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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1287, Tue May 30 23:23:24 2006 UTC
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1    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
4            grouping factors to be specified in the formula as (1|foo/bar).
5    
6    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R (findbars and others): Change check of is.numeric to
9            !is.language to resolve the bug reported by Jacob Wegelin.
10    
11            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
12            code to evaluate inbreeding coefficients without calculating T,
13            based on code in Sargolzaei and Iwaisaki's paper.
14    
15    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
16    
17            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
18            generic and mer methods for isNested and denomDF. This denomDF was
19            an attempt to emulate that in lme but I don't think that makes
20            sense.  Use the trace of the hat matrix instead.
21    
22    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
25            the C code depending on a slot structure that's no longer valid.
26            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
27    
28    
29    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
30    
31            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
32            of lowerTriMatrix generic and methods to tril (also upper to triu)
33            and added a general band extractor.
34    
35    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/pedigree.R (pedigree): Replace sire and dam values outside the
38            allowable range with NAs. Added a corresponding check in the
39            validity check for the pedigree class.
40    
41            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
42            crossprod methods now inherits from symmetricMatrix.
43    
44    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
45    
46            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
47            generics lowerTriMatrix and upperTriMatrix along with methods for
48            the Csparse virtual class.  Also added a C function Csparse_band
49            that implements these methods by calling cholmod_band.
50    
51    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
54            erased when it was NULL.  This led to invalid subselections!
55    
56    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
59            in method for "t" so as not to lose the unit diagonal property.
60    
61    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
64            and methods.  This is now an option to the ranef method for the
65            mer class.
66    
67            * src/cs_utils.c: Ensure that the nz component is -1 for a
68            compressed column-oriented matrix.  Minor formatting cleanup.
69    
70            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
71            objects.
72    
73    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
76            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
77    
78    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
81            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
82    
83            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
84            for the dtCMatrix class.
85    
86    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
89            and methods for it.
90    
91    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
94            arguments, such that M %*% 1:6 now works
95            * Tests/matprod.R: test the above
96    
97    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
100            the ranef.lmer class.
101    
102            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
103            methods to extract the posterior variances from the bVar slot.
104    
105    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
108            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
109    
110            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
111            * tests/simple: (extended)
112    
113            * R/sparseMatrix.R (isTriangular): now using much improved
114            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
115    
116    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
117    
118            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
119            (problem report from Franklin Parlamis).  This should be done
120            generally.
121    
122    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
123    
124            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
125            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
126            update the plot methods.
127    
128    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
129    
130            * R/lmer.R (resid and ranef methods):  Added methods for the
131            "residuals" and "resid" generic but only for linear mixed model
132            fits.  Changed the ranef method to return a list of data frames so
133            that the plot methods now work.
134    
135    2006-03-16  Douglas Bates  <bates@bates2>
136    
137            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
138            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
139    
140            * DESCRIPTION (Date): New release
141    
142    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
145    
146            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
147            * man/KNex.Rd: and other help files
148            * tests/*.R: several ones needed adaption
149            * inst/doc/Comparisons.Rnw: dito
150    
151    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
154    
155            * tests/indexing.R: tests for new [<- methods for sparse matrices.
156    
157    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
160    
161            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
162    
163    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/dMatrix.R: enable things like  M [ M < 10 ]
166            * R/dgeMatrix.R: implement it
167    
168    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/AllClass.R: define "summary.mer" and "*.lmer"
171            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
172            * R/lmer.R (show): now works with summary()
173    
174    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
177            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
178                    support the above
179    
180    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
181    
182            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
183            Use glmFit$prior.weights for weights in a glmm.
184            Allow an option usePQL = FALSE to skip the PQL steps for the
185            Laplace method (and, in time, the AGQ method).
186    
187            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
188            into a separate function internal_mer_Xfactor to be able to call
189            it from internal_bhat.
190    
191    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * tests/Class+Meth.R (tstMatrixClass): function for much better
194            testing; now again of all actual classes.
195    
196            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
197                    use macros and define make_d_matrix_* and make_i_matrix_*
198                    where _i_ is for the ldense routines:
199    
200            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
201            * src/ldense.c (lsyMatrix_as_lgeMatrix):
202    
203            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
204    
205    
206    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
209                    many different kinds of matrices.
210            * R/*.R: quite a few new methods were needed for R CMD check with
211                    new Matrix().  Very good for users playing around.
212    
213    
214    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * src/dgeMatrix.c (dMatrix_validate): new
217            * src/Mutils.c (dense_nonpacked_validate): new
218    
219            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
220    
221    
222    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
225    
226    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
227    
228            * DESCRIPTION (Version): 0.99-6 released to CRAN
229    
230            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
231            segfault in cases with multiple non-nested grouping factors.
232    
233    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
236                    (Depends): also on 'utils'
237    
238            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
239            * R/diagMatrix.R (Diagonal): constructor and methods for
240            diagonal matrices
241    
242            * R/ltTMatrix.R: new "minimal methods"
243    
244    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
247            all methods (and help files).
248    
249    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
252                    for case (dimn.  op  no_dimn.)
253    
254    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
255    
256            * DESCRIPTION (Version): 0.99-2  released to CRAN
257    
258    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
259    
260            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
261            by Julian Faraway.
262    
263    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Auxiliaries.R (try_as): new utility
266            * R/sparseMatrix.R: use try_as() in coercion to original class
267    
268    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
271    
272    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Auxiliaries.R (dimNamesCheck): added
275    
276            * R/Matrix.R (as.array), (as.vector): new
277    
278    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
281                    default.
282            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
283                    "pMatrix" now contains "sparseMatrix"
284    
285    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * tests/Class+Meth.R: new tests; t(t(m)) == m
288    
289            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
290    
291            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
292            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
293    
294            * R/dspMatrix.R: typo in "t" method
295    
296    2005-09-18  Douglas Bates  <bates@wisc.edu>
297    
298            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
299            * R/Tsparse.R: instead of R/gTMatrix.R
300            * R/Csparse.R: new
301            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
302            * src/Tsparse.c: new; many trivial methods calling cholmod_()
303            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
304                            via cholmod
305    
306    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/Auxiliaries.R (non0ind): new function using new C code
309            * src/dgCMatrix.c (compressed_non_0_ij): new utility
310    
311    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
312    
313            * src/chm_common.h: header file required by all C sources that
314            call CHOLMOD functions.  It defines a cholmod_common structure
315            called 'c' whose address is passed as the last argument to
316            (virtually) every CHOLMOD function.
317    
318            * src/Pattern.c: Simple example of the use of CHOLMOD.
319    
320            * src/init.c: initialize and finalize the cholmod_common structure.
321    
322            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
323            LDL and CCOLAMD from the U. of Florida sparse matrix library.
324    
325    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * inst/test-tools.R: new file collecting the utility functions used
328                    in ./tests/*.R
329    
330            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
331            * R/Matrix.R (cbind2): methods for NULL and missing
332    
333    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/AllClass.R: new "index" class for "[" and "[<-":
336                    First cut at "symmetricMatrix" and "triangularMatrix"
337            * R/gTMatrix.R (.ind.prep): new function;
338                    Logical and character indexing now work too.
339            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
340            * tests/indexing.R: new, including *.Rout.save
341            * tests/dgTMatrix.R: new
342    
343    2005-08-29  Douglas Bates  <bates@wisc.edu>
344    
345            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
346            indicator pos not being updated.  Also enforced upper triangular
347            for symmetric case.  Need to coerce edges component of elements of
348            edge list - grr! (Why don't they define their classes cleanly?)
349    
350    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/Matrix.R:  added first "[<-" methods; not yet functional
353            * R/denseMatrix.R: dito
354            * man/Subassign-methods.Rd: new help file for these
355    
356    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * DESCRIPTION (Version): 0.98-6
359    
360            * R/denseMatrix.R: new file for "[" fallback methods for all dense
361            matrices.
362    
363    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
366                    as( <logical>, "matrix")
367    
368            * R/pMatrix.R: coercion to "lgTMatrix"
369    
370            * R/gTMatrix.R: new virtual class to define "[" methods for.
371            * man/gTMatrix-class.Rd:
372            * General slight re-organization of where "[" methods are defined.
373              more to come.
374    
375    2005-08-18  Douglas Bates  <bates@wisc.edu>
376    
377            * DESCRIPTION (Version): 0.98-5  released to CRAN
378    
379            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
380            * .....
381    
382    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
383    
384            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
385            or glmer objects.
386    
387    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
390    
391    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
392    
393            * R/HBMM.R: finish re-writing R-only code.
394    
395    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
396    
397            * man/externalFormats.Rd: move documentation for writeHB and
398            writeMM here.
399    
400            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
401            (suggested by Paul Roecker).
402    
403            * tests/validObj.R (assertError): Comment out test that is failing
404            after recent changes in r-devel.
405    
406    
407  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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