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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1236, Thu Mar 23 15:16:17 2006 UTC
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1    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
4            (problem report from Franklin Parlamis).  This should be done
5            generally.
6    
7    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
10            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
11            update the plot methods.
12    
13    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * R/lmer.R (resid and ranef methods):  Added methods for the
16            "residuals" and "resid" generic but only for linear mixed model
17            fits.  Changed the ranef method to return a list of data frames so
18            that the plot methods now work.
19    
20    2006-03-16  Douglas Bates  <bates@bates2>
21    
22            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
23            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
24    
25            * DESCRIPTION (Date): New release
26    
27    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
30    
31            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
32            * man/KNex.Rd: and other help files
33            * tests/*.R: several ones needed adaption
34            * inst/doc/Comparisons.Rnw: dito
35    
36    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
39    
40            * tests/indexing.R: tests for new [<- methods for sparse matrices.
41    
42    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
45    
46            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
47    
48    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/dMatrix.R: enable things like  M [ M < 10 ]
51            * R/dgeMatrix.R: implement it
52    
53    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/AllClass.R: define "summary.mer" and "*.lmer"
56            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
57            * R/lmer.R (show): now works with summary()
58    
59    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
62            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
63                    support the above
64    
65    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
68            Use glmFit$prior.weights for weights in a glmm.
69            Allow an option usePQL = FALSE to skip the PQL steps for the
70            Laplace method (and, in time, the AGQ method).
71    
72            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
73            into a separate function internal_mer_Xfactor to be able to call
74            it from internal_bhat.
75    
76    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * tests/Class+Meth.R (tstMatrixClass): function for much better
79            testing; now again of all actual classes.
80    
81            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
82                    use macros and define make_d_matrix_* and make_i_matrix_*
83                    where _i_ is for the ldense routines:
84    
85            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
86            * src/ldense.c (lsyMatrix_as_lgeMatrix):
87    
88            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
89    
90    
91    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
94                    many different kinds of matrices.
95            * R/*.R: quite a few new methods were needed for R CMD check with
96                    new Matrix().  Very good for users playing around.
97    
98    
99    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * src/dgeMatrix.c (dMatrix_validate): new
102            * src/Mutils.c (dense_nonpacked_validate): new
103    
104            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
105    
106    
107    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
110    
111    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
112    
113            * DESCRIPTION (Version): 0.99-6 released to CRAN
114    
115            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
116            segfault in cases with multiple non-nested grouping factors.
117    
118    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
121                    (Depends): also on 'utils'
122    
123            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
124            * R/diagMatrix.R (Diagonal): constructor and methods for
125            diagonal matrices
126    
127            * R/ltTMatrix.R: new "minimal methods"
128    
129    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
132            all methods (and help files).
133    
134    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
137                    for case (dimn.  op  no_dimn.)
138    
139    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
140    
141            * DESCRIPTION (Version): 0.99-2  released to CRAN
142    
143    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
146            by Julian Faraway.
147    
148    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Auxiliaries.R (try_as): new utility
151            * R/sparseMatrix.R: use try_as() in coercion to original class
152    
153    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
156    
157    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/Auxiliaries.R (dimNamesCheck): added
160    
161            * R/Matrix.R (as.array), (as.vector): new
162    
163    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
166                    default.
167            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
168                    "pMatrix" now contains "sparseMatrix"
169    
170    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/Class+Meth.R: new tests; t(t(m)) == m
173    
174            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
175    
176            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
177            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
178    
179            * R/dspMatrix.R: typo in "t" method
180    
181    2005-09-18  Douglas Bates  <bates@wisc.edu>
182    
183            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
184            * R/Tsparse.R: instead of R/gTMatrix.R
185            * R/Csparse.R: new
186            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
187            * src/Tsparse.c: new; many trivial methods calling cholmod_()
188            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
189                            via cholmod
190    
191    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Auxiliaries.R (non0ind): new function using new C code
194            * src/dgCMatrix.c (compressed_non_0_ij): new utility
195    
196    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
197    
198            * src/chm_common.h: header file required by all C sources that
199            call CHOLMOD functions.  It defines a cholmod_common structure
200            called 'c' whose address is passed as the last argument to
201            (virtually) every CHOLMOD function.
202    
203            * src/Pattern.c: Simple example of the use of CHOLMOD.
204    
205            * src/init.c: initialize and finalize the cholmod_common structure.
206    
207            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
208            LDL and CCOLAMD from the U. of Florida sparse matrix library.
209    
210    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * inst/test-tools.R: new file collecting the utility functions used
213                    in ./tests/*.R
214    
215            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
216            * R/Matrix.R (cbind2): methods for NULL and missing
217    
218    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/AllClass.R: new "index" class for "[" and "[<-":
221                    First cut at "symmetricMatrix" and "triangularMatrix"
222            * R/gTMatrix.R (.ind.prep): new function;
223                    Logical and character indexing now work too.
224            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
225            * tests/indexing.R: new, including *.Rout.save
226            * tests/dgTMatrix.R: new
227    
228  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
229    
230          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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