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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1257, Wed Apr 19 14:22:07 2006 UTC
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1    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
4            and methods.  This is now an option to the ranef method for the
5            mer class.
6    
7            * src/cs_utils.c: Ensure that the nz component is -1 for a
8            compressed column-oriented matrix.  Minor formatting cleanup.
9    
10            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
11            objects.
12    
13    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
16            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
17    
18    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
21            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
22    
23            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
24            for the dtCMatrix class.
25    
26    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
29            and methods for it.
30    
31    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
34            arguments, such that M %*% 1:6 now works
35            * Tests/matprod.R: test the above
36    
37    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
38    
39            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
40            the ranef.lmer class.
41    
42            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
43            methods to extract the posterior variances from the bVar slot.
44    
45    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
48            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
49    
50            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
51            * tests/simple: (extended)
52    
53            * R/sparseMatrix.R (isTriangular): now using much improved
54            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
55    
56    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
59            (problem report from Franklin Parlamis).  This should be done
60            generally.
61    
62    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
63    
64            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
65            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
66            update the plot methods.
67    
68    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
69    
70            * R/lmer.R (resid and ranef methods):  Added methods for the
71            "residuals" and "resid" generic but only for linear mixed model
72            fits.  Changed the ranef method to return a list of data frames so
73            that the plot methods now work.
74    
75    2006-03-16  Douglas Bates  <bates@bates2>
76    
77            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
78            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
79    
80            * DESCRIPTION (Date): New release
81    
82    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
85    
86            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
87            * man/KNex.Rd: and other help files
88            * tests/*.R: several ones needed adaption
89            * inst/doc/Comparisons.Rnw: dito
90    
91    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
94    
95            * tests/indexing.R: tests for new [<- methods for sparse matrices.
96    
97    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
100    
101            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
102    
103    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/dMatrix.R: enable things like  M [ M < 10 ]
106            * R/dgeMatrix.R: implement it
107    
108    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/AllClass.R: define "summary.mer" and "*.lmer"
111            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
112            * R/lmer.R (show): now works with summary()
113    
114    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
117            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
118                    support the above
119    
120    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
121    
122            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
123            Use glmFit$prior.weights for weights in a glmm.
124            Allow an option usePQL = FALSE to skip the PQL steps for the
125            Laplace method (and, in time, the AGQ method).
126    
127            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
128            into a separate function internal_mer_Xfactor to be able to call
129            it from internal_bhat.
130    
131    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * tests/Class+Meth.R (tstMatrixClass): function for much better
134            testing; now again of all actual classes.
135    
136            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
137                    use macros and define make_d_matrix_* and make_i_matrix_*
138                    where _i_ is for the ldense routines:
139    
140            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
141            * src/ldense.c (lsyMatrix_as_lgeMatrix):
142    
143            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
144    
145    
146    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
149                    many different kinds of matrices.
150            * R/*.R: quite a few new methods were needed for R CMD check with
151                    new Matrix().  Very good for users playing around.
152    
153    
154    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/dgeMatrix.c (dMatrix_validate): new
157            * src/Mutils.c (dense_nonpacked_validate): new
158    
159            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
160    
161    
162    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
165    
166    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
167    
168            * DESCRIPTION (Version): 0.99-6 released to CRAN
169    
170            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
171            segfault in cases with multiple non-nested grouping factors.
172    
173    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
176                    (Depends): also on 'utils'
177    
178            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
179            * R/diagMatrix.R (Diagonal): constructor and methods for
180            diagonal matrices
181    
182            * R/ltTMatrix.R: new "minimal methods"
183    
184    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
187            all methods (and help files).
188    
189    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
192                    for case (dimn.  op  no_dimn.)
193    
194    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * DESCRIPTION (Version): 0.99-2  released to CRAN
197    
198    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
201            by Julian Faraway.
202    
203    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Auxiliaries.R (try_as): new utility
206            * R/sparseMatrix.R: use try_as() in coercion to original class
207    
208    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
211    
212    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/Auxiliaries.R (dimNamesCheck): added
215    
216            * R/Matrix.R (as.array), (as.vector): new
217    
218    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
221                    default.
222            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
223                    "pMatrix" now contains "sparseMatrix"
224    
225    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * tests/Class+Meth.R: new tests; t(t(m)) == m
228    
229            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
230    
231            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
232            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
233    
234            * R/dspMatrix.R: typo in "t" method
235    
236    2005-09-18  Douglas Bates  <bates@wisc.edu>
237    
238            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
239            * R/Tsparse.R: instead of R/gTMatrix.R
240            * R/Csparse.R: new
241            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
242            * src/Tsparse.c: new; many trivial methods calling cholmod_()
243            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
244                            via cholmod
245    
246    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Auxiliaries.R (non0ind): new function using new C code
249            * src/dgCMatrix.c (compressed_non_0_ij): new utility
250    
251    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
252    
253            * src/chm_common.h: header file required by all C sources that
254            call CHOLMOD functions.  It defines a cholmod_common structure
255            called 'c' whose address is passed as the last argument to
256            (virtually) every CHOLMOD function.
257    
258            * src/Pattern.c: Simple example of the use of CHOLMOD.
259    
260            * src/init.c: initialize and finalize the cholmod_common structure.
261    
262            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
263            LDL and CCOLAMD from the U. of Florida sparse matrix library.
264    
265    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * inst/test-tools.R: new file collecting the utility functions used
268                    in ./tests/*.R
269    
270            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
271            * R/Matrix.R (cbind2): methods for NULL and missing
272    
273    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/AllClass.R: new "index" class for "[" and "[<-":
276                    First cut at "symmetricMatrix" and "triangularMatrix"
277            * R/gTMatrix.R (.ind.prep): new function;
278                    Logical and character indexing now work too.
279            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
280            * tests/indexing.R: new, including *.Rout.save
281            * tests/dgTMatrix.R: new
282    
283    2005-08-29  Douglas Bates  <bates@wisc.edu>
284    
285            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
286            indicator pos not being updated.  Also enforced upper triangular
287            for symmetric case.  Need to coerce edges component of elements of
288            edge list - grr! (Why don't they define their classes cleanly?)
289    
290    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Matrix.R:  added first "[<-" methods; not yet functional
293            * R/denseMatrix.R: dito
294            * man/Subassign-methods.Rd: new help file for these
295    
296    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * DESCRIPTION (Version): 0.98-6
299    
300            * R/denseMatrix.R: new file for "[" fallback methods for all dense
301            matrices.
302    
303    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
306                    as( <logical>, "matrix")
307    
308            * R/pMatrix.R: coercion to "lgTMatrix"
309    
310            * R/gTMatrix.R: new virtual class to define "[" methods for.
311            * man/gTMatrix-class.Rd:
312            * General slight re-organization of where "[" methods are defined.
313              more to come.
314    
315    2005-08-18  Douglas Bates  <bates@wisc.edu>
316    
317            * DESCRIPTION (Version): 0.98-5  released to CRAN
318    
319            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
320            * .....
321    
322    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
323    
324            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
325            or glmer objects.
326    
327    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
330    
331    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
332    
333            * R/HBMM.R: finish re-writing R-only code.
334    
335    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
336    
337            * man/externalFormats.Rd: move documentation for writeHB and
338            writeMM here.
339    
340            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
341            (suggested by Paul Roecker).
342    
343            * tests/validObj.R (assertError): Comment out test that is failing
344            after recent changes in r-devel.
345    
346    
347  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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