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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1300, Mon Jun 12 10:52:01 2006 UTC
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1    2006-06-12  Douglas Bates  <bates@R-project.org>
2    
3            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
4            the output from mcmcsamp.
5    
6    2006-06-10  Douglas Bates  <bates@R-project.org>
7    
8            * R/lmer.R (simulestimate): added C code for calculating the trace
9            of the hat matrix.
10    
11    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
14            classes.
15    
16    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/dgTMatrix.R (colSums): etc. All four of
19            colSums(), rowSums(), colMeans(), rowMeans() now should work for
20            all "Matrices".
21    
22    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * R/lmer.R (panel.ci): Add a reference line at zero and a
25            background grid to the qqmath plot of ranef.lmer.
26    
27    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
28    
29            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
30            grouping factors to be specified in the formula as (1|foo/bar).
31    
32    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
33    
34            * R/lmer.R (findbars and others): Change check of is.numeric to
35            !is.language to resolve the bug reported by Jacob Wegelin.
36    
37            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
38            code to evaluate inbreeding coefficients without calculating T,
39            based on code in Sargolzaei and Iwaisaki's paper.
40    
41    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
42    
43            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
44            generic and mer methods for isNested and denomDF. This denomDF was
45            an attempt to emulate that in lme but I don't think that makes
46            sense.  Use the trace of the hat matrix instead.
47    
48    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
51            the C code depending on a slot structure that's no longer valid.
52            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
53    
54    
55    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
56    
57            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
58            of lowerTriMatrix generic and methods to tril (also upper to triu)
59            and added a general band extractor.
60    
61    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/pedigree.R (pedigree): Replace sire and dam values outside the
64            allowable range with NAs. Added a corresponding check in the
65            validity check for the pedigree class.
66    
67            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
68            crossprod methods now inherits from symmetricMatrix.
69    
70    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
71    
72            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
73            generics lowerTriMatrix and upperTriMatrix along with methods for
74            the Csparse virtual class.  Also added a C function Csparse_band
75            that implements these methods by calling cholmod_band.
76    
77    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
80            erased when it was NULL.  This led to invalid subselections!
81    
82    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
83    
84            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
85            in method for "t" so as not to lose the unit diagonal property.
86    
87    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
88    
89            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
90            and methods.  This is now an option to the ranef method for the
91            mer class.
92    
93            * src/cs_utils.c: Ensure that the nz component is -1 for a
94            compressed column-oriented matrix.  Minor formatting cleanup.
95    
96            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
97            objects.
98    
99    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
102            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
103    
104    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
105    
106            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
107            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
108    
109            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
110            for the dtCMatrix class.
111    
112    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
113    
114            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
115            and methods for it.
116    
117    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
120            arguments, such that M %*% 1:6 now works
121            * Tests/matprod.R: test the above
122    
123    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
126            the ranef.lmer class.
127    
128            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
129            methods to extract the posterior variances from the bVar slot.
130    
131    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
134            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
135    
136            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
137            * tests/simple: (extended)
138    
139            * R/sparseMatrix.R (isTriangular): now using much improved
140            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
141    
142    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
143    
144            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
145            (problem report from Franklin Parlamis).  This should be done
146            generally.
147    
148    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
151            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
152            update the plot methods.
153    
154    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
155    
156            * R/lmer.R (resid and ranef methods):  Added methods for the
157            "residuals" and "resid" generic but only for linear mixed model
158            fits.  Changed the ranef method to return a list of data frames so
159            that the plot methods now work.
160    
161    2006-03-16  Douglas Bates  <bates@bates2>
162    
163            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
164            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
165    
166            * DESCRIPTION (Date): New release
167    
168    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
171    
172            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
173            * man/KNex.Rd: and other help files
174            * tests/*.R: several ones needed adaption
175            * inst/doc/Comparisons.Rnw: dito
176    
177    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
180    
181            * tests/indexing.R: tests for new [<- methods for sparse matrices.
182    
183    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
186    
187            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
188    
189    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/dMatrix.R: enable things like  M [ M < 10 ]
192            * R/dgeMatrix.R: implement it
193    
194    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/AllClass.R: define "summary.mer" and "*.lmer"
197            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
198            * R/lmer.R (show): now works with summary()
199    
200    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
203            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
204                    support the above
205    
206    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
209            Use glmFit$prior.weights for weights in a glmm.
210            Allow an option usePQL = FALSE to skip the PQL steps for the
211            Laplace method (and, in time, the AGQ method).
212    
213            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
214            into a separate function internal_mer_Xfactor to be able to call
215            it from internal_bhat.
216    
217    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * tests/Class+Meth.R (tstMatrixClass): function for much better
220            testing; now again of all actual classes.
221    
222            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
223                    use macros and define make_d_matrix_* and make_i_matrix_*
224                    where _i_ is for the ldense routines:
225    
226            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
227            * src/ldense.c (lsyMatrix_as_lgeMatrix):
228    
229            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
230    
231    
232    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
235                    many different kinds of matrices.
236            * R/*.R: quite a few new methods were needed for R CMD check with
237                    new Matrix().  Very good for users playing around.
238    
239    
240    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/dgeMatrix.c (dMatrix_validate): new
243            * src/Mutils.c (dense_nonpacked_validate): new
244    
245            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
246    
247    
248    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
249    
250            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
251    
252    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
253    
254            * DESCRIPTION (Version): 0.99-6 released to CRAN
255    
256            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
257            segfault in cases with multiple non-nested grouping factors.
258    
259    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
262                    (Depends): also on 'utils'
263    
264            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
265            * R/diagMatrix.R (Diagonal): constructor and methods for
266            diagonal matrices
267    
268            * R/ltTMatrix.R: new "minimal methods"
269    
270    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
273            all methods (and help files).
274    
275    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
278                    for case (dimn.  op  no_dimn.)
279    
280    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * DESCRIPTION (Version): 0.99-2  released to CRAN
283    
284    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
287            by Julian Faraway.
288    
289    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/Auxiliaries.R (try_as): new utility
292            * R/sparseMatrix.R: use try_as() in coercion to original class
293    
294    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
297    
298    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/Auxiliaries.R (dimNamesCheck): added
301    
302            * R/Matrix.R (as.array), (as.vector): new
303    
304    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
307                    default.
308            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
309                    "pMatrix" now contains "sparseMatrix"
310    
311    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * tests/Class+Meth.R: new tests; t(t(m)) == m
314    
315            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
316    
317            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
318            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
319    
320            * R/dspMatrix.R: typo in "t" method
321    
322    2005-09-18  Douglas Bates  <bates@wisc.edu>
323    
324            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
325            * R/Tsparse.R: instead of R/gTMatrix.R
326            * R/Csparse.R: new
327            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
328            * src/Tsparse.c: new; many trivial methods calling cholmod_()
329            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
330                            via cholmod
331    
332    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Auxiliaries.R (non0ind): new function using new C code
335            * src/dgCMatrix.c (compressed_non_0_ij): new utility
336    
337    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
338    
339            * src/chm_common.h: header file required by all C sources that
340            call CHOLMOD functions.  It defines a cholmod_common structure
341            called 'c' whose address is passed as the last argument to
342            (virtually) every CHOLMOD function.
343    
344            * src/Pattern.c: Simple example of the use of CHOLMOD.
345    
346            * src/init.c: initialize and finalize the cholmod_common structure.
347    
348            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
349            LDL and CCOLAMD from the U. of Florida sparse matrix library.
350    
351    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * inst/test-tools.R: new file collecting the utility functions used
354                    in ./tests/*.R
355    
356            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
357            * R/Matrix.R (cbind2): methods for NULL and missing
358    
359    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/AllClass.R: new "index" class for "[" and "[<-":
362                    First cut at "symmetricMatrix" and "triangularMatrix"
363            * R/gTMatrix.R (.ind.prep): new function;
364                    Logical and character indexing now work too.
365            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
366            * tests/indexing.R: new, including *.Rout.save
367            * tests/dgTMatrix.R: new
368    
369  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
370    
371          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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