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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1222, Tue Mar 7 11:05:08 2006 UTC
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1    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R: define "summary.mer" and "*.lmer"
4            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
5            * R/lmer.R (show): now works with summary()
6    
7    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
10            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
11                    support the above
12    
13    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
16            Use glmFit$prior.weights for weights in a glmm.
17            Allow an option usePQL = FALSE to skip the PQL steps for the
18            Laplace method (and, in time, the AGQ method).
19    
20            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
21            into a separate function internal_mer_Xfactor to be able to call
22            it from internal_bhat.
23    
24    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * tests/Class+Meth.R (tstMatrixClass): function for much better
27            testing; now again of all actual classes.
28    
29            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
30                    use macros and define make_d_matrix_* and make_i_matrix_*
31                    where _i_ is for the ldense routines:
32    
33            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
34            * src/ldense.c (lsyMatrix_as_lgeMatrix):
35    
36            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
37    
38    
39    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
42                    many different kinds of matrices.
43            * R/*.R: quite a few new methods were needed for R CMD check with
44                    new Matrix().  Very good for users playing around.
45    
46    
47    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * src/dgeMatrix.c (dMatrix_validate): new
50            * src/Mutils.c (dense_nonpacked_validate): new
51    
52            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
53    
54    
55    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
58    
59    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
60    
61            * DESCRIPTION (Version): 0.99-6 released to CRAN
62    
63            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
64            segfault in cases with multiple non-nested grouping factors.
65    
66    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
69                    (Depends): also on 'utils'
70    
71            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
72            * R/diagMatrix.R (Diagonal): constructor and methods for
73            diagonal matrices
74    
75            * R/ltTMatrix.R: new "minimal methods"
76    
77    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
80            all methods (and help files).
81    
82    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
85                    for case (dimn.  op  no_dimn.)
86    
87    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
88    
89            * DESCRIPTION (Version): 0.99-2  released to CRAN
90    
91    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
94            by Julian Faraway.
95    
96    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Auxiliaries.R (try_as): new utility
99            * R/sparseMatrix.R: use try_as() in coercion to original class
100    
101    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
104    
105    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/Auxiliaries.R (dimNamesCheck): added
108    
109            * R/Matrix.R (as.array), (as.vector): new
110    
111    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
114                    default.
115            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
116                    "pMatrix" now contains "sparseMatrix"
117    
118    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * tests/Class+Meth.R: new tests; t(t(m)) == m
121    
122            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
123    
124            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
125            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
126    
127            * R/dspMatrix.R: typo in "t" method
128    
129    2005-09-18  Douglas Bates  <bates@wisc.edu>
130    
131            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
132            * R/Tsparse.R: instead of R/gTMatrix.R
133            * R/Csparse.R: new
134            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
135            * src/Tsparse.c: new; many trivial methods calling cholmod_()
136            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
137                            via cholmod
138    
139    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Auxiliaries.R (non0ind): new function using new C code
142            * src/dgCMatrix.c (compressed_non_0_ij): new utility
143    
144    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
145    
146            * src/chm_common.h: header file required by all C sources that
147            call CHOLMOD functions.  It defines a cholmod_common structure
148            called 'c' whose address is passed as the last argument to
149            (virtually) every CHOLMOD function.
150    
151            * src/Pattern.c: Simple example of the use of CHOLMOD.
152    
153            * src/init.c: initialize and finalize the cholmod_common structure.
154    
155            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
156            LDL and CCOLAMD from the U. of Florida sparse matrix library.
157    
158    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * inst/test-tools.R: new file collecting the utility functions used
161                    in ./tests/*.R
162    
163            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
164            * R/Matrix.R (cbind2): methods for NULL and missing
165    
166    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/AllClass.R: new "index" class for "[" and "[<-":
169                    First cut at "symmetricMatrix" and "triangularMatrix"
170            * R/gTMatrix.R (.ind.prep): new function;
171                    Logical and character indexing now work too.
172            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
173            * tests/indexing.R: new, including *.Rout.save
174            * tests/dgTMatrix.R: new
175    
176    2005-08-29  Douglas Bates  <bates@wisc.edu>
177    
178            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
179            indicator pos not being updated.  Also enforced upper triangular
180            for symmetric case.  Need to coerce edges component of elements of
181            edge list - grr! (Why don't they define their classes cleanly?)
182    
183    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/Matrix.R:  added first "[<-" methods; not yet functional
186            * R/denseMatrix.R: dito
187            * man/Subassign-methods.Rd: new help file for these
188    
189    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * DESCRIPTION (Version): 0.98-6
192    
193            * R/denseMatrix.R: new file for "[" fallback methods for all dense
194            matrices.
195    
196    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
199                    as( <logical>, "matrix")
200    
201            * R/pMatrix.R: coercion to "lgTMatrix"
202    
203            * R/gTMatrix.R: new virtual class to define "[" methods for.
204            * man/gTMatrix-class.Rd:
205            * General slight re-organization of where "[" methods are defined.
206              more to come.
207    
208    2005-08-18  Douglas Bates  <bates@wisc.edu>
209    
210            * DESCRIPTION (Version): 0.98-5  released to CRAN
211    
212            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
213            * .....
214    
215    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
216    
217            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
218            or glmer objects.
219    
220    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
223    
224    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
225    
226            * R/HBMM.R: finish re-writing R-only code.
227    
228    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
229    
230            * man/externalFormats.Rd: move documentation for writeHB and
231            writeMM here.
232    
233            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
234            (suggested by Paul Roecker).
235    
236            * tests/validObj.R (assertError): Comment out test that is failing
237            after recent changes in r-devel.
238    
239    
240  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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