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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1267, Tue May 16 19:12:13 2006 UTC
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1    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/pedigree.R (pedigree): Replace sire and dam values outside the
4            allowable range with NAs. Added a corresponding check in the
5            validity check for the pedigree class.
6    
7            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
8            crossprod methods now inherits from symmetricMatrix.
9    
10    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
13            generics lowerTriMatrix and upperTriMatrix along with methods for
14            the Csparse virtual class.  Also added a C function Csparse_band
15            that implements these methods by calling cholmod_band.
16    
17    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
20            erased when it was NULL.  This led to invalid subselections!
21    
22    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
25            in method for "t" so as not to lose the unit diagonal property.
26    
27    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
28    
29            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
30            and methods.  This is now an option to the ranef method for the
31            mer class.
32    
33            * src/cs_utils.c: Ensure that the nz component is -1 for a
34            compressed column-oriented matrix.  Minor formatting cleanup.
35    
36            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
37            objects.
38    
39    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
42            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
43    
44    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
45    
46            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
47            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
48    
49            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
50            for the dtCMatrix class.
51    
52    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
55            and methods for it.
56    
57    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
60            arguments, such that M %*% 1:6 now works
61            * Tests/matprod.R: test the above
62    
63    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
64    
65            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
66            the ranef.lmer class.
67    
68            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
69            methods to extract the posterior variances from the bVar slot.
70    
71    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
74            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
75    
76            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
77            * tests/simple: (extended)
78    
79            * R/sparseMatrix.R (isTriangular): now using much improved
80            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
81    
82    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
83    
84            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
85            (problem report from Franklin Parlamis).  This should be done
86            generally.
87    
88    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
89    
90            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
91            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
92            update the plot methods.
93    
94    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/lmer.R (resid and ranef methods):  Added methods for the
97            "residuals" and "resid" generic but only for linear mixed model
98            fits.  Changed the ranef method to return a list of data frames so
99            that the plot methods now work.
100    
101    2006-03-16  Douglas Bates  <bates@bates2>
102    
103            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
104            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
105    
106            * DESCRIPTION (Date): New release
107    
108    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
111    
112            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
113            * man/KNex.Rd: and other help files
114            * tests/*.R: several ones needed adaption
115            * inst/doc/Comparisons.Rnw: dito
116    
117    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
120    
121            * tests/indexing.R: tests for new [<- methods for sparse matrices.
122    
123    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
126    
127            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
128    
129    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/dMatrix.R: enable things like  M [ M < 10 ]
132            * R/dgeMatrix.R: implement it
133    
134    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/AllClass.R: define "summary.mer" and "*.lmer"
137            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
138            * R/lmer.R (show): now works with summary()
139    
140    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
143            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
144                    support the above
145    
146    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
147    
148            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
149            Use glmFit$prior.weights for weights in a glmm.
150            Allow an option usePQL = FALSE to skip the PQL steps for the
151            Laplace method (and, in time, the AGQ method).
152    
153            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
154            into a separate function internal_mer_Xfactor to be able to call
155            it from internal_bhat.
156    
157    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * tests/Class+Meth.R (tstMatrixClass): function for much better
160            testing; now again of all actual classes.
161    
162            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
163                    use macros and define make_d_matrix_* and make_i_matrix_*
164                    where _i_ is for the ldense routines:
165    
166            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
167            * src/ldense.c (lsyMatrix_as_lgeMatrix):
168    
169            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
170    
171    
172    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
175                    many different kinds of matrices.
176            * R/*.R: quite a few new methods were needed for R CMD check with
177                    new Matrix().  Very good for users playing around.
178    
179    
180    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * src/dgeMatrix.c (dMatrix_validate): new
183            * src/Mutils.c (dense_nonpacked_validate): new
184    
185            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
186    
187    
188    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
189    
190            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
191    
192    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
193    
194            * DESCRIPTION (Version): 0.99-6 released to CRAN
195    
196            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
197            segfault in cases with multiple non-nested grouping factors.
198    
199    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
202                    (Depends): also on 'utils'
203    
204            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
205            * R/diagMatrix.R (Diagonal): constructor and methods for
206            diagonal matrices
207    
208            * R/ltTMatrix.R: new "minimal methods"
209    
210    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
213            all methods (and help files).
214    
215    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
218                    for case (dimn.  op  no_dimn.)
219    
220    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
221    
222            * DESCRIPTION (Version): 0.99-2  released to CRAN
223    
224    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
225    
226            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
227            by Julian Faraway.
228    
229    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/Auxiliaries.R (try_as): new utility
232            * R/sparseMatrix.R: use try_as() in coercion to original class
233    
234    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
237    
238    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Auxiliaries.R (dimNamesCheck): added
241    
242            * R/Matrix.R (as.array), (as.vector): new
243    
244    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
247                    default.
248            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
249                    "pMatrix" now contains "sparseMatrix"
250    
251    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * tests/Class+Meth.R: new tests; t(t(m)) == m
254    
255            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
256    
257            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
258            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
259    
260            * R/dspMatrix.R: typo in "t" method
261    
262    2005-09-18  Douglas Bates  <bates@wisc.edu>
263    
264            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
265            * R/Tsparse.R: instead of R/gTMatrix.R
266            * R/Csparse.R: new
267            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
268            * src/Tsparse.c: new; many trivial methods calling cholmod_()
269            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
270                            via cholmod
271    
272    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Auxiliaries.R (non0ind): new function using new C code
275            * src/dgCMatrix.c (compressed_non_0_ij): new utility
276    
277    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
278    
279            * src/chm_common.h: header file required by all C sources that
280            call CHOLMOD functions.  It defines a cholmod_common structure
281            called 'c' whose address is passed as the last argument to
282            (virtually) every CHOLMOD function.
283    
284            * src/Pattern.c: Simple example of the use of CHOLMOD.
285    
286            * src/init.c: initialize and finalize the cholmod_common structure.
287    
288            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
289            LDL and CCOLAMD from the U. of Florida sparse matrix library.
290    
291    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * inst/test-tools.R: new file collecting the utility functions used
294                    in ./tests/*.R
295    
296            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
297            * R/Matrix.R (cbind2): methods for NULL and missing
298    
299    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/AllClass.R: new "index" class for "[" and "[<-":
302                    First cut at "symmetricMatrix" and "triangularMatrix"
303            * R/gTMatrix.R (.ind.prep): new function;
304                    Logical and character indexing now work too.
305            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
306            * tests/indexing.R: new, including *.Rout.save
307            * tests/dgTMatrix.R: new
308    
309    2005-08-29  Douglas Bates  <bates@wisc.edu>
310    
311            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
312            indicator pos not being updated.  Also enforced upper triangular
313            for symmetric case.  Need to coerce edges component of elements of
314            edge list - grr! (Why don't they define their classes cleanly?)
315    
316    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/Matrix.R:  added first "[<-" methods; not yet functional
319            * R/denseMatrix.R: dito
320            * man/Subassign-methods.Rd: new help file for these
321    
322    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * DESCRIPTION (Version): 0.98-6
325    
326            * R/denseMatrix.R: new file for "[" fallback methods for all dense
327            matrices.
328    
329    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
332                    as( <logical>, "matrix")
333    
334            * R/pMatrix.R: coercion to "lgTMatrix"
335    
336            * R/gTMatrix.R: new virtual class to define "[" methods for.
337            * man/gTMatrix-class.Rd:
338            * General slight re-organization of where "[" methods are defined.
339              more to come.
340    
341    2005-08-18  Douglas Bates  <bates@wisc.edu>
342    
343            * DESCRIPTION (Version): 0.98-5  released to CRAN
344    
345            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
346            * .....
347    
348    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
349    
350            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
351            or glmer objects.
352    
353    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
356    
357    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
358    
359            * R/HBMM.R: finish re-writing R-only code.
360    
361    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
362    
363            * man/externalFormats.Rd: move documentation for writeHB and
364            writeMM here.
365    
366            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
367            (suggested by Paul Roecker).
368    
369            * tests/validObj.R (assertError): Comment out test that is failing
370            after recent changes in r-devel.
371    
372    
373  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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