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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1259, Tue Apr 25 18:42:22 2006 UTC
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1    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
4            in method for "t" so as not to lose the unit diagonal property.
5    
6    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
9            and methods.  This is now an option to the ranef method for the
10            mer class.
11    
12            * src/cs_utils.c: Ensure that the nz component is -1 for a
13            compressed column-oriented matrix.  Minor formatting cleanup.
14    
15            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
16            objects.
17    
18    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
21            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
22    
23    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
24    
25            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
26            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
27    
28            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
29            for the dtCMatrix class.
30    
31    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
34            and methods for it.
35    
36    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
39            arguments, such that M %*% 1:6 now works
40            * Tests/matprod.R: test the above
41    
42    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
45            the ranef.lmer class.
46    
47            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
48            methods to extract the posterior variances from the bVar slot.
49    
50    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
53            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
54    
55            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
56            * tests/simple: (extended)
57    
58            * R/sparseMatrix.R (isTriangular): now using much improved
59            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
60    
61    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
64            (problem report from Franklin Parlamis).  This should be done
65            generally.
66    
67    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
68    
69            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
70            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
71            update the plot methods.
72    
73    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * R/lmer.R (resid and ranef methods):  Added methods for the
76            "residuals" and "resid" generic but only for linear mixed model
77            fits.  Changed the ranef method to return a list of data frames so
78            that the plot methods now work.
79    
80    2006-03-16  Douglas Bates  <bates@bates2>
81    
82            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
83            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
84    
85            * DESCRIPTION (Date): New release
86    
87    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
90    
91            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
92            * man/KNex.Rd: and other help files
93            * tests/*.R: several ones needed adaption
94            * inst/doc/Comparisons.Rnw: dito
95    
96    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
99    
100            * tests/indexing.R: tests for new [<- methods for sparse matrices.
101    
102    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
105    
106            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
107    
108    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/dMatrix.R: enable things like  M [ M < 10 ]
111            * R/dgeMatrix.R: implement it
112    
113    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/AllClass.R: define "summary.mer" and "*.lmer"
116            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
117            * R/lmer.R (show): now works with summary()
118    
119    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
122            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
123                    support the above
124    
125    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
126    
127            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
128            Use glmFit$prior.weights for weights in a glmm.
129            Allow an option usePQL = FALSE to skip the PQL steps for the
130            Laplace method (and, in time, the AGQ method).
131    
132            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
133            into a separate function internal_mer_Xfactor to be able to call
134            it from internal_bhat.
135    
136    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * tests/Class+Meth.R (tstMatrixClass): function for much better
139            testing; now again of all actual classes.
140    
141            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
142                    use macros and define make_d_matrix_* and make_i_matrix_*
143                    where _i_ is for the ldense routines:
144    
145            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
146            * src/ldense.c (lsyMatrix_as_lgeMatrix):
147    
148            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
149    
150    
151    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
154                    many different kinds of matrices.
155            * R/*.R: quite a few new methods were needed for R CMD check with
156                    new Matrix().  Very good for users playing around.
157    
158    
159    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/dgeMatrix.c (dMatrix_validate): new
162            * src/Mutils.c (dense_nonpacked_validate): new
163    
164            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
165    
166    
167    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
168    
169            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
170    
171    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * DESCRIPTION (Version): 0.99-6 released to CRAN
174    
175            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
176            segfault in cases with multiple non-nested grouping factors.
177    
178    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
181                    (Depends): also on 'utils'
182    
183            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
184            * R/diagMatrix.R (Diagonal): constructor and methods for
185            diagonal matrices
186    
187            * R/ltTMatrix.R: new "minimal methods"
188    
189    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
192            all methods (and help files).
193    
194    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
197                    for case (dimn.  op  no_dimn.)
198    
199    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * DESCRIPTION (Version): 0.99-2  released to CRAN
202    
203    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
206            by Julian Faraway.
207    
208    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Auxiliaries.R (try_as): new utility
211            * R/sparseMatrix.R: use try_as() in coercion to original class
212    
213    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
216    
217    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (dimNamesCheck): added
220    
221            * R/Matrix.R (as.array), (as.vector): new
222    
223    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
226                    default.
227            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
228                    "pMatrix" now contains "sparseMatrix"
229    
230    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * tests/Class+Meth.R: new tests; t(t(m)) == m
233    
234            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
235    
236            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
237            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
238    
239            * R/dspMatrix.R: typo in "t" method
240    
241    2005-09-18  Douglas Bates  <bates@wisc.edu>
242    
243            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
244            * R/Tsparse.R: instead of R/gTMatrix.R
245            * R/Csparse.R: new
246            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
247            * src/Tsparse.c: new; many trivial methods calling cholmod_()
248            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
249                            via cholmod
250    
251    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (non0ind): new function using new C code
254            * src/dgCMatrix.c (compressed_non_0_ij): new utility
255    
256    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
257    
258            * src/chm_common.h: header file required by all C sources that
259            call CHOLMOD functions.  It defines a cholmod_common structure
260            called 'c' whose address is passed as the last argument to
261            (virtually) every CHOLMOD function.
262    
263            * src/Pattern.c: Simple example of the use of CHOLMOD.
264    
265            * src/init.c: initialize and finalize the cholmod_common structure.
266    
267            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
268            LDL and CCOLAMD from the U. of Florida sparse matrix library.
269    
270    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * inst/test-tools.R: new file collecting the utility functions used
273                    in ./tests/*.R
274    
275            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
276            * R/Matrix.R (cbind2): methods for NULL and missing
277    
278    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/AllClass.R: new "index" class for "[" and "[<-":
281                    First cut at "symmetricMatrix" and "triangularMatrix"
282            * R/gTMatrix.R (.ind.prep): new function;
283                    Logical and character indexing now work too.
284            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
285            * tests/indexing.R: new, including *.Rout.save
286            * tests/dgTMatrix.R: new
287    
288  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
289    
290          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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