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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1243, Sun Apr 9 00:02:26 2006 UTC
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1    2006-04-03  Douglas Bates  <bates@dyn-51-232.uwnet.wisc.edu>
2    
3            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
4            the ranef.lmer class.
5    
6            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
7            methods to extract the posterior variances from the bVar slot.
8    
9    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
12            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
13    
14            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
15            * tests/simple: (extended)
16    
17            * R/sparseMatrix.R (isTriangular): now using much improved
18            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
19    
20    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
23            (problem report from Franklin Parlamis).  This should be done
24            generally.
25    
26    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
29            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
30            update the plot methods.
31    
32    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
33    
34            * R/lmer.R (resid and ranef methods):  Added methods for the
35            "residuals" and "resid" generic but only for linear mixed model
36            fits.  Changed the ranef method to return a list of data frames so
37            that the plot methods now work.
38    
39    2006-03-16  Douglas Bates  <bates@bates2>
40    
41            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
42            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
43    
44            * DESCRIPTION (Date): New release
45    
46    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
49    
50            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
51            * man/KNex.Rd: and other help files
52            * tests/*.R: several ones needed adaption
53            * inst/doc/Comparisons.Rnw: dito
54    
55    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
58    
59            * tests/indexing.R: tests for new [<- methods for sparse matrices.
60    
61    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
64    
65            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
66    
67    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/dMatrix.R: enable things like  M [ M < 10 ]
70            * R/dgeMatrix.R: implement it
71    
72    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/AllClass.R: define "summary.mer" and "*.lmer"
75            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
76            * R/lmer.R (show): now works with summary()
77    
78    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
81            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
82                    support the above
83    
84    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
85    
86            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
87            Use glmFit$prior.weights for weights in a glmm.
88            Allow an option usePQL = FALSE to skip the PQL steps for the
89            Laplace method (and, in time, the AGQ method).
90    
91            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
92            into a separate function internal_mer_Xfactor to be able to call
93            it from internal_bhat.
94    
95    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * tests/Class+Meth.R (tstMatrixClass): function for much better
98            testing; now again of all actual classes.
99    
100            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
101                    use macros and define make_d_matrix_* and make_i_matrix_*
102                    where _i_ is for the ldense routines:
103    
104            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
105            * src/ldense.c (lsyMatrix_as_lgeMatrix):
106    
107            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
108    
109    
110    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
113                    many different kinds of matrices.
114            * R/*.R: quite a few new methods were needed for R CMD check with
115                    new Matrix().  Very good for users playing around.
116    
117    
118    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * src/dgeMatrix.c (dMatrix_validate): new
121            * src/Mutils.c (dense_nonpacked_validate): new
122    
123            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
124    
125    
126    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
127    
128            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
129    
130    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
131    
132            * DESCRIPTION (Version): 0.99-6 released to CRAN
133    
134            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
135            segfault in cases with multiple non-nested grouping factors.
136    
137    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
140                    (Depends): also on 'utils'
141    
142            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
143            * R/diagMatrix.R (Diagonal): constructor and methods for
144            diagonal matrices
145    
146            * R/ltTMatrix.R: new "minimal methods"
147    
148    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
151            all methods (and help files).
152    
153    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
156                    for case (dimn.  op  no_dimn.)
157    
158    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
159    
160            * DESCRIPTION (Version): 0.99-2  released to CRAN
161    
162    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
165            by Julian Faraway.
166    
167    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/Auxiliaries.R (try_as): new utility
170            * R/sparseMatrix.R: use try_as() in coercion to original class
171    
172    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
175    
176    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/Auxiliaries.R (dimNamesCheck): added
179    
180            * R/Matrix.R (as.array), (as.vector): new
181    
182    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
185                    default.
186            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
187                    "pMatrix" now contains "sparseMatrix"
188    
189    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * tests/Class+Meth.R: new tests; t(t(m)) == m
192    
193            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
194    
195            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
196            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
197    
198            * R/dspMatrix.R: typo in "t" method
199    
200    2005-09-18  Douglas Bates  <bates@wisc.edu>
201    
202            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
203            * R/Tsparse.R: instead of R/gTMatrix.R
204            * R/Csparse.R: new
205            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
206            * src/Tsparse.c: new; many trivial methods calling cholmod_()
207            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
208                            via cholmod
209    
210    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/Auxiliaries.R (non0ind): new function using new C code
213            * src/dgCMatrix.c (compressed_non_0_ij): new utility
214    
215    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
216    
217            * src/chm_common.h: header file required by all C sources that
218            call CHOLMOD functions.  It defines a cholmod_common structure
219            called 'c' whose address is passed as the last argument to
220            (virtually) every CHOLMOD function.
221    
222            * src/Pattern.c: Simple example of the use of CHOLMOD.
223    
224            * src/init.c: initialize and finalize the cholmod_common structure.
225    
226            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
227            LDL and CCOLAMD from the U. of Florida sparse matrix library.
228    
229    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * inst/test-tools.R: new file collecting the utility functions used
232                    in ./tests/*.R
233    
234            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
235            * R/Matrix.R (cbind2): methods for NULL and missing
236    
237    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/AllClass.R: new "index" class for "[" and "[<-":
240                    First cut at "symmetricMatrix" and "triangularMatrix"
241            * R/gTMatrix.R (.ind.prep): new function;
242                    Logical and character indexing now work too.
243            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
244            * tests/indexing.R: new, including *.Rout.save
245            * tests/dgTMatrix.R: new
246    
247  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
248    
249          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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