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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1315, Mon Jul 10 16:08:05 2006 UTC
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1    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
4    
5            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
6    
7    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * src/lgCMatrix.c (lgCMatrix_diag): new function
10            * R/lgCMatrix.R (diag): for new method
11    
12            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
13                 ==> construction of illegal "*gTMatrix" via new() should
14                 now be much less easy:
15            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
16    
17            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
18                    directly.
19            * man/Matrix.Rd: documents it.
20    
21    2006-07-06  Douglas Bates  <bates@R-project.org>
22    
23            * src/pedigree.c (pedigree_inbreeding): Correction in
24            initialization.  This function is not currently being used and is
25            not fully tested.
26    
27            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
28            Introduced the glmer class.  Added code for mcmcmsamp on glmer
29            objects.  Modified validity check on pedigree objects to account
30            for nonparallel patterns of missingness of parents.
31    
32            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
33            class.
34    
35    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/pMatrix.R: coercion pMatrix -> Tsparse
38    
39    2006-06-12  Douglas Bates  <bates@R-project.org>
40    
41            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
42            the output from mcmcsamp.
43    
44    2006-06-10  Douglas Bates  <bates@R-project.org>
45    
46            * R/lmer.R (simulestimate): added C code for calculating the trace
47            of the hat matrix.
48    
49    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
52            classes.
53            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
54    
55    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dgTMatrix.R (colSums): etc. All four of
58            colSums(), rowSums(), colMeans(), rowMeans() now should work for
59            all "Matrices".
60    
61    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/lmer.R (panel.ci): Add a reference line at zero and a
64            background grid to the qqmath plot of ranef.lmer.
65    
66    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
69            grouping factors to be specified in the formula as (1|foo/bar).
70    
71    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
72    
73            * R/lmer.R (findbars and others): Change check of is.numeric to
74            !is.language to resolve the bug reported by Jacob Wegelin.
75    
76            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
77            code to evaluate inbreeding coefficients without calculating T,
78            based on code in Sargolzaei and Iwaisaki's paper.
79    
80    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
81    
82            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
83            generic and mer methods for isNested and denomDF. This denomDF was
84            an attempt to emulate that in lme but I don't think that makes
85            sense.  Use the trace of the hat matrix instead.
86    
87    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
90            the C code depending on a slot structure that's no longer valid.
91            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
92    
93    
94    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
95    
96            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
97            of lowerTriMatrix generic and methods to tril (also upper to triu)
98            and added a general band extractor.
99    
100    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
101    
102            * R/pedigree.R (pedigree): Replace sire and dam values outside the
103            allowable range with NAs. Added a corresponding check in the
104            validity check for the pedigree class.
105    
106            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
107            crossprod methods now inherits from symmetricMatrix.
108    
109    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
110    
111            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
112            generics lowerTriMatrix and upperTriMatrix along with methods for
113            the Csparse virtual class.  Also added a C function Csparse_band
114            that implements these methods by calling cholmod_band.
115    
116    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
119            erased when it was NULL.  This led to invalid subselections!
120    
121    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
124            in method for "t" so as not to lose the unit diagonal property.
125    
126    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
127    
128            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
129            and methods.  This is now an option to the ranef method for the
130            mer class.
131    
132            * src/cs_utils.c: Ensure that the nz component is -1 for a
133            compressed column-oriented matrix.  Minor formatting cleanup.
134    
135            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
136            objects.
137    
138    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
141            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
142    
143    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
146            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
147    
148            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
149            for the dtCMatrix class.
150    
151    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
152    
153            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
154            and methods for it.
155    
156    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
159            arguments, such that M %*% 1:6 now works
160            * Tests/matprod.R: test the above
161    
162    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
165            the ranef.lmer class.
166    
167            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
168            methods to extract the posterior variances from the bVar slot.
169    
170    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
173            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
174    
175            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
176            * tests/simple: (extended)
177    
178            * R/sparseMatrix.R (isTriangular): now using much improved
179            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
180    
181    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
182    
183            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
184            (problem report from Franklin Parlamis).  This should be done
185            generally.
186    
187    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
188    
189            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
190            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
191            update the plot methods.
192    
193    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * R/lmer.R (resid and ranef methods):  Added methods for the
196            "residuals" and "resid" generic but only for linear mixed model
197            fits.  Changed the ranef method to return a list of data frames so
198            that the plot methods now work.
199    
200    2006-03-16  Douglas Bates  <bates@bates2>
201    
202            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
203            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
204    
205            * DESCRIPTION (Date): New release
206    
207    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
210    
211            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
212            * man/KNex.Rd: and other help files
213            * tests/*.R: several ones needed adaption
214            * inst/doc/Comparisons.Rnw: dito
215    
216    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
219    
220            * tests/indexing.R: tests for new [<- methods for sparse matrices.
221    
222    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
225    
226            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
227    
228    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/dMatrix.R: enable things like  M [ M < 10 ]
231            * R/dgeMatrix.R: implement it
232    
233    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/AllClass.R: define "summary.mer" and "*.lmer"
236            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
237            * R/lmer.R (show): now works with summary()
238    
239    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
242            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
243                    support the above
244    
245    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
248            Use glmFit$prior.weights for weights in a glmm.
249            Allow an option usePQL = FALSE to skip the PQL steps for the
250            Laplace method (and, in time, the AGQ method).
251    
252            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
253            into a separate function internal_mer_Xfactor to be able to call
254            it from internal_bhat.
255    
256    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * tests/Class+Meth.R (tstMatrixClass): function for much better
259            testing; now again of all actual classes.
260    
261            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
262                    use macros and define make_d_matrix_* and make_i_matrix_*
263                    where _i_ is for the ldense routines:
264    
265            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
266            * src/ldense.c (lsyMatrix_as_lgeMatrix):
267    
268            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
269    
270    
271    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
274                    many different kinds of matrices.
275            * R/*.R: quite a few new methods were needed for R CMD check with
276                    new Matrix().  Very good for users playing around.
277    
278    
279    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/dgeMatrix.c (dMatrix_validate): new
282            * src/Mutils.c (dense_nonpacked_validate): new
283    
284            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
285    
286    
287    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
288    
289            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
290    
291    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
292    
293            * DESCRIPTION (Version): 0.99-6 released to CRAN
294    
295            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
296            segfault in cases with multiple non-nested grouping factors.
297    
298    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
301                    (Depends): also on 'utils'
302    
303            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
304            * R/diagMatrix.R (Diagonal): constructor and methods for
305            diagonal matrices
306    
307            * R/ltTMatrix.R: new "minimal methods"
308    
309    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
312            all methods (and help files).
313    
314    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
317                    for case (dimn.  op  no_dimn.)
318    
319    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
320    
321            * DESCRIPTION (Version): 0.99-2  released to CRAN
322    
323    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
326            by Julian Faraway.
327    
328    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Auxiliaries.R (try_as): new utility
331            * R/sparseMatrix.R: use try_as() in coercion to original class
332    
333    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
336    
337    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Auxiliaries.R (dimNamesCheck): added
340    
341            * R/Matrix.R (as.array), (as.vector): new
342    
343    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
346                    default.
347            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
348                    "pMatrix" now contains "sparseMatrix"
349    
350    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * tests/Class+Meth.R: new tests; t(t(m)) == m
353    
354            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
355    
356            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
357            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
358    
359            * R/dspMatrix.R: typo in "t" method
360    
361    2005-09-18  Douglas Bates  <bates@wisc.edu>
362    
363            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
364            * R/Tsparse.R: instead of R/gTMatrix.R
365            * R/Csparse.R: new
366            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
367            * src/Tsparse.c: new; many trivial methods calling cholmod_()
368            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
369                            via cholmod
370    
371    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/Auxiliaries.R (non0ind): new function using new C code
374            * src/dgCMatrix.c (compressed_non_0_ij): new utility
375    
376    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
377    
378            * src/chm_common.h: header file required by all C sources that
379            call CHOLMOD functions.  It defines a cholmod_common structure
380            called 'c' whose address is passed as the last argument to
381            (virtually) every CHOLMOD function.
382    
383            * src/Pattern.c: Simple example of the use of CHOLMOD.
384    
385            * src/init.c: initialize and finalize the cholmod_common structure.
386    
387            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
388            LDL and CCOLAMD from the U. of Florida sparse matrix library.
389    
390    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * inst/test-tools.R: new file collecting the utility functions used
393                    in ./tests/*.R
394    
395            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
396            * R/Matrix.R (cbind2): methods for NULL and missing
397    
398    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/AllClass.R: new "index" class for "[" and "[<-":
401                    First cut at "symmetricMatrix" and "triangularMatrix"
402            * R/gTMatrix.R (.ind.prep): new function;
403                    Logical and character indexing now work too.
404            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
405            * tests/indexing.R: new, including *.Rout.save
406            * tests/dgTMatrix.R: new
407    
408  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
409    
410          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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