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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1228, Wed Mar 15 17:43:34 2006 UTC
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1    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
4    
5            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
6            * man/KNex.Rd: and other help files
7            * tests/*.R: several ones needed adaption
8            * inst/doc/Comparisons.Rnw: dito
9    
10    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
13    
14            * tests/indexing.R: tests for new [<- methods for sparse matrices.
15    
16    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
19    
20            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
21    
22    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/dMatrix.R: enable things like  M [ M < 10 ]
25            * R/dgeMatrix.R: implement it
26    
27    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/AllClass.R: define "summary.mer" and "*.lmer"
30            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
31            * R/lmer.R (show): now works with summary()
32    
33    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
36            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
37                    support the above
38    
39    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
40    
41            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
42            Use glmFit$prior.weights for weights in a glmm.
43            Allow an option usePQL = FALSE to skip the PQL steps for the
44            Laplace method (and, in time, the AGQ method).
45    
46            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
47            into a separate function internal_mer_Xfactor to be able to call
48            it from internal_bhat.
49    
50    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * tests/Class+Meth.R (tstMatrixClass): function for much better
53            testing; now again of all actual classes.
54    
55            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
56                    use macros and define make_d_matrix_* and make_i_matrix_*
57                    where _i_ is for the ldense routines:
58    
59            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
60            * src/ldense.c (lsyMatrix_as_lgeMatrix):
61    
62            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
63    
64    
65    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
68                    many different kinds of matrices.
69            * R/*.R: quite a few new methods were needed for R CMD check with
70                    new Matrix().  Very good for users playing around.
71    
72    
73    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * src/dgeMatrix.c (dMatrix_validate): new
76            * src/Mutils.c (dense_nonpacked_validate): new
77    
78            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
79    
80    
81    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
84    
85    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * DESCRIPTION (Version): 0.99-6 released to CRAN
88    
89            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
90            segfault in cases with multiple non-nested grouping factors.
91    
92    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
95                    (Depends): also on 'utils'
96    
97            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
98            * R/diagMatrix.R (Diagonal): constructor and methods for
99            diagonal matrices
100    
101            * R/ltTMatrix.R: new "minimal methods"
102    
103    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
106            all methods (and help files).
107    
108    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
111                    for case (dimn.  op  no_dimn.)
112    
113    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * DESCRIPTION (Version): 0.99-2  released to CRAN
116    
117    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
120            by Julian Faraway.
121    
122    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Auxiliaries.R (try_as): new utility
125            * R/sparseMatrix.R: use try_as() in coercion to original class
126    
127    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
130    
131    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/Auxiliaries.R (dimNamesCheck): added
134    
135            * R/Matrix.R (as.array), (as.vector): new
136    
137    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
140                    default.
141            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
142                    "pMatrix" now contains "sparseMatrix"
143    
144    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * tests/Class+Meth.R: new tests; t(t(m)) == m
147    
148            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
149    
150            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
151            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
152    
153            * R/dspMatrix.R: typo in "t" method
154    
155    2005-09-18  Douglas Bates  <bates@wisc.edu>
156    
157            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
158            * R/Tsparse.R: instead of R/gTMatrix.R
159            * R/Csparse.R: new
160            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
161            * src/Tsparse.c: new; many trivial methods calling cholmod_()
162            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
163                            via cholmod
164    
165    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/Auxiliaries.R (non0ind): new function using new C code
168            * src/dgCMatrix.c (compressed_non_0_ij): new utility
169    
170    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
171    
172            * src/chm_common.h: header file required by all C sources that
173            call CHOLMOD functions.  It defines a cholmod_common structure
174            called 'c' whose address is passed as the last argument to
175            (virtually) every CHOLMOD function.
176    
177            * src/Pattern.c: Simple example of the use of CHOLMOD.
178    
179            * src/init.c: initialize and finalize the cholmod_common structure.
180    
181            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
182            LDL and CCOLAMD from the U. of Florida sparse matrix library.
183    
184    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * inst/test-tools.R: new file collecting the utility functions used
187                    in ./tests/*.R
188    
189            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
190            * R/Matrix.R (cbind2): methods for NULL and missing
191    
192    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/AllClass.R: new "index" class for "[" and "[<-":
195                    First cut at "symmetricMatrix" and "triangularMatrix"
196            * R/gTMatrix.R (.ind.prep): new function;
197                    Logical and character indexing now work too.
198            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
199            * tests/indexing.R: new, including *.Rout.save
200            * tests/dgTMatrix.R: new
201    
202  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
203    
204          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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