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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1230, Thu Mar 16 20:03:41 2006 UTC
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1    2006-03-16  Douglas Bates  <bates@bates2>
2    
3            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
4            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
5    
6            * DESCRIPTION (Date): New release
7    
8    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
11    
12            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
13            * man/KNex.Rd: and other help files
14            * tests/*.R: several ones needed adaption
15            * inst/doc/Comparisons.Rnw: dito
16    
17    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
20    
21            * tests/indexing.R: tests for new [<- methods for sparse matrices.
22    
23    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
26    
27            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
28    
29    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/dMatrix.R: enable things like  M [ M < 10 ]
32            * R/dgeMatrix.R: implement it
33    
34    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/AllClass.R: define "summary.mer" and "*.lmer"
37            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
38            * R/lmer.R (show): now works with summary()
39    
40    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
43            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
44                    support the above
45    
46    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
47    
48            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
49            Use glmFit$prior.weights for weights in a glmm.
50            Allow an option usePQL = FALSE to skip the PQL steps for the
51            Laplace method (and, in time, the AGQ method).
52    
53            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
54            into a separate function internal_mer_Xfactor to be able to call
55            it from internal_bhat.
56    
57    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * tests/Class+Meth.R (tstMatrixClass): function for much better
60            testing; now again of all actual classes.
61    
62            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
63                    use macros and define make_d_matrix_* and make_i_matrix_*
64                    where _i_ is for the ldense routines:
65    
66            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
67            * src/ldense.c (lsyMatrix_as_lgeMatrix):
68    
69            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
70    
71    
72    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
75                    many different kinds of matrices.
76            * R/*.R: quite a few new methods were needed for R CMD check with
77                    new Matrix().  Very good for users playing around.
78    
79    
80    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/dgeMatrix.c (dMatrix_validate): new
83            * src/Mutils.c (dense_nonpacked_validate): new
84    
85            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
86    
87    
88    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
89    
90            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
91    
92    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * DESCRIPTION (Version): 0.99-6 released to CRAN
95    
96            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
97            segfault in cases with multiple non-nested grouping factors.
98    
99    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
102                    (Depends): also on 'utils'
103    
104            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
105            * R/diagMatrix.R (Diagonal): constructor and methods for
106            diagonal matrices
107    
108            * R/ltTMatrix.R: new "minimal methods"
109    
110    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
113            all methods (and help files).
114    
115    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
118                    for case (dimn.  op  no_dimn.)
119    
120    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
121    
122            * DESCRIPTION (Version): 0.99-2  released to CRAN
123    
124    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
125    
126            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
127            by Julian Faraway.
128    
129    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/Auxiliaries.R (try_as): new utility
132            * R/sparseMatrix.R: use try_as() in coercion to original class
133    
134    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
137    
138    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Auxiliaries.R (dimNamesCheck): added
141    
142            * R/Matrix.R (as.array), (as.vector): new
143    
144    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
147                    default.
148            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
149                    "pMatrix" now contains "sparseMatrix"
150    
151    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * tests/Class+Meth.R: new tests; t(t(m)) == m
154    
155            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
156    
157            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
158            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
159    
160            * R/dspMatrix.R: typo in "t" method
161    
162    2005-09-18  Douglas Bates  <bates@wisc.edu>
163    
164            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
165            * R/Tsparse.R: instead of R/gTMatrix.R
166            * R/Csparse.R: new
167            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
168            * src/Tsparse.c: new; many trivial methods calling cholmod_()
169            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
170                            via cholmod
171    
172    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Auxiliaries.R (non0ind): new function using new C code
175            * src/dgCMatrix.c (compressed_non_0_ij): new utility
176    
177    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
178    
179            * src/chm_common.h: header file required by all C sources that
180            call CHOLMOD functions.  It defines a cholmod_common structure
181            called 'c' whose address is passed as the last argument to
182            (virtually) every CHOLMOD function.
183    
184            * src/Pattern.c: Simple example of the use of CHOLMOD.
185    
186            * src/init.c: initialize and finalize the cholmod_common structure.
187    
188            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
189            LDL and CCOLAMD from the U. of Florida sparse matrix library.
190    
191    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * inst/test-tools.R: new file collecting the utility functions used
194                    in ./tests/*.R
195    
196            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
197            * R/Matrix.R (cbind2): methods for NULL and missing
198    
199    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/AllClass.R: new "index" class for "[" and "[<-":
202                    First cut at "symmetricMatrix" and "triangularMatrix"
203            * R/gTMatrix.R (.ind.prep): new function;
204                    Logical and character indexing now work too.
205            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
206            * tests/indexing.R: new, including *.Rout.save
207            * tests/dgTMatrix.R: new
208    
209    2005-08-29  Douglas Bates  <bates@wisc.edu>
210    
211            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
212            indicator pos not being updated.  Also enforced upper triangular
213            for symmetric case.  Need to coerce edges component of elements of
214            edge list - grr! (Why don't they define their classes cleanly?)
215    
216    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Matrix.R:  added first "[<-" methods; not yet functional
219            * R/denseMatrix.R: dito
220            * man/Subassign-methods.Rd: new help file for these
221    
222    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * DESCRIPTION (Version): 0.98-6
225    
226            * R/denseMatrix.R: new file for "[" fallback methods for all dense
227            matrices.
228    
229    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
232                    as( <logical>, "matrix")
233    
234            * R/pMatrix.R: coercion to "lgTMatrix"
235    
236            * R/gTMatrix.R: new virtual class to define "[" methods for.
237            * man/gTMatrix-class.Rd:
238            * General slight re-organization of where "[" methods are defined.
239              more to come.
240    
241    2005-08-18  Douglas Bates  <bates@wisc.edu>
242    
243            * DESCRIPTION (Version): 0.98-5  released to CRAN
244    
245            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
246            * .....
247    
248    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
249    
250            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
251            or glmer objects.
252    
253    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
256    
257    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
258    
259            * R/HBMM.R: finish re-writing R-only code.
260    
261    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
262    
263            * man/externalFormats.Rd: move documentation for writeHB and
264            writeMM here.
265    
266            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
267            (suggested by Paul Roecker).
268    
269            * tests/validObj.R (assertError): Comment out test that is failing
270            after recent changes in r-devel.
271    
272    
273  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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