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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1247, Thu Apr 13 11:12:51 2006 UTC
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1    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
4            and methods for it.
5    
6    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
9            arguments, such that M %*% 1:6 now works
10            * Tests/matprod.R: test the above
11    
12    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
15            the ranef.lmer class.
16    
17            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
18            methods to extract the posterior variances from the bVar slot.
19    
20    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
23            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
24    
25            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
26            * tests/simple: (extended)
27    
28            * R/sparseMatrix.R (isTriangular): now using much improved
29            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
30    
31    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
34            (problem report from Franklin Parlamis).  This should be done
35            generally.
36    
37    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
38    
39            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
40            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
41            update the plot methods.
42    
43    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/lmer.R (resid and ranef methods):  Added methods for the
46            "residuals" and "resid" generic but only for linear mixed model
47            fits.  Changed the ranef method to return a list of data frames so
48            that the plot methods now work.
49    
50    2006-03-16  Douglas Bates  <bates@bates2>
51    
52            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
53            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
54    
55            * DESCRIPTION (Date): New release
56    
57    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
60    
61            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
62            * man/KNex.Rd: and other help files
63            * tests/*.R: several ones needed adaption
64            * inst/doc/Comparisons.Rnw: dito
65    
66    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
69    
70            * tests/indexing.R: tests for new [<- methods for sparse matrices.
71    
72    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
75    
76            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
77    
78    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/dMatrix.R: enable things like  M [ M < 10 ]
81            * R/dgeMatrix.R: implement it
82    
83    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/AllClass.R: define "summary.mer" and "*.lmer"
86            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
87            * R/lmer.R (show): now works with summary()
88    
89    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
92            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
93                    support the above
94    
95    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
96    
97            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
98            Use glmFit$prior.weights for weights in a glmm.
99            Allow an option usePQL = FALSE to skip the PQL steps for the
100            Laplace method (and, in time, the AGQ method).
101    
102            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
103            into a separate function internal_mer_Xfactor to be able to call
104            it from internal_bhat.
105    
106    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * tests/Class+Meth.R (tstMatrixClass): function for much better
109            testing; now again of all actual classes.
110    
111            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
112                    use macros and define make_d_matrix_* and make_i_matrix_*
113                    where _i_ is for the ldense routines:
114    
115            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
116            * src/ldense.c (lsyMatrix_as_lgeMatrix):
117    
118            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
119    
120    
121    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
124                    many different kinds of matrices.
125            * R/*.R: quite a few new methods were needed for R CMD check with
126                    new Matrix().  Very good for users playing around.
127    
128    
129    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/dgeMatrix.c (dMatrix_validate): new
132            * src/Mutils.c (dense_nonpacked_validate): new
133    
134            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
135    
136    
137    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
140    
141    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * DESCRIPTION (Version): 0.99-6 released to CRAN
144    
145            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
146            segfault in cases with multiple non-nested grouping factors.
147    
148    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
151                    (Depends): also on 'utils'
152    
153            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
154            * R/diagMatrix.R (Diagonal): constructor and methods for
155            diagonal matrices
156    
157            * R/ltTMatrix.R: new "minimal methods"
158    
159    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
162            all methods (and help files).
163    
164    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
167                    for case (dimn.  op  no_dimn.)
168    
169    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
170    
171            * DESCRIPTION (Version): 0.99-2  released to CRAN
172    
173    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
176            by Julian Faraway.
177    
178    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Auxiliaries.R (try_as): new utility
181            * R/sparseMatrix.R: use try_as() in coercion to original class
182    
183    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
186    
187    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Auxiliaries.R (dimNamesCheck): added
190    
191            * R/Matrix.R (as.array), (as.vector): new
192    
193    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
196                    default.
197            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
198                    "pMatrix" now contains "sparseMatrix"
199    
200    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * tests/Class+Meth.R: new tests; t(t(m)) == m
203    
204            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
205    
206            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
207            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
208    
209            * R/dspMatrix.R: typo in "t" method
210    
211    2005-09-18  Douglas Bates  <bates@wisc.edu>
212    
213            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
214            * R/Tsparse.R: instead of R/gTMatrix.R
215            * R/Csparse.R: new
216            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
217            * src/Tsparse.c: new; many trivial methods calling cholmod_()
218            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
219                            via cholmod
220    
221    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/Auxiliaries.R (non0ind): new function using new C code
224            * src/dgCMatrix.c (compressed_non_0_ij): new utility
225    
226    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
227    
228            * src/chm_common.h: header file required by all C sources that
229            call CHOLMOD functions.  It defines a cholmod_common structure
230            called 'c' whose address is passed as the last argument to
231            (virtually) every CHOLMOD function.
232    
233            * src/Pattern.c: Simple example of the use of CHOLMOD.
234    
235            * src/init.c: initialize and finalize the cholmod_common structure.
236    
237            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
238            LDL and CCOLAMD from the U. of Florida sparse matrix library.
239    
240    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * inst/test-tools.R: new file collecting the utility functions used
243                    in ./tests/*.R
244    
245            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
246            * R/Matrix.R (cbind2): methods for NULL and missing
247    
248    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/AllClass.R: new "index" class for "[" and "[<-":
251                    First cut at "symmetricMatrix" and "triangularMatrix"
252            * R/gTMatrix.R (.ind.prep): new function;
253                    Logical and character indexing now work too.
254            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
255            * tests/indexing.R: new, including *.Rout.save
256            * tests/dgTMatrix.R: new
257    
258  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
259    
260          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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