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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1226, Mon Mar 13 14:07:58 2006 UTC
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1    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
4    
5            * tests/indexing.R: tests for new [<- methods for sparse matrices.
6    
7    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
10    
11            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
12    
13    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/dMatrix.R: enable things like  M [ M < 10 ]
16            * R/dgeMatrix.R: implement it
17    
18    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/AllClass.R: define "summary.mer" and "*.lmer"
21            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
22            * R/lmer.R (show): now works with summary()
23    
24    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
27            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
28                    support the above
29    
30    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
33            Use glmFit$prior.weights for weights in a glmm.
34            Allow an option usePQL = FALSE to skip the PQL steps for the
35            Laplace method (and, in time, the AGQ method).
36    
37            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
38            into a separate function internal_mer_Xfactor to be able to call
39            it from internal_bhat.
40    
41    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * tests/Class+Meth.R (tstMatrixClass): function for much better
44            testing; now again of all actual classes.
45    
46            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
47                    use macros and define make_d_matrix_* and make_i_matrix_*
48                    where _i_ is for the ldense routines:
49    
50            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
51            * src/ldense.c (lsyMatrix_as_lgeMatrix):
52    
53            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
54    
55    
56    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
59                    many different kinds of matrices.
60            * R/*.R: quite a few new methods were needed for R CMD check with
61                    new Matrix().  Very good for users playing around.
62    
63    
64    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/dgeMatrix.c (dMatrix_validate): new
67            * src/Mutils.c (dense_nonpacked_validate): new
68    
69            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
70    
71    
72    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
75    
76    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
77    
78            * DESCRIPTION (Version): 0.99-6 released to CRAN
79    
80            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
81            segfault in cases with multiple non-nested grouping factors.
82    
83    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
86                    (Depends): also on 'utils'
87    
88            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
89            * R/diagMatrix.R (Diagonal): constructor and methods for
90            diagonal matrices
91    
92            * R/ltTMatrix.R: new "minimal methods"
93    
94    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
97            all methods (and help files).
98    
99    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
102                    for case (dimn.  op  no_dimn.)
103    
104    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
105    
106            * DESCRIPTION (Version): 0.99-2  released to CRAN
107    
108    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
111            by Julian Faraway.
112    
113    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/Auxiliaries.R (try_as): new utility
116            * R/sparseMatrix.R: use try_as() in coercion to original class
117    
118    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
121    
122    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Auxiliaries.R (dimNamesCheck): added
125    
126            * R/Matrix.R (as.array), (as.vector): new
127    
128    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
131                    default.
132            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
133                    "pMatrix" now contains "sparseMatrix"
134    
135    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * tests/Class+Meth.R: new tests; t(t(m)) == m
138    
139            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
140    
141            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
142            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
143    
144            * R/dspMatrix.R: typo in "t" method
145    
146    2005-09-18  Douglas Bates  <bates@wisc.edu>
147    
148            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
149            * R/Tsparse.R: instead of R/gTMatrix.R
150            * R/Csparse.R: new
151            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
152            * src/Tsparse.c: new; many trivial methods calling cholmod_()
153            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
154                            via cholmod
155    
156    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (non0ind): new function using new C code
159            * src/dgCMatrix.c (compressed_non_0_ij): new utility
160    
161    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
162    
163            * src/chm_common.h: header file required by all C sources that
164            call CHOLMOD functions.  It defines a cholmod_common structure
165            called 'c' whose address is passed as the last argument to
166            (virtually) every CHOLMOD function.
167    
168            * src/Pattern.c: Simple example of the use of CHOLMOD.
169    
170            * src/init.c: initialize and finalize the cholmod_common structure.
171    
172            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
173            LDL and CCOLAMD from the U. of Florida sparse matrix library.
174    
175    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * inst/test-tools.R: new file collecting the utility functions used
178                    in ./tests/*.R
179    
180            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
181            * R/Matrix.R (cbind2): methods for NULL and missing
182    
183    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/AllClass.R: new "index" class for "[" and "[<-":
186                    First cut at "symmetricMatrix" and "triangularMatrix"
187            * R/gTMatrix.R (.ind.prep): new function;
188                    Logical and character indexing now work too.
189            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
190            * tests/indexing.R: new, including *.Rout.save
191            * tests/dgTMatrix.R: new
192    
193    2005-08-29  Douglas Bates  <bates@wisc.edu>
194    
195            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
196            indicator pos not being updated.  Also enforced upper triangular
197            for symmetric case.  Need to coerce edges component of elements of
198            edge list - grr! (Why don't they define their classes cleanly?)
199    
200    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R:  added first "[<-" methods; not yet functional
203            * R/denseMatrix.R: dito
204            * man/Subassign-methods.Rd: new help file for these
205    
206    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * DESCRIPTION (Version): 0.98-6
209    
210            * R/denseMatrix.R: new file for "[" fallback methods for all dense
211            matrices.
212    
213    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
216                    as( <logical>, "matrix")
217    
218            * R/pMatrix.R: coercion to "lgTMatrix"
219    
220            * R/gTMatrix.R: new virtual class to define "[" methods for.
221            * man/gTMatrix-class.Rd:
222            * General slight re-organization of where "[" methods are defined.
223              more to come.
224    
225    2005-08-18  Douglas Bates  <bates@wisc.edu>
226    
227            * DESCRIPTION (Version): 0.98-5  released to CRAN
228    
229            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
230            * .....
231    
232    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
233    
234            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
235            or glmer objects.
236    
237    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
240    
241    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
242    
243            * R/HBMM.R: finish re-writing R-only code.
244    
245    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
246    
247            * man/externalFormats.Rd: move documentation for writeHB and
248            writeMM here.
249    
250            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
251            (suggested by Paul Roecker).
252    
253            * tests/validObj.R (assertError): Comment out test that is failing
254            after recent changes in r-devel.
255    
256    
257  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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