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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1271, Thu May 18 06:47:09 2006 UTC
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1    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
4            the C code depending on a slot structure that's no longer valid.
5            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
6    
7    
8    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
9    
10            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
11            of lowerTriMatrix generic and methods to tril (also upper to triu)
12            and added a general band extractor.
13    
14    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
15    
16            * R/pedigree.R (pedigree): Replace sire and dam values outside the
17            allowable range with NAs. Added a corresponding check in the
18            validity check for the pedigree class.
19    
20            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
21            crossprod methods now inherits from symmetricMatrix.
22    
23    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
24    
25            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
26            generics lowerTriMatrix and upperTriMatrix along with methods for
27            the Csparse virtual class.  Also added a C function Csparse_band
28            that implements these methods by calling cholmod_band.
29    
30    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
33            erased when it was NULL.  This led to invalid subselections!
34    
35    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
38            in method for "t" so as not to lose the unit diagonal property.
39    
40    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
43            and methods.  This is now an option to the ranef method for the
44            mer class.
45    
46            * src/cs_utils.c: Ensure that the nz component is -1 for a
47            compressed column-oriented matrix.  Minor formatting cleanup.
48    
49            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
50            objects.
51    
52    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
55            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
56    
57    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
58    
59            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
60            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
61    
62            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
63            for the dtCMatrix class.
64    
65    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
68            and methods for it.
69    
70    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
73            arguments, such that M %*% 1:6 now works
74            * Tests/matprod.R: test the above
75    
76    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
77    
78            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
79            the ranef.lmer class.
80    
81            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
82            methods to extract the posterior variances from the bVar slot.
83    
84    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
87            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
88    
89            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
90            * tests/simple: (extended)
91    
92            * R/sparseMatrix.R (isTriangular): now using much improved
93            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
94    
95    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
96    
97            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
98            (problem report from Franklin Parlamis).  This should be done
99            generally.
100    
101    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
102    
103            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
104            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
105            update the plot methods.
106    
107    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * R/lmer.R (resid and ranef methods):  Added methods for the
110            "residuals" and "resid" generic but only for linear mixed model
111            fits.  Changed the ranef method to return a list of data frames so
112            that the plot methods now work.
113    
114    2006-03-16  Douglas Bates  <bates@bates2>
115    
116            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
117            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
118    
119            * DESCRIPTION (Date): New release
120    
121    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
124    
125            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
126            * man/KNex.Rd: and other help files
127            * tests/*.R: several ones needed adaption
128            * inst/doc/Comparisons.Rnw: dito
129    
130    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
133    
134            * tests/indexing.R: tests for new [<- methods for sparse matrices.
135    
136    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
139    
140            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
141    
142    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dMatrix.R: enable things like  M [ M < 10 ]
145            * R/dgeMatrix.R: implement it
146    
147    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/AllClass.R: define "summary.mer" and "*.lmer"
150            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
151            * R/lmer.R (show): now works with summary()
152    
153    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
156            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
157                    support the above
158    
159    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
162            Use glmFit$prior.weights for weights in a glmm.
163            Allow an option usePQL = FALSE to skip the PQL steps for the
164            Laplace method (and, in time, the AGQ method).
165    
166            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
167            into a separate function internal_mer_Xfactor to be able to call
168            it from internal_bhat.
169    
170    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/Class+Meth.R (tstMatrixClass): function for much better
173            testing; now again of all actual classes.
174    
175            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
176                    use macros and define make_d_matrix_* and make_i_matrix_*
177                    where _i_ is for the ldense routines:
178    
179            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
180            * src/ldense.c (lsyMatrix_as_lgeMatrix):
181    
182            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
183    
184    
185    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
188                    many different kinds of matrices.
189            * R/*.R: quite a few new methods were needed for R CMD check with
190                    new Matrix().  Very good for users playing around.
191    
192    
193    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/dgeMatrix.c (dMatrix_validate): new
196            * src/Mutils.c (dense_nonpacked_validate): new
197    
198            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
199    
200    
201    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
202    
203            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
204    
205    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
206    
207            * DESCRIPTION (Version): 0.99-6 released to CRAN
208    
209            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
210            segfault in cases with multiple non-nested grouping factors.
211    
212    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
215                    (Depends): also on 'utils'
216    
217            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
218            * R/diagMatrix.R (Diagonal): constructor and methods for
219            diagonal matrices
220    
221            * R/ltTMatrix.R: new "minimal methods"
222    
223    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
226            all methods (and help files).
227    
228    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
231                    for case (dimn.  op  no_dimn.)
232    
233    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
234    
235            * DESCRIPTION (Version): 0.99-2  released to CRAN
236    
237    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
240            by Julian Faraway.
241    
242    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/Auxiliaries.R (try_as): new utility
245            * R/sparseMatrix.R: use try_as() in coercion to original class
246    
247    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
250    
251    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (dimNamesCheck): added
254    
255            * R/Matrix.R (as.array), (as.vector): new
256    
257    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
260                    default.
261            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
262                    "pMatrix" now contains "sparseMatrix"
263    
264    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/Class+Meth.R: new tests; t(t(m)) == m
267    
268            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
269    
270            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
271            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
272    
273            * R/dspMatrix.R: typo in "t" method
274    
275    2005-09-18  Douglas Bates  <bates@wisc.edu>
276    
277            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
278            * R/Tsparse.R: instead of R/gTMatrix.R
279            * R/Csparse.R: new
280            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
281            * src/Tsparse.c: new; many trivial methods calling cholmod_()
282            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
283                            via cholmod
284    
285    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/Auxiliaries.R (non0ind): new function using new C code
288            * src/dgCMatrix.c (compressed_non_0_ij): new utility
289    
290    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
291    
292            * src/chm_common.h: header file required by all C sources that
293            call CHOLMOD functions.  It defines a cholmod_common structure
294            called 'c' whose address is passed as the last argument to
295            (virtually) every CHOLMOD function.
296    
297            * src/Pattern.c: Simple example of the use of CHOLMOD.
298    
299            * src/init.c: initialize and finalize the cholmod_common structure.
300    
301            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
302            LDL and CCOLAMD from the U. of Florida sparse matrix library.
303    
304    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * inst/test-tools.R: new file collecting the utility functions used
307                    in ./tests/*.R
308    
309            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
310            * R/Matrix.R (cbind2): methods for NULL and missing
311    
312    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/AllClass.R: new "index" class for "[" and "[<-":
315                    First cut at "symmetricMatrix" and "triangularMatrix"
316            * R/gTMatrix.R (.ind.prep): new function;
317                    Logical and character indexing now work too.
318            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
319            * tests/indexing.R: new, including *.Rout.save
320            * tests/dgTMatrix.R: new
321    
322    2005-08-29  Douglas Bates  <bates@wisc.edu>
323    
324            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
325            indicator pos not being updated.  Also enforced upper triangular
326            for symmetric case.  Need to coerce edges component of elements of
327            edge list - grr! (Why don't they define their classes cleanly?)
328    
329    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R:  added first "[<-" methods; not yet functional
332            * R/denseMatrix.R: dito
333            * man/Subassign-methods.Rd: new help file for these
334    
335    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * DESCRIPTION (Version): 0.98-6
338    
339            * R/denseMatrix.R: new file for "[" fallback methods for all dense
340            matrices.
341    
342    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
345                    as( <logical>, "matrix")
346    
347            * R/pMatrix.R: coercion to "lgTMatrix"
348    
349            * R/gTMatrix.R: new virtual class to define "[" methods for.
350            * man/gTMatrix-class.Rd:
351            * General slight re-organization of where "[" methods are defined.
352              more to come.
353    
354    2005-08-18  Douglas Bates  <bates@wisc.edu>
355    
356            * DESCRIPTION (Version): 0.98-5  released to CRAN
357    
358            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
359            * .....
360    
361    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
362    
363            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
364            or glmer objects.
365    
366    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
369    
370    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
371    
372            * R/HBMM.R: finish re-writing R-only code.
373    
374    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
375    
376            * man/externalFormats.Rd: move documentation for writeHB and
377            writeMM here.
378    
379            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
380            (suggested by Paul Roecker).
381    
382            * tests/validObj.R (assertError): Comment out test that is failing
383            after recent changes in r-devel.
384    
385    
386  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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