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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1232, Tue Mar 21 11:07:55 2006 UTC
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1    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (resid and ranef methods):  Added methods for the
4            "residuals" and "resid" generic but only for linear mixed model
5            fits.  Changed the ranef method to return a list of data frames so
6            that the plot methods now work.
7    
8    2006-03-16  Douglas Bates  <bates@bates2>
9    
10            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
11            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
12    
13            * DESCRIPTION (Date): New release
14    
15    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
18    
19            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
20            * man/KNex.Rd: and other help files
21            * tests/*.R: several ones needed adaption
22            * inst/doc/Comparisons.Rnw: dito
23    
24    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
27    
28            * tests/indexing.R: tests for new [<- methods for sparse matrices.
29    
30    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
33    
34            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
35    
36    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dMatrix.R: enable things like  M [ M < 10 ]
39            * R/dgeMatrix.R: implement it
40    
41    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/AllClass.R: define "summary.mer" and "*.lmer"
44            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
45            * R/lmer.R (show): now works with summary()
46    
47    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
50            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
51                    support the above
52    
53    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
54    
55            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
56            Use glmFit$prior.weights for weights in a glmm.
57            Allow an option usePQL = FALSE to skip the PQL steps for the
58            Laplace method (and, in time, the AGQ method).
59    
60            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
61            into a separate function internal_mer_Xfactor to be able to call
62            it from internal_bhat.
63    
64    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * tests/Class+Meth.R (tstMatrixClass): function for much better
67            testing; now again of all actual classes.
68    
69            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
70                    use macros and define make_d_matrix_* and make_i_matrix_*
71                    where _i_ is for the ldense routines:
72    
73            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
74            * src/ldense.c (lsyMatrix_as_lgeMatrix):
75    
76            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
77    
78    
79    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
82                    many different kinds of matrices.
83            * R/*.R: quite a few new methods were needed for R CMD check with
84                    new Matrix().  Very good for users playing around.
85    
86    
87    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/dgeMatrix.c (dMatrix_validate): new
90            * src/Mutils.c (dense_nonpacked_validate): new
91    
92            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
93    
94    
95    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
96    
97            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
98    
99    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
100    
101            * DESCRIPTION (Version): 0.99-6 released to CRAN
102    
103            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
104            segfault in cases with multiple non-nested grouping factors.
105    
106    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
109                    (Depends): also on 'utils'
110    
111            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
112            * R/diagMatrix.R (Diagonal): constructor and methods for
113            diagonal matrices
114    
115            * R/ltTMatrix.R: new "minimal methods"
116    
117    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
120            all methods (and help files).
121    
122    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
125                    for case (dimn.  op  no_dimn.)
126    
127    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * DESCRIPTION (Version): 0.99-2  released to CRAN
130    
131    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
134            by Julian Faraway.
135    
136    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/Auxiliaries.R (try_as): new utility
139            * R/sparseMatrix.R: use try_as() in coercion to original class
140    
141    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
144    
145    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/Auxiliaries.R (dimNamesCheck): added
148    
149            * R/Matrix.R (as.array), (as.vector): new
150    
151    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
154                    default.
155            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
156                    "pMatrix" now contains "sparseMatrix"
157    
158    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * tests/Class+Meth.R: new tests; t(t(m)) == m
161    
162            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
163    
164            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
165            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
166    
167            * R/dspMatrix.R: typo in "t" method
168    
169    2005-09-18  Douglas Bates  <bates@wisc.edu>
170    
171            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
172            * R/Tsparse.R: instead of R/gTMatrix.R
173            * R/Csparse.R: new
174            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
175            * src/Tsparse.c: new; many trivial methods calling cholmod_()
176            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
177                            via cholmod
178    
179    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/Auxiliaries.R (non0ind): new function using new C code
182            * src/dgCMatrix.c (compressed_non_0_ij): new utility
183    
184    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
185    
186            * src/chm_common.h: header file required by all C sources that
187            call CHOLMOD functions.  It defines a cholmod_common structure
188            called 'c' whose address is passed as the last argument to
189            (virtually) every CHOLMOD function.
190    
191            * src/Pattern.c: Simple example of the use of CHOLMOD.
192    
193            * src/init.c: initialize and finalize the cholmod_common structure.
194    
195            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
196            LDL and CCOLAMD from the U. of Florida sparse matrix library.
197    
198    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * inst/test-tools.R: new file collecting the utility functions used
201                    in ./tests/*.R
202    
203            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
204            * R/Matrix.R (cbind2): methods for NULL and missing
205    
206    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/AllClass.R: new "index" class for "[" and "[<-":
209                    First cut at "symmetricMatrix" and "triangularMatrix"
210            * R/gTMatrix.R (.ind.prep): new function;
211                    Logical and character indexing now work too.
212            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
213            * tests/indexing.R: new, including *.Rout.save
214            * tests/dgTMatrix.R: new
215    
216    2005-08-29  Douglas Bates  <bates@wisc.edu>
217    
218            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
219            indicator pos not being updated.  Also enforced upper triangular
220            for symmetric case.  Need to coerce edges component of elements of
221            edge list - grr! (Why don't they define their classes cleanly?)
222    
223    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Matrix.R:  added first "[<-" methods; not yet functional
226            * R/denseMatrix.R: dito
227            * man/Subassign-methods.Rd: new help file for these
228    
229    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * DESCRIPTION (Version): 0.98-6
232    
233            * R/denseMatrix.R: new file for "[" fallback methods for all dense
234            matrices.
235    
236    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
239                    as( <logical>, "matrix")
240    
241            * R/pMatrix.R: coercion to "lgTMatrix"
242    
243            * R/gTMatrix.R: new virtual class to define "[" methods for.
244            * man/gTMatrix-class.Rd:
245            * General slight re-organization of where "[" methods are defined.
246              more to come.
247    
248    2005-08-18  Douglas Bates  <bates@wisc.edu>
249    
250            * DESCRIPTION (Version): 0.98-5  released to CRAN
251    
252            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
253            * .....
254    
255    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
256    
257            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
258            or glmer objects.
259    
260    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
263    
264    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
265    
266            * R/HBMM.R: finish re-writing R-only code.
267    
268    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
269    
270            * man/externalFormats.Rd: move documentation for writeHB and
271            writeMM here.
272    
273            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
274            (suggested by Paul Roecker).
275    
276            * tests/validObj.R (assertError): Comment out test that is failing
277            after recent changes in r-devel.
278    
279    
280  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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