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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1284, Sat May 27 20:01:11 2006 UTC
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1    2006-05-27  Douglas Bates  <bates@.stat.wisc.edu>
2    
3            * R/lmer.R (findbars and others): Change check of is.numeric to
4            !is.language to resolve the bug reported by Jacob Wegelin.
5    
6            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
7            code to evaluate inbreeding coefficients without calculating T,
8            based on code in Sargolzaei and Iwaisaki's paper.
9    
10    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
13            generic and mer methods for isNested and denomDF. This denomDF was
14            an attempt to emulate that in lme but I don't think that makes
15            sense.  Use the trace of the hat matrix instead.
16    
17    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
20            the C code depending on a slot structure that's no longer valid.
21            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
22    
23    
24    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
25    
26            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
27            of lowerTriMatrix generic and methods to tril (also upper to triu)
28            and added a general band extractor.
29    
30    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * R/pedigree.R (pedigree): Replace sire and dam values outside the
33            allowable range with NAs. Added a corresponding check in the
34            validity check for the pedigree class.
35    
36            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
37            crossprod methods now inherits from symmetricMatrix.
38    
39    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
40    
41            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
42            generics lowerTriMatrix and upperTriMatrix along with methods for
43            the Csparse virtual class.  Also added a C function Csparse_band
44            that implements these methods by calling cholmod_band.
45    
46    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
49            erased when it was NULL.  This led to invalid subselections!
50    
51    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
54            in method for "t" so as not to lose the unit diagonal property.
55    
56    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
59            and methods.  This is now an option to the ranef method for the
60            mer class.
61    
62            * src/cs_utils.c: Ensure that the nz component is -1 for a
63            compressed column-oriented matrix.  Minor formatting cleanup.
64    
65            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
66            objects.
67    
68    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
71            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
72    
73    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
76            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
77    
78            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
79            for the dtCMatrix class.
80    
81    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
84            and methods for it.
85    
86    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
89            arguments, such that M %*% 1:6 now works
90            * Tests/matprod.R: test the above
91    
92    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
95            the ranef.lmer class.
96    
97            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
98            methods to extract the posterior variances from the bVar slot.
99    
100    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
103            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
104    
105            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
106            * tests/simple: (extended)
107    
108            * R/sparseMatrix.R (isTriangular): now using much improved
109            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
110    
111    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
112    
113            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
114            (problem report from Franklin Parlamis).  This should be done
115            generally.
116    
117    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
120            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
121            update the plot methods.
122    
123    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/lmer.R (resid and ranef methods):  Added methods for the
126            "residuals" and "resid" generic but only for linear mixed model
127            fits.  Changed the ranef method to return a list of data frames so
128            that the plot methods now work.
129    
130    2006-03-16  Douglas Bates  <bates@bates2>
131    
132            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
133            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
134    
135            * DESCRIPTION (Date): New release
136    
137    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
140    
141            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
142            * man/KNex.Rd: and other help files
143            * tests/*.R: several ones needed adaption
144            * inst/doc/Comparisons.Rnw: dito
145    
146    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
149    
150            * tests/indexing.R: tests for new [<- methods for sparse matrices.
151    
152    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
155    
156            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
157    
158    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/dMatrix.R: enable things like  M [ M < 10 ]
161            * R/dgeMatrix.R: implement it
162    
163    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/AllClass.R: define "summary.mer" and "*.lmer"
166            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
167            * R/lmer.R (show): now works with summary()
168    
169    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
172            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
173                    support the above
174    
175    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
176    
177            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
178            Use glmFit$prior.weights for weights in a glmm.
179            Allow an option usePQL = FALSE to skip the PQL steps for the
180            Laplace method (and, in time, the AGQ method).
181    
182            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
183            into a separate function internal_mer_Xfactor to be able to call
184            it from internal_bhat.
185    
186    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * tests/Class+Meth.R (tstMatrixClass): function for much better
189            testing; now again of all actual classes.
190    
191            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
192                    use macros and define make_d_matrix_* and make_i_matrix_*
193                    where _i_ is for the ldense routines:
194    
195            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
196            * src/ldense.c (lsyMatrix_as_lgeMatrix):
197    
198            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
199    
200    
201    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
204                    many different kinds of matrices.
205            * R/*.R: quite a few new methods were needed for R CMD check with
206                    new Matrix().  Very good for users playing around.
207    
208    
209    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * src/dgeMatrix.c (dMatrix_validate): new
212            * src/Mutils.c (dense_nonpacked_validate): new
213    
214            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
215    
216    
217    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
218    
219            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
220    
221    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
222    
223            * DESCRIPTION (Version): 0.99-6 released to CRAN
224    
225            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
226            segfault in cases with multiple non-nested grouping factors.
227    
228    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
231                    (Depends): also on 'utils'
232    
233            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
234            * R/diagMatrix.R (Diagonal): constructor and methods for
235            diagonal matrices
236    
237            * R/ltTMatrix.R: new "minimal methods"
238    
239    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
242            all methods (and help files).
243    
244    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
247                    for case (dimn.  op  no_dimn.)
248    
249    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
250    
251            * DESCRIPTION (Version): 0.99-2  released to CRAN
252    
253    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
254    
255            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
256            by Julian Faraway.
257    
258    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Auxiliaries.R (try_as): new utility
261            * R/sparseMatrix.R: use try_as() in coercion to original class
262    
263    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
266    
267    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Auxiliaries.R (dimNamesCheck): added
270    
271            * R/Matrix.R (as.array), (as.vector): new
272    
273    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
276                    default.
277            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
278                    "pMatrix" now contains "sparseMatrix"
279    
280    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * tests/Class+Meth.R: new tests; t(t(m)) == m
283    
284            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
285    
286            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
287            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
288    
289            * R/dspMatrix.R: typo in "t" method
290    
291    2005-09-18  Douglas Bates  <bates@wisc.edu>
292    
293            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
294            * R/Tsparse.R: instead of R/gTMatrix.R
295            * R/Csparse.R: new
296            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
297            * src/Tsparse.c: new; many trivial methods calling cholmod_()
298            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
299                            via cholmod
300    
301    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/Auxiliaries.R (non0ind): new function using new C code
304            * src/dgCMatrix.c (compressed_non_0_ij): new utility
305    
306    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
307    
308            * src/chm_common.h: header file required by all C sources that
309            call CHOLMOD functions.  It defines a cholmod_common structure
310            called 'c' whose address is passed as the last argument to
311            (virtually) every CHOLMOD function.
312    
313            * src/Pattern.c: Simple example of the use of CHOLMOD.
314    
315            * src/init.c: initialize and finalize the cholmod_common structure.
316    
317            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
318            LDL and CCOLAMD from the U. of Florida sparse matrix library.
319    
320    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * inst/test-tools.R: new file collecting the utility functions used
323                    in ./tests/*.R
324    
325            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
326            * R/Matrix.R (cbind2): methods for NULL and missing
327    
328    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/AllClass.R: new "index" class for "[" and "[<-":
331                    First cut at "symmetricMatrix" and "triangularMatrix"
332            * R/gTMatrix.R (.ind.prep): new function;
333                    Logical and character indexing now work too.
334            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
335            * tests/indexing.R: new, including *.Rout.save
336            * tests/dgTMatrix.R: new
337    
338    2005-08-29  Douglas Bates  <bates@wisc.edu>
339    
340            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
341            indicator pos not being updated.  Also enforced upper triangular
342            for symmetric case.  Need to coerce edges component of elements of
343            edge list - grr! (Why don't they define their classes cleanly?)
344    
345    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Matrix.R:  added first "[<-" methods; not yet functional
348            * R/denseMatrix.R: dito
349            * man/Subassign-methods.Rd: new help file for these
350    
351    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * DESCRIPTION (Version): 0.98-6
354    
355            * R/denseMatrix.R: new file for "[" fallback methods for all dense
356            matrices.
357    
358    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
361                    as( <logical>, "matrix")
362    
363            * R/pMatrix.R: coercion to "lgTMatrix"
364    
365            * R/gTMatrix.R: new virtual class to define "[" methods for.
366            * man/gTMatrix-class.Rd:
367            * General slight re-organization of where "[" methods are defined.
368              more to come.
369    
370    2005-08-18  Douglas Bates  <bates@wisc.edu>
371    
372            * DESCRIPTION (Version): 0.98-5  released to CRAN
373    
374            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
375            * .....
376    
377    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
378    
379            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
380            or glmer objects.
381    
382    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
385    
386    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
387    
388            * R/HBMM.R: finish re-writing R-only code.
389    
390    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
391    
392            * man/externalFormats.Rd: move documentation for writeHB and
393            writeMM here.
394    
395            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
396            (suggested by Paul Roecker).
397    
398            * tests/validObj.R (assertError): Comment out test that is failing
399            after recent changes in r-devel.
400    
401    
402  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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