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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1264, Mon May 15 21:05:20 2006 UTC
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1    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
4            erased when it was NULL.  This led to invalid subselections!
5    
6    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
9            in method for "t" so as not to lose the unit diagonal property.
10    
11    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
14            and methods.  This is now an option to the ranef method for the
15            mer class.
16    
17            * src/cs_utils.c: Ensure that the nz component is -1 for a
18            compressed column-oriented matrix.  Minor formatting cleanup.
19    
20            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
21            objects.
22    
23    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
26            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
27    
28    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
31            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
32    
33            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
34            for the dtCMatrix class.
35    
36    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
37    
38            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
39            and methods for it.
40    
41    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
44            arguments, such that M %*% 1:6 now works
45            * Tests/matprod.R: test the above
46    
47    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
50            the ranef.lmer class.
51    
52            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
53            methods to extract the posterior variances from the bVar slot.
54    
55    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
58            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
59    
60            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
61            * tests/simple: (extended)
62    
63            * R/sparseMatrix.R (isTriangular): now using much improved
64            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
65    
66    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
69            (problem report from Franklin Parlamis).  This should be done
70            generally.
71    
72    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
75            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
76            update the plot methods.
77    
78    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * R/lmer.R (resid and ranef methods):  Added methods for the
81            "residuals" and "resid" generic but only for linear mixed model
82            fits.  Changed the ranef method to return a list of data frames so
83            that the plot methods now work.
84    
85    2006-03-16  Douglas Bates  <bates@bates2>
86    
87            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
88            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
89    
90            * DESCRIPTION (Date): New release
91    
92    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
95    
96            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
97            * man/KNex.Rd: and other help files
98            * tests/*.R: several ones needed adaption
99            * inst/doc/Comparisons.Rnw: dito
100    
101    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
104    
105            * tests/indexing.R: tests for new [<- methods for sparse matrices.
106    
107    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
110    
111            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
112    
113    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/dMatrix.R: enable things like  M [ M < 10 ]
116            * R/dgeMatrix.R: implement it
117    
118    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/AllClass.R: define "summary.mer" and "*.lmer"
121            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
122            * R/lmer.R (show): now works with summary()
123    
124    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
127            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
128                    support the above
129    
130    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
131    
132            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
133            Use glmFit$prior.weights for weights in a glmm.
134            Allow an option usePQL = FALSE to skip the PQL steps for the
135            Laplace method (and, in time, the AGQ method).
136    
137            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
138            into a separate function internal_mer_Xfactor to be able to call
139            it from internal_bhat.
140    
141    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * tests/Class+Meth.R (tstMatrixClass): function for much better
144            testing; now again of all actual classes.
145    
146            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
147                    use macros and define make_d_matrix_* and make_i_matrix_*
148                    where _i_ is for the ldense routines:
149    
150            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
151            * src/ldense.c (lsyMatrix_as_lgeMatrix):
152    
153            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
154    
155    
156    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
159                    many different kinds of matrices.
160            * R/*.R: quite a few new methods were needed for R CMD check with
161                    new Matrix().  Very good for users playing around.
162    
163    
164    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * src/dgeMatrix.c (dMatrix_validate): new
167            * src/Mutils.c (dense_nonpacked_validate): new
168    
169            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
170    
171    
172    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
173    
174            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
175    
176    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
177    
178            * DESCRIPTION (Version): 0.99-6 released to CRAN
179    
180            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
181            segfault in cases with multiple non-nested grouping factors.
182    
183    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
186                    (Depends): also on 'utils'
187    
188            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
189            * R/diagMatrix.R (Diagonal): constructor and methods for
190            diagonal matrices
191    
192            * R/ltTMatrix.R: new "minimal methods"
193    
194    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
197            all methods (and help files).
198    
199    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
202                    for case (dimn.  op  no_dimn.)
203    
204    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
205    
206            * DESCRIPTION (Version): 0.99-2  released to CRAN
207    
208    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
211            by Julian Faraway.
212    
213    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Auxiliaries.R (try_as): new utility
216            * R/sparseMatrix.R: use try_as() in coercion to original class
217    
218    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
221    
222    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Auxiliaries.R (dimNamesCheck): added
225    
226            * R/Matrix.R (as.array), (as.vector): new
227    
228    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
231                    default.
232            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
233                    "pMatrix" now contains "sparseMatrix"
234    
235    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * tests/Class+Meth.R: new tests; t(t(m)) == m
238    
239            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
240    
241            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
242            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
243    
244            * R/dspMatrix.R: typo in "t" method
245    
246    2005-09-18  Douglas Bates  <bates@wisc.edu>
247    
248            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
249            * R/Tsparse.R: instead of R/gTMatrix.R
250            * R/Csparse.R: new
251            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
252            * src/Tsparse.c: new; many trivial methods calling cholmod_()
253            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
254                            via cholmod
255    
256    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Auxiliaries.R (non0ind): new function using new C code
259            * src/dgCMatrix.c (compressed_non_0_ij): new utility
260    
261    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
262    
263            * src/chm_common.h: header file required by all C sources that
264            call CHOLMOD functions.  It defines a cholmod_common structure
265            called 'c' whose address is passed as the last argument to
266            (virtually) every CHOLMOD function.
267    
268            * src/Pattern.c: Simple example of the use of CHOLMOD.
269    
270            * src/init.c: initialize and finalize the cholmod_common structure.
271    
272            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
273            LDL and CCOLAMD from the U. of Florida sparse matrix library.
274    
275    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * inst/test-tools.R: new file collecting the utility functions used
278                    in ./tests/*.R
279    
280            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
281            * R/Matrix.R (cbind2): methods for NULL and missing
282    
283    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/AllClass.R: new "index" class for "[" and "[<-":
286                    First cut at "symmetricMatrix" and "triangularMatrix"
287            * R/gTMatrix.R (.ind.prep): new function;
288                    Logical and character indexing now work too.
289            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
290            * tests/indexing.R: new, including *.Rout.save
291            * tests/dgTMatrix.R: new
292    
293    2005-08-29  Douglas Bates  <bates@wisc.edu>
294    
295            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
296            indicator pos not being updated.  Also enforced upper triangular
297            for symmetric case.  Need to coerce edges component of elements of
298            edge list - grr! (Why don't they define their classes cleanly?)
299    
300    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Matrix.R:  added first "[<-" methods; not yet functional
303            * R/denseMatrix.R: dito
304            * man/Subassign-methods.Rd: new help file for these
305    
306    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * DESCRIPTION (Version): 0.98-6
309    
310            * R/denseMatrix.R: new file for "[" fallback methods for all dense
311            matrices.
312    
313    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
316                    as( <logical>, "matrix")
317    
318            * R/pMatrix.R: coercion to "lgTMatrix"
319    
320            * R/gTMatrix.R: new virtual class to define "[" methods for.
321            * man/gTMatrix-class.Rd:
322            * General slight re-organization of where "[" methods are defined.
323              more to come.
324    
325    2005-08-18  Douglas Bates  <bates@wisc.edu>
326    
327            * DESCRIPTION (Version): 0.98-5  released to CRAN
328    
329            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
330            * .....
331    
332    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
333    
334            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
335            or glmer objects.
336    
337    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
340    
341    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
342    
343            * R/HBMM.R: finish re-writing R-only code.
344    
345    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
346    
347            * man/externalFormats.Rd: move documentation for writeHB and
348            writeMM here.
349    
350            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
351            (suggested by Paul Roecker).
352    
353            * tests/validObj.R (assertError): Comment out test that is failing
354            after recent changes in r-devel.
355    
356    
357  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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