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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1283, Sat May 27 19:51:01 2006 UTC
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1    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
4            generic and mer methods for isNested and denomDF. This denomDF was
5            an attempt to emulate that in lme but I don't think that makes
6            sense.  Use the trace of the hat matrix instead.
7    
8    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
11            the C code depending on a slot structure that's no longer valid.
12            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
13    
14    
15    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
16    
17            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
18            of lowerTriMatrix generic and methods to tril (also upper to triu)
19            and added a general band extractor.
20    
21    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * R/pedigree.R (pedigree): Replace sire and dam values outside the
24            allowable range with NAs. Added a corresponding check in the
25            validity check for the pedigree class.
26    
27            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
28            crossprod methods now inherits from symmetricMatrix.
29    
30    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
33            generics lowerTriMatrix and upperTriMatrix along with methods for
34            the Csparse virtual class.  Also added a C function Csparse_band
35            that implements these methods by calling cholmod_band.
36    
37    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
40            erased when it was NULL.  This led to invalid subselections!
41    
42    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
45            in method for "t" so as not to lose the unit diagonal property.
46    
47    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
50            and methods.  This is now an option to the ranef method for the
51            mer class.
52    
53            * src/cs_utils.c: Ensure that the nz component is -1 for a
54            compressed column-oriented matrix.  Minor formatting cleanup.
55    
56            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
57            objects.
58    
59    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
62            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
63    
64    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
67            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
68    
69            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
70            for the dtCMatrix class.
71    
72    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
75            and methods for it.
76    
77    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
80            arguments, such that M %*% 1:6 now works
81            * Tests/matprod.R: test the above
82    
83    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
86            the ranef.lmer class.
87    
88            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
89            methods to extract the posterior variances from the bVar slot.
90    
91    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
94            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
95    
96            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
97            * tests/simple: (extended)
98    
99            * R/sparseMatrix.R (isTriangular): now using much improved
100            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
101    
102    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
105            (problem report from Franklin Parlamis).  This should be done
106            generally.
107    
108    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
111            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
112            update the plot methods.
113    
114    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
115    
116            * R/lmer.R (resid and ranef methods):  Added methods for the
117            "residuals" and "resid" generic but only for linear mixed model
118            fits.  Changed the ranef method to return a list of data frames so
119            that the plot methods now work.
120    
121    2006-03-16  Douglas Bates  <bates@bates2>
122    
123            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
124            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
125    
126            * DESCRIPTION (Date): New release
127    
128    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
131    
132            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
133            * man/KNex.Rd: and other help files
134            * tests/*.R: several ones needed adaption
135            * inst/doc/Comparisons.Rnw: dito
136    
137    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
140    
141            * tests/indexing.R: tests for new [<- methods for sparse matrices.
142    
143    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
146    
147            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
148    
149    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dMatrix.R: enable things like  M [ M < 10 ]
152            * R/dgeMatrix.R: implement it
153    
154    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/AllClass.R: define "summary.mer" and "*.lmer"
157            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
158            * R/lmer.R (show): now works with summary()
159    
160    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
163            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
164                    support the above
165    
166    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
167    
168            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
169            Use glmFit$prior.weights for weights in a glmm.
170            Allow an option usePQL = FALSE to skip the PQL steps for the
171            Laplace method (and, in time, the AGQ method).
172    
173            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
174            into a separate function internal_mer_Xfactor to be able to call
175            it from internal_bhat.
176    
177    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * tests/Class+Meth.R (tstMatrixClass): function for much better
180            testing; now again of all actual classes.
181    
182            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
183                    use macros and define make_d_matrix_* and make_i_matrix_*
184                    where _i_ is for the ldense routines:
185    
186            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
187            * src/ldense.c (lsyMatrix_as_lgeMatrix):
188    
189            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
190    
191    
192    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
195                    many different kinds of matrices.
196            * R/*.R: quite a few new methods were needed for R CMD check with
197                    new Matrix().  Very good for users playing around.
198    
199    
200    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * src/dgeMatrix.c (dMatrix_validate): new
203            * src/Mutils.c (dense_nonpacked_validate): new
204    
205            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
206    
207    
208    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
211    
212    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
213    
214            * DESCRIPTION (Version): 0.99-6 released to CRAN
215    
216            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
217            segfault in cases with multiple non-nested grouping factors.
218    
219    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
222                    (Depends): also on 'utils'
223    
224            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
225            * R/diagMatrix.R (Diagonal): constructor and methods for
226            diagonal matrices
227    
228            * R/ltTMatrix.R: new "minimal methods"
229    
230    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
233            all methods (and help files).
234    
235    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
238                    for case (dimn.  op  no_dimn.)
239    
240    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
241    
242            * DESCRIPTION (Version): 0.99-2  released to CRAN
243    
244    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
245    
246            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
247            by Julian Faraway.
248    
249    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/Auxiliaries.R (try_as): new utility
252            * R/sparseMatrix.R: use try_as() in coercion to original class
253    
254    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
257    
258    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Auxiliaries.R (dimNamesCheck): added
261    
262            * R/Matrix.R (as.array), (as.vector): new
263    
264    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
267                    default.
268            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
269                    "pMatrix" now contains "sparseMatrix"
270    
271    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * tests/Class+Meth.R: new tests; t(t(m)) == m
274    
275            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
276    
277            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
278            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
279    
280            * R/dspMatrix.R: typo in "t" method
281    
282    2005-09-18  Douglas Bates  <bates@wisc.edu>
283    
284            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
285            * R/Tsparse.R: instead of R/gTMatrix.R
286            * R/Csparse.R: new
287            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
288            * src/Tsparse.c: new; many trivial methods calling cholmod_()
289            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
290                            via cholmod
291    
292    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/Auxiliaries.R (non0ind): new function using new C code
295            * src/dgCMatrix.c (compressed_non_0_ij): new utility
296    
297    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
298    
299            * src/chm_common.h: header file required by all C sources that
300            call CHOLMOD functions.  It defines a cholmod_common structure
301            called 'c' whose address is passed as the last argument to
302            (virtually) every CHOLMOD function.
303    
304            * src/Pattern.c: Simple example of the use of CHOLMOD.
305    
306            * src/init.c: initialize and finalize the cholmod_common structure.
307    
308            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
309            LDL and CCOLAMD from the U. of Florida sparse matrix library.
310    
311    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * inst/test-tools.R: new file collecting the utility functions used
314                    in ./tests/*.R
315    
316            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
317            * R/Matrix.R (cbind2): methods for NULL and missing
318    
319    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/AllClass.R: new "index" class for "[" and "[<-":
322                    First cut at "symmetricMatrix" and "triangularMatrix"
323            * R/gTMatrix.R (.ind.prep): new function;
324                    Logical and character indexing now work too.
325            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
326            * tests/indexing.R: new, including *.Rout.save
327            * tests/dgTMatrix.R: new
328    
329  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
330    
331          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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