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revision 917, Thu Sep 15 18:03:55 2005 UTC revision 1288, Thu Jun 1 20:41:20 2006 UTC
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1    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (panel.ci): Add a reference line at zero and a
4            background grid to the qqmath plot of ranef.lmer.
5    
6    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
9            grouping factors to be specified in the formula as (1|foo/bar).
10    
11    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/lmer.R (findbars and others): Change check of is.numeric to
14            !is.language to resolve the bug reported by Jacob Wegelin.
15    
16            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
17            code to evaluate inbreeding coefficients without calculating T,
18            based on code in Sargolzaei and Iwaisaki's paper.
19    
20    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
23            generic and mer methods for isNested and denomDF. This denomDF was
24            an attempt to emulate that in lme but I don't think that makes
25            sense.  Use the trace of the hat matrix instead.
26    
27    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
30            the C code depending on a slot structure that's no longer valid.
31            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
32    
33    
34    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
35    
36            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
37            of lowerTriMatrix generic and methods to tril (also upper to triu)
38            and added a general band extractor.
39    
40    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * R/pedigree.R (pedigree): Replace sire and dam values outside the
43            allowable range with NAs. Added a corresponding check in the
44            validity check for the pedigree class.
45    
46            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
47            crossprod methods now inherits from symmetricMatrix.
48    
49    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
50    
51            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
52            generics lowerTriMatrix and upperTriMatrix along with methods for
53            the Csparse virtual class.  Also added a C function Csparse_band
54            that implements these methods by calling cholmod_band.
55    
56    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
59            erased when it was NULL.  This led to invalid subselections!
60    
61    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
64            in method for "t" so as not to lose the unit diagonal property.
65    
66    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
69            and methods.  This is now an option to the ranef method for the
70            mer class.
71    
72            * src/cs_utils.c: Ensure that the nz component is -1 for a
73            compressed column-oriented matrix.  Minor formatting cleanup.
74    
75            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
76            objects.
77    
78    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
81            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
82    
83    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
86            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
87    
88            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
89            for the dtCMatrix class.
90    
91    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
94            and methods for it.
95    
96    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
99            arguments, such that M %*% 1:6 now works
100            * Tests/matprod.R: test the above
101    
102    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
105            the ranef.lmer class.
106    
107            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
108            methods to extract the posterior variances from the bVar slot.
109    
110    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
113            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
114    
115            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
116            * tests/simple: (extended)
117    
118            * R/sparseMatrix.R (isTriangular): now using much improved
119            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
120    
121    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
124            (problem report from Franklin Parlamis).  This should be done
125            generally.
126    
127    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
130            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
131            update the plot methods.
132    
133    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
134    
135            * R/lmer.R (resid and ranef methods):  Added methods for the
136            "residuals" and "resid" generic but only for linear mixed model
137            fits.  Changed the ranef method to return a list of data frames so
138            that the plot methods now work.
139    
140    2006-03-16  Douglas Bates  <bates@bates2>
141    
142            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
143            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
144    
145            * DESCRIPTION (Date): New release
146    
147    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
150    
151            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
152            * man/KNex.Rd: and other help files
153            * tests/*.R: several ones needed adaption
154            * inst/doc/Comparisons.Rnw: dito
155    
156    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
159    
160            * tests/indexing.R: tests for new [<- methods for sparse matrices.
161    
162    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
165    
166            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
167    
168    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/dMatrix.R: enable things like  M [ M < 10 ]
171            * R/dgeMatrix.R: implement it
172    
173    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/AllClass.R: define "summary.mer" and "*.lmer"
176            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
177            * R/lmer.R (show): now works with summary()
178    
179    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
182            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
183                    support the above
184    
185    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
186    
187            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
188            Use glmFit$prior.weights for weights in a glmm.
189            Allow an option usePQL = FALSE to skip the PQL steps for the
190            Laplace method (and, in time, the AGQ method).
191    
192            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
193            into a separate function internal_mer_Xfactor to be able to call
194            it from internal_bhat.
195    
196    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * tests/Class+Meth.R (tstMatrixClass): function for much better
199            testing; now again of all actual classes.
200    
201            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
202                    use macros and define make_d_matrix_* and make_i_matrix_*
203                    where _i_ is for the ldense routines:
204    
205            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
206            * src/ldense.c (lsyMatrix_as_lgeMatrix):
207    
208            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
209    
210    
211    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
214                    many different kinds of matrices.
215            * R/*.R: quite a few new methods were needed for R CMD check with
216                    new Matrix().  Very good for users playing around.
217    
218    
219    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * src/dgeMatrix.c (dMatrix_validate): new
222            * src/Mutils.c (dense_nonpacked_validate): new
223    
224            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
225    
226    
227    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
230    
231    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
232    
233            * DESCRIPTION (Version): 0.99-6 released to CRAN
234    
235            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
236            segfault in cases with multiple non-nested grouping factors.
237    
238    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
241                    (Depends): also on 'utils'
242    
243            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
244            * R/diagMatrix.R (Diagonal): constructor and methods for
245            diagonal matrices
246    
247            * R/ltTMatrix.R: new "minimal methods"
248    
249    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
252            all methods (and help files).
253    
254    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
257                    for case (dimn.  op  no_dimn.)
258    
259    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * DESCRIPTION (Version): 0.99-2  released to CRAN
262    
263    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
266            by Julian Faraway.
267    
268    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Auxiliaries.R (try_as): new utility
271            * R/sparseMatrix.R: use try_as() in coercion to original class
272    
273    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
276    
277    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Auxiliaries.R (dimNamesCheck): added
280    
281            * R/Matrix.R (as.array), (as.vector): new
282    
283    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
286                    default.
287            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
288                    "pMatrix" now contains "sparseMatrix"
289    
290    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * tests/Class+Meth.R: new tests; t(t(m)) == m
293    
294            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
295    
296            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
297            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
298    
299            * R/dspMatrix.R: typo in "t" method
300    
301    2005-09-18  Douglas Bates  <bates@wisc.edu>
302    
303            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
304            * R/Tsparse.R: instead of R/gTMatrix.R
305            * R/Csparse.R: new
306            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
307            * src/Tsparse.c: new; many trivial methods calling cholmod_()
308            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
309                            via cholmod
310    
311    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Auxiliaries.R (non0ind): new function using new C code
314            * src/dgCMatrix.c (compressed_non_0_ij): new utility
315    
316  2005-09-15  Douglas Bates  <bates@localhost.localdomain>  2005-09-15  Douglas Bates  <bates@localhost.localdomain>
317    
318          * src/chm_common.h: header file required by all C sources that          * src/chm_common.h: header file required by all C sources that

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