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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1313, Thu Jul 6 17:24:01 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            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
13            class.
14    
15    2006-06-12  Douglas Bates  <bates@R-project.org>
16    
17            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
18            the output from mcmcsamp.
19    
20    2006-06-10  Douglas Bates  <bates@R-project.org>
21    
22            * R/lmer.R (simulestimate): added C code for calculating the trace
23            of the hat matrix.
24    
25    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
28            classes.
29    
30    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgTMatrix.R (colSums): etc. All four of
33            colSums(), rowSums(), colMeans(), rowMeans() now should work for
34            all "Matrices".
35    
36    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
37    
38            * R/lmer.R (panel.ci): Add a reference line at zero and a
39            background grid to the qqmath plot of ranef.lmer.
40    
41    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
42    
43            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
44            grouping factors to be specified in the formula as (1|foo/bar).
45    
46    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
47    
48            * R/lmer.R (findbars and others): Change check of is.numeric to
49            !is.language to resolve the bug reported by Jacob Wegelin.
50    
51            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
52            code to evaluate inbreeding coefficients without calculating T,
53            based on code in Sargolzaei and Iwaisaki's paper.
54    
55    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
58            generic and mer methods for isNested and denomDF. This denomDF was
59            an attempt to emulate that in lme but I don't think that makes
60            sense.  Use the trace of the hat matrix instead.
61    
62    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
65            the C code depending on a slot structure that's no longer valid.
66            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
67    
68    
69    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
70    
71            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
72            of lowerTriMatrix generic and methods to tril (also upper to triu)
73            and added a general band extractor.
74    
75    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
76    
77            * R/pedigree.R (pedigree): Replace sire and dam values outside the
78            allowable range with NAs. Added a corresponding check in the
79            validity check for the pedigree class.
80    
81            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
82            crossprod methods now inherits from symmetricMatrix.
83    
84    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
85    
86            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
87            generics lowerTriMatrix and upperTriMatrix along with methods for
88            the Csparse virtual class.  Also added a C function Csparse_band
89            that implements these methods by calling cholmod_band.
90    
91    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
94            erased when it was NULL.  This led to invalid subselections!
95    
96    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
97    
98            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
99            in method for "t" so as not to lose the unit diagonal property.
100    
101    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
102    
103            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
104            and methods.  This is now an option to the ranef method for the
105            mer class.
106    
107            * src/cs_utils.c: Ensure that the nz component is -1 for a
108            compressed column-oriented matrix.  Minor formatting cleanup.
109    
110            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
111            objects.
112    
113    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
116            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
117    
118    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
121            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
122    
123            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
124            for the dtCMatrix class.
125    
126    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
127    
128            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
129            and methods for it.
130    
131    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
134            arguments, such that M %*% 1:6 now works
135            * Tests/matprod.R: test the above
136    
137    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
140            the ranef.lmer class.
141    
142            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
143            methods to extract the posterior variances from the bVar slot.
144    
145    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
148            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
149    
150            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
151            * tests/simple: (extended)
152    
153            * R/sparseMatrix.R (isTriangular): now using much improved
154            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
155    
156    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
157    
158            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
159            (problem report from Franklin Parlamis).  This should be done
160            generally.
161    
162    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
165            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
166            update the plot methods.
167    
168    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/lmer.R (resid and ranef methods):  Added methods for the
171            "residuals" and "resid" generic but only for linear mixed model
172            fits.  Changed the ranef method to return a list of data frames so
173            that the plot methods now work.
174    
175    2006-03-16  Douglas Bates  <bates@bates2>
176    
177            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
178            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
179    
180            * DESCRIPTION (Date): New release
181    
182    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
185    
186            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
187            * man/KNex.Rd: and other help files
188            * tests/*.R: several ones needed adaption
189            * inst/doc/Comparisons.Rnw: dito
190    
191    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
194    
195            * tests/indexing.R: tests for new [<- methods for sparse matrices.
196    
197    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
200    
201            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
202    
203    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/dMatrix.R: enable things like  M [ M < 10 ]
206            * R/dgeMatrix.R: implement it
207    
208    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/AllClass.R: define "summary.mer" and "*.lmer"
211            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
212            * R/lmer.R (show): now works with summary()
213    
214    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
217            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
218                    support the above
219    
220    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
221    
222            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
223            Use glmFit$prior.weights for weights in a glmm.
224            Allow an option usePQL = FALSE to skip the PQL steps for the
225            Laplace method (and, in time, the AGQ method).
226    
227            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
228            into a separate function internal_mer_Xfactor to be able to call
229            it from internal_bhat.
230    
231    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * tests/Class+Meth.R (tstMatrixClass): function for much better
234            testing; now again of all actual classes.
235    
236            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
237                    use macros and define make_d_matrix_* and make_i_matrix_*
238                    where _i_ is for the ldense routines:
239    
240            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
241            * src/ldense.c (lsyMatrix_as_lgeMatrix):
242    
243            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
244    
245    
246    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
249                    many different kinds of matrices.
250            * R/*.R: quite a few new methods were needed for R CMD check with
251                    new Matrix().  Very good for users playing around.
252    
253    
254    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * src/dgeMatrix.c (dMatrix_validate): new
257            * src/Mutils.c (dense_nonpacked_validate): new
258    
259            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
260    
261    
262    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
265    
266    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
267    
268            * DESCRIPTION (Version): 0.99-6 released to CRAN
269    
270            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
271            segfault in cases with multiple non-nested grouping factors.
272    
273    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
276                    (Depends): also on 'utils'
277    
278            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
279            * R/diagMatrix.R (Diagonal): constructor and methods for
280            diagonal matrices
281    
282            * R/ltTMatrix.R: new "minimal methods"
283    
284    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
287            all methods (and help files).
288    
289    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
292                    for case (dimn.  op  no_dimn.)
293    
294    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
295    
296            * DESCRIPTION (Version): 0.99-2  released to CRAN
297    
298    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
299    
300            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
301            by Julian Faraway.
302    
303    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/Auxiliaries.R (try_as): new utility
306            * R/sparseMatrix.R: use try_as() in coercion to original class
307    
308    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
311    
312    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (dimNamesCheck): added
315    
316            * R/Matrix.R (as.array), (as.vector): new
317    
318    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
321                    default.
322            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
323                    "pMatrix" now contains "sparseMatrix"
324    
325    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * tests/Class+Meth.R: new tests; t(t(m)) == m
328    
329            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
330    
331            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
332            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
333    
334            * R/dspMatrix.R: typo in "t" method
335    
336    2005-09-18  Douglas Bates  <bates@wisc.edu>
337    
338            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
339            * R/Tsparse.R: instead of R/gTMatrix.R
340            * R/Csparse.R: new
341            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
342            * src/Tsparse.c: new; many trivial methods calling cholmod_()
343            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
344                            via cholmod
345    
346    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Auxiliaries.R (non0ind): new function using new C code
349            * src/dgCMatrix.c (compressed_non_0_ij): new utility
350    
351    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
352    
353            * src/chm_common.h: header file required by all C sources that
354            call CHOLMOD functions.  It defines a cholmod_common structure
355            called 'c' whose address is passed as the last argument to
356            (virtually) every CHOLMOD function.
357    
358            * src/Pattern.c: Simple example of the use of CHOLMOD.
359    
360            * src/init.c: initialize and finalize the cholmod_common structure.
361    
362            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
363            LDL and CCOLAMD from the U. of Florida sparse matrix library.
364    
365    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * inst/test-tools.R: new file collecting the utility functions used
368                    in ./tests/*.R
369    
370            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
371            * R/Matrix.R (cbind2): methods for NULL and missing
372    
373    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/AllClass.R: new "index" class for "[" and "[<-":
376                    First cut at "symmetricMatrix" and "triangularMatrix"
377            * R/gTMatrix.R (.ind.prep): new function;
378                    Logical and character indexing now work too.
379            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
380            * tests/indexing.R: new, including *.Rout.save
381            * tests/dgTMatrix.R: new
382    
383    2005-08-29  Douglas Bates  <bates@wisc.edu>
384    
385            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
386            indicator pos not being updated.  Also enforced upper triangular
387            for symmetric case.  Need to coerce edges component of elements of
388            edge list - grr! (Why don't they define their classes cleanly?)
389    
390    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R:  added first "[<-" methods; not yet functional
393            * R/denseMatrix.R: dito
394            * man/Subassign-methods.Rd: new help file for these
395    
396    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * DESCRIPTION (Version): 0.98-6
399    
400            * R/denseMatrix.R: new file for "[" fallback methods for all dense
401            matrices.
402    
403    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
406                    as( <logical>, "matrix")
407    
408            * R/pMatrix.R: coercion to "lgTMatrix"
409    
410            * R/gTMatrix.R: new virtual class to define "[" methods for.
411            * man/gTMatrix-class.Rd:
412            * General slight re-organization of where "[" methods are defined.
413              more to come.
414    
415    2005-08-18  Douglas Bates  <bates@wisc.edu>
416    
417            * DESCRIPTION (Version): 0.98-5  released to CRAN
418    
419            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
420            * .....
421    
422    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
423    
424            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
425            or glmer objects.
426    
427    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
430    
431    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
432    
433            * R/HBMM.R: finish re-writing R-only code.
434    
435    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
436    
437            * man/externalFormats.Rd: move documentation for writeHB and
438            writeMM here.
439    
440            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
441            (suggested by Paul Roecker).
442    
443            * tests/validObj.R (assertError): Comment out test that is failing
444            after recent changes in r-devel.
445    
446    
447  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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