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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1295, Fri Jun 9 21:47:22 2006 UTC
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1    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
4            classes.
5    
6    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/dgTMatrix.R (colSums): etc. All four of
9            colSums(), rowSums(), colMeans(), rowMeans() now should work for
10            all "Matrices".
11    
12    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * R/lmer.R (panel.ci): Add a reference line at zero and a
15            background grid to the qqmath plot of ranef.lmer.
16    
17    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
20            grouping factors to be specified in the formula as (1|foo/bar).
21    
22    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * R/lmer.R (findbars and others): Change check of is.numeric to
25            !is.language to resolve the bug reported by Jacob Wegelin.
26    
27            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
28            code to evaluate inbreeding coefficients without calculating T,
29            based on code in Sargolzaei and Iwaisaki's paper.
30    
31    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
34            generic and mer methods for isNested and denomDF. This denomDF was
35            an attempt to emulate that in lme but I don't think that makes
36            sense.  Use the trace of the hat matrix instead.
37    
38    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
41            the C code depending on a slot structure that's no longer valid.
42            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
43    
44    
45    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
46    
47            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
48            of lowerTriMatrix generic and methods to tril (also upper to triu)
49            and added a general band extractor.
50    
51    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * R/pedigree.R (pedigree): Replace sire and dam values outside the
54            allowable range with NAs. Added a corresponding check in the
55            validity check for the pedigree class.
56    
57            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
58            crossprod methods now inherits from symmetricMatrix.
59    
60    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
63            generics lowerTriMatrix and upperTriMatrix along with methods for
64            the Csparse virtual class.  Also added a C function Csparse_band
65            that implements these methods by calling cholmod_band.
66    
67    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
70            erased when it was NULL.  This led to invalid subselections!
71    
72    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
75            in method for "t" so as not to lose the unit diagonal property.
76    
77    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
78    
79            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
80            and methods.  This is now an option to the ranef method for the
81            mer class.
82    
83            * src/cs_utils.c: Ensure that the nz component is -1 for a
84            compressed column-oriented matrix.  Minor formatting cleanup.
85    
86            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
87            objects.
88    
89    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
92            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
93    
94    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
97            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
98    
99            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
100            for the dtCMatrix class.
101    
102    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
105            and methods for it.
106    
107    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
110            arguments, such that M %*% 1:6 now works
111            * Tests/matprod.R: test the above
112    
113    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
116            the ranef.lmer class.
117    
118            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
119            methods to extract the posterior variances from the bVar slot.
120    
121    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
124            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
125    
126            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
127            * tests/simple: (extended)
128    
129            * R/sparseMatrix.R (isTriangular): now using much improved
130            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
131    
132    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
135            (problem report from Franklin Parlamis).  This should be done
136            generally.
137    
138    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
139    
140            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
141            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
142            update the plot methods.
143    
144    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
145    
146            * R/lmer.R (resid and ranef methods):  Added methods for the
147            "residuals" and "resid" generic but only for linear mixed model
148            fits.  Changed the ranef method to return a list of data frames so
149            that the plot methods now work.
150    
151    2006-03-16  Douglas Bates  <bates@bates2>
152    
153            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
154            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
155    
156            * DESCRIPTION (Date): New release
157    
158    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
161    
162            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
163            * man/KNex.Rd: and other help files
164            * tests/*.R: several ones needed adaption
165            * inst/doc/Comparisons.Rnw: dito
166    
167    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
170    
171            * tests/indexing.R: tests for new [<- methods for sparse matrices.
172    
173    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
176    
177            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
178    
179    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dMatrix.R: enable things like  M [ M < 10 ]
182            * R/dgeMatrix.R: implement it
183    
184    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/AllClass.R: define "summary.mer" and "*.lmer"
187            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
188            * R/lmer.R (show): now works with summary()
189    
190    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
193            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
194                    support the above
195    
196    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
197    
198            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
199            Use glmFit$prior.weights for weights in a glmm.
200            Allow an option usePQL = FALSE to skip the PQL steps for the
201            Laplace method (and, in time, the AGQ method).
202    
203            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
204            into a separate function internal_mer_Xfactor to be able to call
205            it from internal_bhat.
206    
207    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * tests/Class+Meth.R (tstMatrixClass): function for much better
210            testing; now again of all actual classes.
211    
212            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
213                    use macros and define make_d_matrix_* and make_i_matrix_*
214                    where _i_ is for the ldense routines:
215    
216            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
217            * src/ldense.c (lsyMatrix_as_lgeMatrix):
218    
219            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
220    
221    
222    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
225                    many different kinds of matrices.
226            * R/*.R: quite a few new methods were needed for R CMD check with
227                    new Matrix().  Very good for users playing around.
228    
229    
230    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * src/dgeMatrix.c (dMatrix_validate): new
233            * src/Mutils.c (dense_nonpacked_validate): new
234    
235            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
236    
237    
238    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
239    
240            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
241    
242    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * DESCRIPTION (Version): 0.99-6 released to CRAN
245    
246            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
247            segfault in cases with multiple non-nested grouping factors.
248    
249    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
252                    (Depends): also on 'utils'
253    
254            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
255            * R/diagMatrix.R (Diagonal): constructor and methods for
256            diagonal matrices
257    
258            * R/ltTMatrix.R: new "minimal methods"
259    
260    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
263            all methods (and help files).
264    
265    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
268                    for case (dimn.  op  no_dimn.)
269    
270    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * DESCRIPTION (Version): 0.99-2  released to CRAN
273    
274    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
277            by Julian Faraway.
278    
279    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Auxiliaries.R (try_as): new utility
282            * R/sparseMatrix.R: use try_as() in coercion to original class
283    
284    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
287    
288    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/Auxiliaries.R (dimNamesCheck): added
291    
292            * R/Matrix.R (as.array), (as.vector): new
293    
294    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
297                    default.
298            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
299                    "pMatrix" now contains "sparseMatrix"
300    
301    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * tests/Class+Meth.R: new tests; t(t(m)) == m
304    
305            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
306    
307            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
308            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
309    
310            * R/dspMatrix.R: typo in "t" method
311    
312    2005-09-18  Douglas Bates  <bates@wisc.edu>
313    
314            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
315            * R/Tsparse.R: instead of R/gTMatrix.R
316            * R/Csparse.R: new
317            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
318            * src/Tsparse.c: new; many trivial methods calling cholmod_()
319            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
320                            via cholmod
321    
322    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Auxiliaries.R (non0ind): new function using new C code
325            * src/dgCMatrix.c (compressed_non_0_ij): new utility
326    
327    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
328    
329            * src/chm_common.h: header file required by all C sources that
330            call CHOLMOD functions.  It defines a cholmod_common structure
331            called 'c' whose address is passed as the last argument to
332            (virtually) every CHOLMOD function.
333    
334            * src/Pattern.c: Simple example of the use of CHOLMOD.
335    
336            * src/init.c: initialize and finalize the cholmod_common structure.
337    
338            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
339            LDL and CCOLAMD from the U. of Florida sparse matrix library.
340    
341    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * inst/test-tools.R: new file collecting the utility functions used
344                    in ./tests/*.R
345    
346            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
347            * R/Matrix.R (cbind2): methods for NULL and missing
348    
349    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/AllClass.R: new "index" class for "[" and "[<-":
352                    First cut at "symmetricMatrix" and "triangularMatrix"
353            * R/gTMatrix.R (.ind.prep): new function;
354                    Logical and character indexing now work too.
355            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
356            * tests/indexing.R: new, including *.Rout.save
357            * tests/dgTMatrix.R: new
358    
359    2005-08-29  Douglas Bates  <bates@wisc.edu>
360    
361            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
362            indicator pos not being updated.  Also enforced upper triangular
363            for symmetric case.  Need to coerce edges component of elements of
364            edge list - grr! (Why don't they define their classes cleanly?)
365    
366    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Matrix.R:  added first "[<-" methods; not yet functional
369            * R/denseMatrix.R: dito
370            * man/Subassign-methods.Rd: new help file for these
371    
372    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * DESCRIPTION (Version): 0.98-6
375    
376            * R/denseMatrix.R: new file for "[" fallback methods for all dense
377            matrices.
378    
379    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
382                    as( <logical>, "matrix")
383    
384            * R/pMatrix.R: coercion to "lgTMatrix"
385    
386            * R/gTMatrix.R: new virtual class to define "[" methods for.
387            * man/gTMatrix-class.Rd:
388            * General slight re-organization of where "[" methods are defined.
389              more to come.
390    
391    2005-08-18  Douglas Bates  <bates@wisc.edu>
392    
393            * DESCRIPTION (Version): 0.98-5  released to CRAN
394    
395            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
396            * .....
397    
398    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
399    
400            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
401            or glmer objects.
402    
403    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
406    
407    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
408    
409            * R/HBMM.R: finish re-writing R-only code.
410    
411    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
412    
413            * man/externalFormats.Rd: move documentation for writeHB and
414            writeMM here.
415    
416            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
417            (suggested by Paul Roecker).
418    
419            * tests/validObj.R (assertError): Comment out test that is failing
420            after recent changes in r-devel.
421    
422    
423  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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