SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 854, Tue Aug 16 18:05:01 2005 UTC revision 1298, Sat Jun 10 19:56:18 2006 UTC
# Line 1  Line 1 
1    2006-06-10  Douglas Bates  <bates@R-project.org>
2    
3            * R/lmer.R (simulestimate): added
4    
5    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
8            classes.
9    
10    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/dgTMatrix.R (colSums): etc. All four of
13            colSums(), rowSums(), colMeans(), rowMeans() now should work for
14            all "Matrices".
15    
16    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
17    
18            * R/lmer.R (panel.ci): Add a reference line at zero and a
19            background grid to the qqmath plot of ranef.lmer.
20    
21    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
24            grouping factors to be specified in the formula as (1|foo/bar).
25    
26    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/lmer.R (findbars and others): Change check of is.numeric to
29            !is.language to resolve the bug reported by Jacob Wegelin.
30    
31            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
32            code to evaluate inbreeding coefficients without calculating T,
33            based on code in Sargolzaei and Iwaisaki's paper.
34    
35    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
38            generic and mer methods for isNested and denomDF. This denomDF was
39            an attempt to emulate that in lme but I don't think that makes
40            sense.  Use the trace of the hat matrix instead.
41    
42    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
45            the C code depending on a slot structure that's no longer valid.
46            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
47    
48    
49    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
50    
51            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
52            of lowerTriMatrix generic and methods to tril (also upper to triu)
53            and added a general band extractor.
54    
55    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * R/pedigree.R (pedigree): Replace sire and dam values outside the
58            allowable range with NAs. Added a corresponding check in the
59            validity check for the pedigree class.
60    
61            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
62            crossprod methods now inherits from symmetricMatrix.
63    
64    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
67            generics lowerTriMatrix and upperTriMatrix along with methods for
68            the Csparse virtual class.  Also added a C function Csparse_band
69            that implements these methods by calling cholmod_band.
70    
71    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
74            erased when it was NULL.  This led to invalid subselections!
75    
76    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
77    
78            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
79            in method for "t" so as not to lose the unit diagonal property.
80    
81    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
84            and methods.  This is now an option to the ranef method for the
85            mer class.
86    
87            * src/cs_utils.c: Ensure that the nz component is -1 for a
88            compressed column-oriented matrix.  Minor formatting cleanup.
89    
90            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
91            objects.
92    
93    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
96            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
97    
98    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
101            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
102    
103            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
104            for the dtCMatrix class.
105    
106    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
107    
108            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
109            and methods for it.
110    
111    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
114            arguments, such that M %*% 1:6 now works
115            * Tests/matprod.R: test the above
116    
117    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
120            the ranef.lmer class.
121    
122            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
123            methods to extract the posterior variances from the bVar slot.
124    
125    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
128            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
129    
130            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
131            * tests/simple: (extended)
132    
133            * R/sparseMatrix.R (isTriangular): now using much improved
134            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
135    
136    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
139            (problem report from Franklin Parlamis).  This should be done
140            generally.
141    
142    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
143    
144            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
145            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
146            update the plot methods.
147    
148    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * R/lmer.R (resid and ranef methods):  Added methods for the
151            "residuals" and "resid" generic but only for linear mixed model
152            fits.  Changed the ranef method to return a list of data frames so
153            that the plot methods now work.
154    
155    2006-03-16  Douglas Bates  <bates@bates2>
156    
157            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
158            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
159    
160            * DESCRIPTION (Date): New release
161    
162    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
165    
166            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
167            * man/KNex.Rd: and other help files
168            * tests/*.R: several ones needed adaption
169            * inst/doc/Comparisons.Rnw: dito
170    
171    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
174    
175            * tests/indexing.R: tests for new [<- methods for sparse matrices.
176    
177    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
180    
181            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
182    
183    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/dMatrix.R: enable things like  M [ M < 10 ]
186            * R/dgeMatrix.R: implement it
187    
188    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/AllClass.R: define "summary.mer" and "*.lmer"
191            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
192            * R/lmer.R (show): now works with summary()
193    
194    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
197            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
198                    support the above
199    
200    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
201    
202            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
203            Use glmFit$prior.weights for weights in a glmm.
204            Allow an option usePQL = FALSE to skip the PQL steps for the
205            Laplace method (and, in time, the AGQ method).
206    
207            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
208            into a separate function internal_mer_Xfactor to be able to call
209            it from internal_bhat.
210    
211    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * tests/Class+Meth.R (tstMatrixClass): function for much better
214            testing; now again of all actual classes.
215    
216            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
217                    use macros and define make_d_matrix_* and make_i_matrix_*
218                    where _i_ is for the ldense routines:
219    
220            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
221            * src/ldense.c (lsyMatrix_as_lgeMatrix):
222    
223            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
224    
225    
226    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
229                    many different kinds of matrices.
230            * R/*.R: quite a few new methods were needed for R CMD check with
231                    new Matrix().  Very good for users playing around.
232    
233    
234    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/dgeMatrix.c (dMatrix_validate): new
237            * src/Mutils.c (dense_nonpacked_validate): new
238    
239            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
240    
241    
242    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
245    
246    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * DESCRIPTION (Version): 0.99-6 released to CRAN
249    
250            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
251            segfault in cases with multiple non-nested grouping factors.
252    
253    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
256                    (Depends): also on 'utils'
257    
258            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
259            * R/diagMatrix.R (Diagonal): constructor and methods for
260            diagonal matrices
261    
262            * R/ltTMatrix.R: new "minimal methods"
263    
264    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
267            all methods (and help files).
268    
269    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
272                    for case (dimn.  op  no_dimn.)
273    
274    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * DESCRIPTION (Version): 0.99-2  released to CRAN
277    
278    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
281            by Julian Faraway.
282    
283    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Auxiliaries.R (try_as): new utility
286            * R/sparseMatrix.R: use try_as() in coercion to original class
287    
288    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
291    
292    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/Auxiliaries.R (dimNamesCheck): added
295    
296            * R/Matrix.R (as.array), (as.vector): new
297    
298    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
301                    default.
302            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
303                    "pMatrix" now contains "sparseMatrix"
304    
305    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * tests/Class+Meth.R: new tests; t(t(m)) == m
308    
309            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
310    
311            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
312            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
313    
314            * R/dspMatrix.R: typo in "t" method
315    
316    2005-09-18  Douglas Bates  <bates@wisc.edu>
317    
318            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
319            * R/Tsparse.R: instead of R/gTMatrix.R
320            * R/Csparse.R: new
321            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
322            * src/Tsparse.c: new; many trivial methods calling cholmod_()
323            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
324                            via cholmod
325    
326    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Auxiliaries.R (non0ind): new function using new C code
329            * src/dgCMatrix.c (compressed_non_0_ij): new utility
330    
331    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
332    
333            * src/chm_common.h: header file required by all C sources that
334            call CHOLMOD functions.  It defines a cholmod_common structure
335            called 'c' whose address is passed as the last argument to
336            (virtually) every CHOLMOD function.
337    
338            * src/Pattern.c: Simple example of the use of CHOLMOD.
339    
340            * src/init.c: initialize and finalize the cholmod_common structure.
341    
342            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
343            LDL and CCOLAMD from the U. of Florida sparse matrix library.
344    
345    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * inst/test-tools.R: new file collecting the utility functions used
348                    in ./tests/*.R
349    
350            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
351            * R/Matrix.R (cbind2): methods for NULL and missing
352    
353    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/AllClass.R: new "index" class for "[" and "[<-":
356                    First cut at "symmetricMatrix" and "triangularMatrix"
357            * R/gTMatrix.R (.ind.prep): new function;
358                    Logical and character indexing now work too.
359            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
360            * tests/indexing.R: new, including *.Rout.save
361            * tests/dgTMatrix.R: new
362    
363    2005-08-29  Douglas Bates  <bates@wisc.edu>
364    
365            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
366            indicator pos not being updated.  Also enforced upper triangular
367            for symmetric case.  Need to coerce edges component of elements of
368            edge list - grr! (Why don't they define their classes cleanly?)
369    
370    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/Matrix.R:  added first "[<-" methods; not yet functional
373            * R/denseMatrix.R: dito
374            * man/Subassign-methods.Rd: new help file for these
375    
376    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * DESCRIPTION (Version): 0.98-6
379    
380            * R/denseMatrix.R: new file for "[" fallback methods for all dense
381            matrices.
382    
383    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
386                    as( <logical>, "matrix")
387    
388            * R/pMatrix.R: coercion to "lgTMatrix"
389    
390            * R/gTMatrix.R: new virtual class to define "[" methods for.
391            * man/gTMatrix-class.Rd:
392            * General slight re-organization of where "[" methods are defined.
393              more to come.
394    
395    2005-08-18  Douglas Bates  <bates@wisc.edu>
396    
397            * DESCRIPTION (Version): 0.98-5  released to CRAN
398    
399            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
400            * .....
401    
402    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
403    
404            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
405            or glmer objects.
406    
407    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
410    
411    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
412    
413            * R/HBMM.R: finish re-writing R-only code.
414    
415  2005-08-15  Douglas Bates  <bates@localhost.localdomain>  2005-08-15  Douglas Bates  <bates@localhost.localdomain>
416    
417          * man/externalFormats.Rd: move documentation for writeHB and          * man/externalFormats.Rd: move documentation for writeHB and

Legend:
Removed from v.854  
changed lines
  Added in v.1298

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge