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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1253, Wed Apr 19 09:17:14 2006 UTC
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1    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
4            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
5    
6    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
9            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
10    
11            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
12            for the dtCMatrix class.
13    
14    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
15    
16            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
17            and methods for it.
18    
19    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
22            arguments, such that M %*% 1:6 now works
23            * Tests/matprod.R: test the above
24    
25    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
26    
27            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
28            the ranef.lmer class.
29    
30            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
31            methods to extract the posterior variances from the bVar slot.
32    
33    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
36            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
37    
38            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
39            * tests/simple: (extended)
40    
41            * R/sparseMatrix.R (isTriangular): now using much improved
42            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
43    
44    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
45    
46            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
47            (problem report from Franklin Parlamis).  This should be done
48            generally.
49    
50    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
53            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
54            update the plot methods.
55    
56    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * R/lmer.R (resid and ranef methods):  Added methods for the
59            "residuals" and "resid" generic but only for linear mixed model
60            fits.  Changed the ranef method to return a list of data frames so
61            that the plot methods now work.
62    
63    2006-03-16  Douglas Bates  <bates@bates2>
64    
65            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
66            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
67    
68            * DESCRIPTION (Date): New release
69    
70    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
73    
74            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
75            * man/KNex.Rd: and other help files
76            * tests/*.R: several ones needed adaption
77            * inst/doc/Comparisons.Rnw: dito
78    
79    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
82    
83            * tests/indexing.R: tests for new [<- methods for sparse matrices.
84    
85    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
88    
89            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
90    
91    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dMatrix.R: enable things like  M [ M < 10 ]
94            * R/dgeMatrix.R: implement it
95    
96    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/AllClass.R: define "summary.mer" and "*.lmer"
99            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
100            * R/lmer.R (show): now works with summary()
101    
102    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
105            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
106                    support the above
107    
108    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
111            Use glmFit$prior.weights for weights in a glmm.
112            Allow an option usePQL = FALSE to skip the PQL steps for the
113            Laplace method (and, in time, the AGQ method).
114    
115            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
116            into a separate function internal_mer_Xfactor to be able to call
117            it from internal_bhat.
118    
119    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * tests/Class+Meth.R (tstMatrixClass): function for much better
122            testing; now again of all actual classes.
123    
124            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
125                    use macros and define make_d_matrix_* and make_i_matrix_*
126                    where _i_ is for the ldense routines:
127    
128            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
129            * src/ldense.c (lsyMatrix_as_lgeMatrix):
130    
131            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
132    
133    
134    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
137                    many different kinds of matrices.
138            * R/*.R: quite a few new methods were needed for R CMD check with
139                    new Matrix().  Very good for users playing around.
140    
141    
142    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * src/dgeMatrix.c (dMatrix_validate): new
145            * src/Mutils.c (dense_nonpacked_validate): new
146    
147            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
148    
149    
150    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
153    
154    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
155    
156            * DESCRIPTION (Version): 0.99-6 released to CRAN
157    
158            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
159            segfault in cases with multiple non-nested grouping factors.
160    
161    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
164                    (Depends): also on 'utils'
165    
166            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
167            * R/diagMatrix.R (Diagonal): constructor and methods for
168            diagonal matrices
169    
170            * R/ltTMatrix.R: new "minimal methods"
171    
172    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
175            all methods (and help files).
176    
177    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
180                    for case (dimn.  op  no_dimn.)
181    
182    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
183    
184            * DESCRIPTION (Version): 0.99-2  released to CRAN
185    
186    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
187    
188            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
189            by Julian Faraway.
190    
191    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Auxiliaries.R (try_as): new utility
194            * R/sparseMatrix.R: use try_as() in coercion to original class
195    
196    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
199    
200    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Auxiliaries.R (dimNamesCheck): added
203    
204            * R/Matrix.R (as.array), (as.vector): new
205    
206    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
209                    default.
210            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
211                    "pMatrix" now contains "sparseMatrix"
212    
213    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * tests/Class+Meth.R: new tests; t(t(m)) == m
216    
217            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
218    
219            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
220            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
221    
222            * R/dspMatrix.R: typo in "t" method
223    
224    2005-09-18  Douglas Bates  <bates@wisc.edu>
225    
226            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
227            * R/Tsparse.R: instead of R/gTMatrix.R
228            * R/Csparse.R: new
229            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
230            * src/Tsparse.c: new; many trivial methods calling cholmod_()
231            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
232                            via cholmod
233    
234    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Auxiliaries.R (non0ind): new function using new C code
237            * src/dgCMatrix.c (compressed_non_0_ij): new utility
238    
239    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
240    
241            * src/chm_common.h: header file required by all C sources that
242            call CHOLMOD functions.  It defines a cholmod_common structure
243            called 'c' whose address is passed as the last argument to
244            (virtually) every CHOLMOD function.
245    
246            * src/Pattern.c: Simple example of the use of CHOLMOD.
247    
248            * src/init.c: initialize and finalize the cholmod_common structure.
249    
250            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
251            LDL and CCOLAMD from the U. of Florida sparse matrix library.
252    
253    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * inst/test-tools.R: new file collecting the utility functions used
256                    in ./tests/*.R
257    
258            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
259            * R/Matrix.R (cbind2): methods for NULL and missing
260    
261    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/AllClass.R: new "index" class for "[" and "[<-":
264                    First cut at "symmetricMatrix" and "triangularMatrix"
265            * R/gTMatrix.R (.ind.prep): new function;
266                    Logical and character indexing now work too.
267            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
268            * tests/indexing.R: new, including *.Rout.save
269            * tests/dgTMatrix.R: new
270    
271    2005-08-29  Douglas Bates  <bates@wisc.edu>
272    
273            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
274            indicator pos not being updated.  Also enforced upper triangular
275            for symmetric case.  Need to coerce edges component of elements of
276            edge list - grr! (Why don't they define their classes cleanly?)
277    
278    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/Matrix.R:  added first "[<-" methods; not yet functional
281            * R/denseMatrix.R: dito
282            * man/Subassign-methods.Rd: new help file for these
283    
284    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.98-6
287    
288            * R/denseMatrix.R: new file for "[" fallback methods for all dense
289            matrices.
290    
291    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
294                    as( <logical>, "matrix")
295    
296            * R/pMatrix.R: coercion to "lgTMatrix"
297    
298            * R/gTMatrix.R: new virtual class to define "[" methods for.
299            * man/gTMatrix-class.Rd:
300            * General slight re-organization of where "[" methods are defined.
301              more to come.
302    
303    2005-08-18  Douglas Bates  <bates@wisc.edu>
304    
305            * DESCRIPTION (Version): 0.98-5  released to CRAN
306    
307            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
308            * .....
309    
310    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
311    
312            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
313            or glmer objects.
314    
315    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
318    
319    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
320    
321            * R/HBMM.R: finish re-writing R-only code.
322    
323    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
324    
325            * man/externalFormats.Rd: move documentation for writeHB and
326            writeMM here.
327    
328            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
329            (suggested by Paul Roecker).
330    
331            * tests/validObj.R (assertError): Comment out test that is failing
332            after recent changes in r-devel.
333    
334    
335  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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