Hornik and Michael Hahsler.
69    
70    2005-05-10  Douglas Bates  <bates@bates1-home>
71    
72            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
73            logical sparse matrices.  These will also be used in the symbolic
74            analysis for lmer objects.
75    
76            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
77            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
78    
79    2005-05-06  Douglas Bates  <bates@bates1-home>
80    
81            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
82            colMeans, colSums, rowMeans and rowSums.
83    
84    2005-04-18  Douglas Bates  <bates@bates1-home>
85    
86            * src/lgCMatrix.[ch]: code for _validate method and stub for
87            multiplication operation.
88    
89            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
90            to dgetrs.
91    
92            * src/init.c: Fix cut-and-paste error in definition of
93            dgeMatrix_matrix_solve
94    
95            * src/{many files}: Tighten code by using ALLOC_SLOT.
96    
97    2005-04-15  Douglas Bates  <bates@bates1-home>
98    
99            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
100    
101            * DESCRIPTION: Eliminate import of stats.
102    
103    
104    2005-04-06  Douglas Bates  <bates@bates1-home>
105    
106            * R/AllClass.R : add logical sparse matrix classes
107    
108    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/dgTMatrix.R: add "[" method for triplet matrices
111            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
112    
113    2005-03-31  Douglas Bates  <bates@bates1-home>
114    
115            * DESCRIPTION (Version): release 0.95-5 to CRAN
116    
117            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
118            * R/sparseMatrix.R: %*%, crossprod()
119            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
120            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
121            * src/lmer.c (lmer_fitted): fix thinko
122    
123    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/AllClass.R: add two virtual sparse classes ``on top''
126    
127    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
130                    correspondingly fix examples and tests/ since new()
131                    doesn't work for virtual classes.
132    
133    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Matrix.R (as.matrix): method and one for unname()
136            * tests/dpoMatrix.R: tests should now be less platform dependent;
137              also run for R 2.1.0; using as.matrix()
138    
139    2005-03-15  Douglas Bates  <bates@bates1-home>
140    
141            * R/pMatrix.R: "pMatrix" class added
142            * ....
143    
144    2005-03-14  Douglas Bates  <bates@bates1-home>
145    
146            * R/dtpMatrix.R: Add unpack method and an example.
147    
148            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
149            of general symmetric matrices and associated S4 methods.
150    
151    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
152            +
153    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/dgeMatrix.R (setAs): and many other files: more coercion,
156              crossprod() and "%*%" methods added; tests, too.
157            * tests/matprod.R: new, for testing these
158    
159    2005-03-03  Douglas Bates  <bates@bates1-home>
160    
161            * src/lmer.c (lmer_fitted): Added.
162    
163    2005-03-02  Douglas Bates  <bates@bates1-home>
164    
165            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
166    
167    2005-02-28  Douglas Bates  <bates@bates1-home>
168    
169            * src/*.c,po/,inst/po: Internationalization and localization of
170            the package.
171    
172            * src/ldl.[ch]: Removed these as their contents are referenced in the
173            R_ldl.c file.
174    
175            * src/flame.[ch]: Removed these source files.
176    
177            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
178    
179            * src/LU.[ch],src/init.c: absorb in factorizations
180    
181            * src/Mutils.h: prepare for internationalization
182    
183            * src/cblas.h: move the enum definitions to Mutils.h and remove
184            this file
185    
186    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
189    
190            * R/dtrMatrix.R: fix t() method
191    
192            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
193            * NAMESPACE: export them (and import generics from "methods")
194            * tests/group-methods.R : and test them.
195    
196            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
197            border case
198    
199    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * DESCRIPTION (Version): 0.95-2  released to CRAN
202    
203            * src/dgBCMatrix.c:
204            * src/lmer.c: many changes
205            * ...
206    
207    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Matrix.R: add more sophisticated show() method.
210    
211    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
212    
213            * */* : almost complete reorganization of classes.
214    
215    2005-01-26  Douglas Bates  <bates@bates7>
216    
217            * R/AllGeneric.R: Added matrix exponential generic expm and a method
218            for the geMatrix class.
219    
220    2005-01-24  Douglas Bates  <bates@bates7>
221    
222            * src/Makefile (clean): Remove *.a and *.so
223    
224            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
225    
226    2005-01-23  Douglas Bates  <bates@bates7>
227    
228            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
229            had an effect in cases with more than 2 grouping factors.
230    
231    2005-01-03  Douglas Bates  <bates@bates1-home>
232    
233            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
234    
235    2004-12-23  Douglas Bates  <bates@bates1-home>
236    
237            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
238            and R_useDynamicSymbols (suggested by B.D.Ripley).
239    
240    2004-12-14  Douglas Bates  <bates@bates1-home>
241    
242            * R/sscMatrix.R: Add determinant methods
243    
244            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
245            for tripletMatrix to matrix.
246    
247  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@bates1-home>
248    
249            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
250            no longer used.
251    
252          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
253          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
254    

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