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revision 868, Fri Aug 19 17:01:11 2005 UTC revision 1213, Tue Feb 7 23:44:07 2006 UTC
# Line 1  Line 1 
1    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
4            Use glmFit$prior.weights for weights in a glmm.
5            Allow an option usePQL = FALSE to skip the PQL steps for the
6            Laplace method (and, in time, the AGQ method).
7    
8            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
9            into a separate function internal_mer_Xfactor to be able to call
10            it from internal_bhat.
11    
12    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * tests/Class+Meth.R (tstMatrixClass): function for much better
15            testing; now again of all actual classes.
16    
17            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
18                    use macros and define make_d_matrix_* and make_i_matrix_*
19                    where _i_ is for the ldense routines:
20    
21            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
22            * src/ldense.c (lsyMatrix_as_lgeMatrix):
23    
24            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
25    
26    
27    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
30                    many different kinds of matrices.
31            * R/*.R: quite a few new methods were needed for R CMD check with
32                    new Matrix().  Very good for users playing around.
33    
34    
35    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * src/dgeMatrix.c (dMatrix_validate): new
38            * src/Mutils.c (dense_nonpacked_validate): new
39    
40            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
41    
42    
43    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
46    
47    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * DESCRIPTION (Version): 0.99-6 released to CRAN
50    
51            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
52            segfault in cases with multiple non-nested grouping factors.
53    
54    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
57                    (Depends): also on 'utils'
58    
59            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
60            * R/diagMatrix.R (Diagonal): constructor and methods for
61            diagonal matrices
62    
63            * R/ltTMatrix.R: new "minimal methods"
64    
65    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
68            all methods (and help files).
69    
70    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
73                    for case (dimn.  op  no_dimn.)
74    
75    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
76    
77            * DESCRIPTION (Version): 0.99-2  released to CRAN
78    
79    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
82            by Julian Faraway.
83    
84    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Auxiliaries.R (try_as): new utility
87            * R/sparseMatrix.R: use try_as() in coercion to original class
88    
89    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
92    
93    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Auxiliaries.R (dimNamesCheck): added
96    
97            * R/Matrix.R (as.array), (as.vector): new
98    
99    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
102                    default.
103            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
104                    "pMatrix" now contains "sparseMatrix"
105    
106    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * tests/Class+Meth.R: new tests; t(t(m)) == m
109    
110            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
111    
112            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
113            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
114    
115            * R/dspMatrix.R: typo in "t" method
116    
117    2005-09-18  Douglas Bates  <bates@wisc.edu>
118    
119            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
120            * R/Tsparse.R: instead of R/gTMatrix.R
121            * R/Csparse.R: new
122            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
123            * src/Tsparse.c: new; many trivial methods calling cholmod_()
124            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
125                            via cholmod
126    
127    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Auxiliaries.R (non0ind): new function using new C code
130            * src/dgCMatrix.c (compressed_non_0_ij): new utility
131    
132    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
133    
134            * src/chm_common.h: header file required by all C sources that
135            call CHOLMOD functions.  It defines a cholmod_common structure
136            called 'c' whose address is passed as the last argument to
137            (virtually) every CHOLMOD function.
138    
139            * src/Pattern.c: Simple example of the use of CHOLMOD.
140    
141            * src/init.c: initialize and finalize the cholmod_common structure.
142    
143            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
144            LDL and CCOLAMD from the U. of Florida sparse matrix library.
145    
146    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * inst/test-tools.R: new file collecting the utility functions used
149                    in ./tests/*.R
150    
151            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
152            * R/Matrix.R (cbind2): methods for NULL and missing
153    
154    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/AllClass.R: new "index" class for "[" and "[<-":
157                    First cut at "symmetricMatrix" and "triangularMatrix"
158            * R/gTMatrix.R (.ind.prep): new function;
159                    Logical and character indexing now work too.
160            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
161            * tests/indexing.R: new, including *.Rout.save
162            * tests/dgTMatrix.R: new
163    
164    2005-08-29  Douglas Bates  <bates@wisc.edu>
165    
166            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
167            indicator pos not being updated.  Also enforced upper triangular
168            for symmetric case.  Need to coerce edges component of elements of
169            edge list - grr! (Why don't they define their classes cleanly?)
170    
171    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Matrix.R:  added first "[<-" methods; not yet functional
174            * R/denseMatrix.R: dito
175            * man/Subassign-methods.Rd: new help file for these
176    
177    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * DESCRIPTION (Version): 0.98-6
180    
181            * R/denseMatrix.R: new file for "[" fallback methods for all dense
182            matrices.
183    
184  2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186          * src/lgCMatrix.c (lcsc_to_matrix): new; need for          * src/lgCMatrix.c (lcsc_to_matrix): new; need for
# Line 10  Line 193 
193          * General slight re-organization of where "[" methods are defined.          * General slight re-organization of where "[" methods are defined.
194            more to come.            more to come.
195    
196    2005-08-18  Douglas Bates  <bates@wisc.edu>
197    
198            * DESCRIPTION (Version): 0.98-5  released to CRAN
199    
200            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
201            * .....
202    
203  2005-08-18  Douglas Bates  <bates@localhost.localdomain>  2005-08-18  Douglas Bates  <bates@localhost.localdomain>
204    

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