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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1312, Thu Jul 6 15:29:56 2006 UTC
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1    2006-07-06  Douglas Bates  <bates@R-project.org>
2    
3            * src/pedigree.c (pedigree_inbreeding): Correction in
4            initialization.  This function is not currently being used and is
5            not fully tested.
6    
7            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
8            Introduced the glmer class.  Added code for mcmcmsamp on glmer
9            objects.  Modified validity check on pedigree objects to account
10            for nonparallel patterns of missingness of parents.
11    
12    2006-06-12  Douglas Bates  <bates@R-project.org>
13    
14            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
15            the output from mcmcsamp.
16    
17    2006-06-10  Douglas Bates  <bates@R-project.org>
18    
19            * R/lmer.R (simulestimate): added C code for calculating the trace
20            of the hat matrix.
21    
22    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
25            classes.
26    
27    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/dgTMatrix.R (colSums): etc. All four of
30            colSums(), rowSums(), colMeans(), rowMeans() now should work for
31            all "Matrices".
32    
33    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/lmer.R (panel.ci): Add a reference line at zero and a
36            background grid to the qqmath plot of ranef.lmer.
37    
38    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
41            grouping factors to be specified in the formula as (1|foo/bar).
42    
43    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/lmer.R (findbars and others): Change check of is.numeric to
46            !is.language to resolve the bug reported by Jacob Wegelin.
47    
48            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
49            code to evaluate inbreeding coefficients without calculating T,
50            based on code in Sargolzaei and Iwaisaki's paper.
51    
52    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
55            generic and mer methods for isNested and denomDF. This denomDF was
56            an attempt to emulate that in lme but I don't think that makes
57            sense.  Use the trace of the hat matrix instead.
58    
59    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
62            the C code depending on a slot structure that's no longer valid.
63            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
64    
65    
66    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
67    
68            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
69            of lowerTriMatrix generic and methods to tril (also upper to triu)
70            and added a general band extractor.
71    
72    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/pedigree.R (pedigree): Replace sire and dam values outside the
75            allowable range with NAs. Added a corresponding check in the
76            validity check for the pedigree class.
77    
78            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
79            crossprod methods now inherits from symmetricMatrix.
80    
81    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
84            generics lowerTriMatrix and upperTriMatrix along with methods for
85            the Csparse virtual class.  Also added a C function Csparse_band
86            that implements these methods by calling cholmod_band.
87    
88    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
91            erased when it was NULL.  This led to invalid subselections!
92    
93    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
94    
95            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
96            in method for "t" so as not to lose the unit diagonal property.
97    
98    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
101            and methods.  This is now an option to the ranef method for the
102            mer class.
103    
104            * src/cs_utils.c: Ensure that the nz component is -1 for a
105            compressed column-oriented matrix.  Minor formatting cleanup.
106    
107            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
108            objects.
109    
110    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
113            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
114    
115    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
118            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
119    
120            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
121            for the dtCMatrix class.
122    
123    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
126            and methods for it.
127    
128    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
131            arguments, such that M %*% 1:6 now works
132            * Tests/matprod.R: test the above
133    
134    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
135    
136            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
137            the ranef.lmer class.
138    
139            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
140            methods to extract the posterior variances from the bVar slot.
141    
142    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
145            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
146    
147            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
148            * tests/simple: (extended)
149    
150            * R/sparseMatrix.R (isTriangular): now using much improved
151            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
152    
153    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
156            (problem report from Franklin Parlamis).  This should be done
157            generally.
158    
159    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
162            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
163            update the plot methods.
164    
165    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
166    
167            * R/lmer.R (resid and ranef methods):  Added methods for the
168            "residuals" and "resid" generic but only for linear mixed model
169            fits.  Changed the ranef method to return a list of data frames so
170            that the plot methods now work.
171    
172    2006-03-16  Douglas Bates  <bates@bates2>
173    
174            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
175            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
176    
177            * DESCRIPTION (Date): New release
178    
179    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
182    
183            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
184            * man/KNex.Rd: and other help files
185            * tests/*.R: several ones needed adaption
186            * inst/doc/Comparisons.Rnw: dito
187    
188    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
191    
192            * tests/indexing.R: tests for new [<- methods for sparse matrices.
193    
194    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
197    
198            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
199    
200    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/dMatrix.R: enable things like  M [ M < 10 ]
203            * R/dgeMatrix.R: implement it
204    
205    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/AllClass.R: define "summary.mer" and "*.lmer"
208            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
209            * R/lmer.R (show): now works with summary()
210    
211    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
214            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
215                    support the above
216    
217    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
218    
219            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
220            Use glmFit$prior.weights for weights in a glmm.
221            Allow an option usePQL = FALSE to skip the PQL steps for the
222            Laplace method (and, in time, the AGQ method).
223    
224            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
225            into a separate function internal_mer_Xfactor to be able to call
226            it from internal_bhat.
227    
228    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * tests/Class+Meth.R (tstMatrixClass): function for much better
231            testing; now again of all actual classes.
232    
233            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
234                    use macros and define make_d_matrix_* and make_i_matrix_*
235                    where _i_ is for the ldense routines:
236    
237            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
238            * src/ldense.c (lsyMatrix_as_lgeMatrix):
239    
240            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
241    
242    
243    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
246                    many different kinds of matrices.
247            * R/*.R: quite a few new methods were needed for R CMD check with
248                    new Matrix().  Very good for users playing around.
249    
250    
251    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * src/dgeMatrix.c (dMatrix_validate): new
254            * src/Mutils.c (dense_nonpacked_validate): new
255    
256            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
257    
258    
259    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
262    
263    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * DESCRIPTION (Version): 0.99-6 released to CRAN
266    
267            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
268            segfault in cases with multiple non-nested grouping factors.
269    
270    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
273                    (Depends): also on 'utils'
274    
275            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
276            * R/diagMatrix.R (Diagonal): constructor and methods for
277            diagonal matrices
278    
279            * R/ltTMatrix.R: new "minimal methods"
280    
281    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
284            all methods (and help files).
285    
286    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
289                    for case (dimn.  op  no_dimn.)
290    
291    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
292    
293            * DESCRIPTION (Version): 0.99-2  released to CRAN
294    
295    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
298            by Julian Faraway.
299    
300    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Auxiliaries.R (try_as): new utility
303            * R/sparseMatrix.R: use try_as() in coercion to original class
304    
305    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
308    
309    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Auxiliaries.R (dimNamesCheck): added
312    
313            * R/Matrix.R (as.array), (as.vector): new
314    
315    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
318                    default.
319            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
320                    "pMatrix" now contains "sparseMatrix"
321    
322    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * tests/Class+Meth.R: new tests; t(t(m)) == m
325    
326            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
327    
328            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
329            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
330    
331            * R/dspMatrix.R: typo in "t" method
332    
333    2005-09-18  Douglas Bates  <bates@wisc.edu>
334    
335            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
336            * R/Tsparse.R: instead of R/gTMatrix.R
337            * R/Csparse.R: new
338            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
339            * src/Tsparse.c: new; many trivial methods calling cholmod_()
340            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
341                            via cholmod
342    
343    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Auxiliaries.R (non0ind): new function using new C code
346            * src/dgCMatrix.c (compressed_non_0_ij): new utility
347    
348    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
349    
350            * src/chm_common.h: header file required by all C sources that
351            call CHOLMOD functions.  It defines a cholmod_common structure
352            called 'c' whose address is passed as the last argument to
353            (virtually) every CHOLMOD function.
354    
355            * src/Pattern.c: Simple example of the use of CHOLMOD.
356    
357            * src/init.c: initialize and finalize the cholmod_common structure.
358    
359            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
360            LDL and CCOLAMD from the U. of Florida sparse matrix library.
361    
362    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * inst/test-tools.R: new file collecting the utility functions used
365                    in ./tests/*.R
366    
367            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
368            * R/Matrix.R (cbind2): methods for NULL and missing
369    
370    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/AllClass.R: new "index" class for "[" and "[<-":
373                    First cut at "symmetricMatrix" and "triangularMatrix"
374            * R/gTMatrix.R (.ind.prep): new function;
375                    Logical and character indexing now work too.
376            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
377            * tests/indexing.R: new, including *.Rout.save
378            * tests/dgTMatrix.R: new
379    
380    2005-08-29  Douglas Bates  <bates@wisc.edu>
381    
382            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
383            indicator pos not being updated.  Also enforced upper triangular
384            for symmetric case.  Need to coerce edges component of elements of
385            edge list - grr! (Why don't they define their classes cleanly?)
386    
387    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/Matrix.R:  added first "[<-" methods; not yet functional
390            * R/denseMatrix.R: dito
391            * man/Subassign-methods.Rd: new help file for these
392    
393    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * DESCRIPTION (Version): 0.98-6
396    
397            * R/denseMatrix.R: new file for "[" fallback methods for all dense
398            matrices.
399    
400    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
403                    as( <logical>, "matrix")
404    
405            * R/pMatrix.R: coercion to "lgTMatrix"
406    
407            * R/gTMatrix.R: new virtual class to define "[" methods for.
408            * man/gTMatrix-class.Rd:
409            * General slight re-organization of where "[" methods are defined.
410              more to come.
411    
412    2005-08-18  Douglas Bates  <bates@wisc.edu>
413    
414            * DESCRIPTION (Version): 0.98-5  released to CRAN
415    
416            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
417            * .....
418    
419    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
420    
421            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
422            or glmer objects.
423    
424    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
427    
428    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
429    
430            * R/HBMM.R: finish re-writing R-only code.
431    
432    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
433    
434            * man/externalFormats.Rd: move documentation for writeHB and
435            writeMM here.
436    
437            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
438            (suggested by Paul Roecker).
439    
440            * tests/validObj.R (assertError): Comment out test that is failing
441            after recent changes in r-devel.
442    
443    
444  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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