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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1290, Thu Jun 8 09:30:21 2006 UTC
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1    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgTMatrix.R (colSums): etc. All four of
4            colSums(), rowSums(), colMeans(), rowMeans() now should work for
5            all "Matrices".
6    
7    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/lmer.R (panel.ci): Add a reference line at zero and a
10            background grid to the qqmath plot of ranef.lmer.
11    
12    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
15            grouping factors to be specified in the formula as (1|foo/bar).
16    
17    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * R/lmer.R (findbars and others): Change check of is.numeric to
20            !is.language to resolve the bug reported by Jacob Wegelin.
21    
22            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
23            code to evaluate inbreeding coefficients without calculating T,
24            based on code in Sargolzaei and Iwaisaki's paper.
25    
26    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
29            generic and mer methods for isNested and denomDF. This denomDF was
30            an attempt to emulate that in lme but I don't think that makes
31            sense.  Use the trace of the hat matrix instead.
32    
33    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
36            the C code depending on a slot structure that's no longer valid.
37            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
38    
39    
40    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
41    
42            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
43            of lowerTriMatrix generic and methods to tril (also upper to triu)
44            and added a general band extractor.
45    
46    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
47    
48            * R/pedigree.R (pedigree): Replace sire and dam values outside the
49            allowable range with NAs. Added a corresponding check in the
50            validity check for the pedigree class.
51    
52            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
53            crossprod methods now inherits from symmetricMatrix.
54    
55    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
58            generics lowerTriMatrix and upperTriMatrix along with methods for
59            the Csparse virtual class.  Also added a C function Csparse_band
60            that implements these methods by calling cholmod_band.
61    
62    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
65            erased when it was NULL.  This led to invalid subselections!
66    
67    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
68    
69            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
70            in method for "t" so as not to lose the unit diagonal property.
71    
72    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
75            and methods.  This is now an option to the ranef method for the
76            mer class.
77    
78            * src/cs_utils.c: Ensure that the nz component is -1 for a
79            compressed column-oriented matrix.  Minor formatting cleanup.
80    
81            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
82            objects.
83    
84    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
87            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
88    
89    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
90    
91            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
92            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
93    
94            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
95            for the dtCMatrix class.
96    
97    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
100            and methods for it.
101    
102    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
105            arguments, such that M %*% 1:6 now works
106            * Tests/matprod.R: test the above
107    
108    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
111            the ranef.lmer class.
112    
113            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
114            methods to extract the posterior variances from the bVar slot.
115    
116    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
119            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
120    
121            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
122            * tests/simple: (extended)
123    
124            * R/sparseMatrix.R (isTriangular): now using much improved
125            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
126    
127    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
130            (problem report from Franklin Parlamis).  This should be done
131            generally.
132    
133    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
134    
135            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
136            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
137            update the plot methods.
138    
139    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
140    
141            * R/lmer.R (resid and ranef methods):  Added methods for the
142            "residuals" and "resid" generic but only for linear mixed model
143            fits.  Changed the ranef method to return a list of data frames so
144            that the plot methods now work.
145    
146    2006-03-16  Douglas Bates  <bates@bates2>
147    
148            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
149            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
150    
151            * DESCRIPTION (Date): New release
152    
153    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
156    
157            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
158            * man/KNex.Rd: and other help files
159            * tests/*.R: several ones needed adaption
160            * inst/doc/Comparisons.Rnw: dito
161    
162    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
165    
166            * tests/indexing.R: tests for new [<- methods for sparse matrices.
167    
168    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
171    
172            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
173    
174    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dMatrix.R: enable things like  M [ M < 10 ]
177            * R/dgeMatrix.R: implement it
178    
179    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/AllClass.R: define "summary.mer" and "*.lmer"
182            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
183            * R/lmer.R (show): now works with summary()
184    
185    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
188            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
189                    support the above
190    
191    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
192    
193            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
194            Use glmFit$prior.weights for weights in a glmm.
195            Allow an option usePQL = FALSE to skip the PQL steps for the
196            Laplace method (and, in time, the AGQ method).
197    
198            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
199            into a separate function internal_mer_Xfactor to be able to call
200            it from internal_bhat.
201    
202    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * tests/Class+Meth.R (tstMatrixClass): function for much better
205            testing; now again of all actual classes.
206    
207            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
208                    use macros and define make_d_matrix_* and make_i_matrix_*
209                    where _i_ is for the ldense routines:
210    
211            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
212            * src/ldense.c (lsyMatrix_as_lgeMatrix):
213    
214            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
215    
216    
217    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
220                    many different kinds of matrices.
221            * R/*.R: quite a few new methods were needed for R CMD check with
222                    new Matrix().  Very good for users playing around.
223    
224    
225    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/dgeMatrix.c (dMatrix_validate): new
228            * src/Mutils.c (dense_nonpacked_validate): new
229    
230            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
231    
232    
233    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
234    
235            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
236    
237    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * DESCRIPTION (Version): 0.99-6 released to CRAN
240    
241            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
242            segfault in cases with multiple non-nested grouping factors.
243    
244    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
247                    (Depends): also on 'utils'
248    
249            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
250            * R/diagMatrix.R (Diagonal): constructor and methods for
251            diagonal matrices
252    
253            * R/ltTMatrix.R: new "minimal methods"
254    
255    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
258            all methods (and help files).
259    
260    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
263                    for case (dimn.  op  no_dimn.)
264    
265    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
266    
267            * DESCRIPTION (Version): 0.99-2  released to CRAN
268    
269    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
270    
271            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
272            by Julian Faraway.
273    
274    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Auxiliaries.R (try_as): new utility
277            * R/sparseMatrix.R: use try_as() in coercion to original class
278    
279    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
282    
283    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Auxiliaries.R (dimNamesCheck): added
286    
287            * R/Matrix.R (as.array), (as.vector): new
288    
289    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
292                    default.
293            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
294                    "pMatrix" now contains "sparseMatrix"
295    
296    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * tests/Class+Meth.R: new tests; t(t(m)) == m
299    
300            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
301    
302            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
303            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
304    
305            * R/dspMatrix.R: typo in "t" method
306    
307    2005-09-18  Douglas Bates  <bates@wisc.edu>
308    
309            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
310            * R/Tsparse.R: instead of R/gTMatrix.R
311            * R/Csparse.R: new
312            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
313            * src/Tsparse.c: new; many trivial methods calling cholmod_()
314            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
315                            via cholmod
316    
317    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Auxiliaries.R (non0ind): new function using new C code
320            * src/dgCMatrix.c (compressed_non_0_ij): new utility
321    
322    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
323    
324            * src/chm_common.h: header file required by all C sources that
325            call CHOLMOD functions.  It defines a cholmod_common structure
326            called 'c' whose address is passed as the last argument to
327            (virtually) every CHOLMOD function.
328    
329            * src/Pattern.c: Simple example of the use of CHOLMOD.
330    
331            * src/init.c: initialize and finalize the cholmod_common structure.
332    
333            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
334            LDL and CCOLAMD from the U. of Florida sparse matrix library.
335    
336    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * inst/test-tools.R: new file collecting the utility functions used
339                    in ./tests/*.R
340    
341            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
342            * R/Matrix.R (cbind2): methods for NULL and missing
343    
344    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/AllClass.R: new "index" class for "[" and "[<-":
347                    First cut at "symmetricMatrix" and "triangularMatrix"
348            * R/gTMatrix.R (.ind.prep): new function;
349                    Logical and character indexing now work too.
350            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
351            * tests/indexing.R: new, including *.Rout.save
352            * tests/dgTMatrix.R: new
353    
354    2005-08-29  Douglas Bates  <bates@wisc.edu>
355    
356            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
357            indicator pos not being updated.  Also enforced upper triangular
358            for symmetric case.  Need to coerce edges component of elements of
359            edge list - grr! (Why don't they define their classes cleanly?)
360    
361    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Matrix.R:  added first "[<-" methods; not yet functional
364            * R/denseMatrix.R: dito
365            * man/Subassign-methods.Rd: new help file for these
366    
367    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * DESCRIPTION (Version): 0.98-6
370    
371            * R/denseMatrix.R: new file for "[" fallback methods for all dense
372            matrices.
373    
374    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
377                    as( <logical>, "matrix")
378    
379            * R/pMatrix.R: coercion to "lgTMatrix"
380    
381            * R/gTMatrix.R: new virtual class to define "[" methods for.
382            * man/gTMatrix-class.Rd:
383            * General slight re-organization of where "[" methods are defined.
384              more to come.
385    
386    2005-08-18  Douglas Bates  <bates@wisc.edu>
387    
388            * DESCRIPTION (Version): 0.98-5  released to CRAN
389    
390            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
391            * .....
392    
393    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
394    
395            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
396            or glmer objects.
397    
398    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
401    
402    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
403    
404            * R/HBMM.R: finish re-writing R-only code.
405    
406    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
407    
408            * man/externalFormats.Rd: move documentation for writeHB and
409            writeMM here.
410    
411            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
412            (suggested by Paul Roecker).
413    
414            * tests/validObj.R (assertError): Comment out test that is failing
415            after recent changes in r-devel.
416    
417    
418  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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