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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1245, Wed Apr 12 20:31:18 2006 UTC
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1    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
4            arguments, such that M %*% 1:6 now works
5            * Tests/matprod.R: test the above
6    
7    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
10            the ranef.lmer class.
11    
12            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
13            methods to extract the posterior variances from the bVar slot.
14    
15    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
18            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
19    
20            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
21            * tests/simple: (extended)
22    
23            * R/sparseMatrix.R (isTriangular): now using much improved
24            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
25    
26    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
29            (problem report from Franklin Parlamis).  This should be done
30            generally.
31    
32    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
33    
34            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
35            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
36            update the plot methods.
37    
38    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * R/lmer.R (resid and ranef methods):  Added methods for the
41            "residuals" and "resid" generic but only for linear mixed model
42            fits.  Changed the ranef method to return a list of data frames so
43            that the plot methods now work.
44    
45    2006-03-16  Douglas Bates  <bates@bates2>
46    
47            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
48            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
49    
50            * DESCRIPTION (Date): New release
51    
52    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
55    
56            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
57            * man/KNex.Rd: and other help files
58            * tests/*.R: several ones needed adaption
59            * inst/doc/Comparisons.Rnw: dito
60    
61    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
64    
65            * tests/indexing.R: tests for new [<- methods for sparse matrices.
66    
67    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
70    
71            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
72    
73    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/dMatrix.R: enable things like  M [ M < 10 ]
76            * R/dgeMatrix.R: implement it
77    
78    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/AllClass.R: define "summary.mer" and "*.lmer"
81            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
82            * R/lmer.R (show): now works with summary()
83    
84    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
87            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
88                    support the above
89    
90    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
91    
92            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
93            Use glmFit$prior.weights for weights in a glmm.
94            Allow an option usePQL = FALSE to skip the PQL steps for the
95            Laplace method (and, in time, the AGQ method).
96    
97            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
98            into a separate function internal_mer_Xfactor to be able to call
99            it from internal_bhat.
100    
101    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * tests/Class+Meth.R (tstMatrixClass): function for much better
104            testing; now again of all actual classes.
105    
106            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
107                    use macros and define make_d_matrix_* and make_i_matrix_*
108                    where _i_ is for the ldense routines:
109    
110            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
111            * src/ldense.c (lsyMatrix_as_lgeMatrix):
112    
113            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
114    
115    
116    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
119                    many different kinds of matrices.
120            * R/*.R: quite a few new methods were needed for R CMD check with
121                    new Matrix().  Very good for users playing around.
122    
123    
124    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * src/dgeMatrix.c (dMatrix_validate): new
127            * src/Mutils.c (dense_nonpacked_validate): new
128    
129            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
130    
131    
132    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
135    
136    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * DESCRIPTION (Version): 0.99-6 released to CRAN
139    
140            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
141            segfault in cases with multiple non-nested grouping factors.
142    
143    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
146                    (Depends): also on 'utils'
147    
148            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
149            * R/diagMatrix.R (Diagonal): constructor and methods for
150            diagonal matrices
151    
152            * R/ltTMatrix.R: new "minimal methods"
153    
154    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
157            all methods (and help files).
158    
159    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
162                    for case (dimn.  op  no_dimn.)
163    
164    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * DESCRIPTION (Version): 0.99-2  released to CRAN
167    
168    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
171            by Julian Faraway.
172    
173    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/Auxiliaries.R (try_as): new utility
176            * R/sparseMatrix.R: use try_as() in coercion to original class
177    
178    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
181    
182    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/Auxiliaries.R (dimNamesCheck): added
185    
186            * R/Matrix.R (as.array), (as.vector): new
187    
188    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
191                    default.
192            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
193                    "pMatrix" now contains "sparseMatrix"
194    
195    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * tests/Class+Meth.R: new tests; t(t(m)) == m
198    
199            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
200    
201            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
202            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
203    
204            * R/dspMatrix.R: typo in "t" method
205    
206    2005-09-18  Douglas Bates  <bates@wisc.edu>
207    
208            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
209            * R/Tsparse.R: instead of R/gTMatrix.R
210            * R/Csparse.R: new
211            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
212            * src/Tsparse.c: new; many trivial methods calling cholmod_()
213            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
214                            via cholmod
215    
216    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Auxiliaries.R (non0ind): new function using new C code
219            * src/dgCMatrix.c (compressed_non_0_ij): new utility
220    
221    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
222    
223            * src/chm_common.h: header file required by all C sources that
224            call CHOLMOD functions.  It defines a cholmod_common structure
225            called 'c' whose address is passed as the last argument to
226            (virtually) every CHOLMOD function.
227    
228            * src/Pattern.c: Simple example of the use of CHOLMOD.
229    
230            * src/init.c: initialize and finalize the cholmod_common structure.
231    
232            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
233            LDL and CCOLAMD from the U. of Florida sparse matrix library.
234    
235    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * inst/test-tools.R: new file collecting the utility functions used
238                    in ./tests/*.R
239    
240            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
241            * R/Matrix.R (cbind2): methods for NULL and missing
242    
243    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/AllClass.R: new "index" class for "[" and "[<-":
246                    First cut at "symmetricMatrix" and "triangularMatrix"
247            * R/gTMatrix.R (.ind.prep): new function;
248                    Logical and character indexing now work too.
249            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
250            * tests/indexing.R: new, including *.Rout.save
251            * tests/dgTMatrix.R: new
252    
253    2005-08-29  Douglas Bates  <bates@wisc.edu>
254    
255            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
256            indicator pos not being updated.  Also enforced upper triangular
257            for symmetric case.  Need to coerce edges component of elements of
258            edge list - grr! (Why don't they define their classes cleanly?)
259    
260    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Matrix.R:  added first "[<-" methods; not yet functional
263            * R/denseMatrix.R: dito
264            * man/Subassign-methods.Rd: new help file for these
265    
266    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * DESCRIPTION (Version): 0.98-6
269    
270            * R/denseMatrix.R: new file for "[" fallback methods for all dense
271            matrices.
272    
273    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
276                    as( <logical>, "matrix")
277    
278            * R/pMatrix.R: coercion to "lgTMatrix"
279    
280            * R/gTMatrix.R: new virtual class to define "[" methods for.
281            * man/gTMatrix-class.Rd:
282            * General slight re-organization of where "[" methods are defined.
283              more to come.
284    
285    2005-08-18  Douglas Bates  <bates@wisc.edu>
286    
287            * DESCRIPTION (Version): 0.98-5  released to CRAN
288    
289            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
290            * .....
291    
292    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
293    
294            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
295            or glmer objects.
296    
297    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
300    
301    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
302    
303            * R/HBMM.R: finish re-writing R-only code.
304    
305    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
306    
307            * man/externalFormats.Rd: move documentation for writeHB and
308            writeMM here.
309    
310            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
311            (suggested by Paul Roecker).
312    
313            * tests/validObj.R (assertError): Comment out test that is failing
314            after recent changes in r-devel.
315    
316    
317  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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