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 876, Sat Aug 27 22:50:57 2005 UTC revision 1268, Wed May 17 17:42:09 2006 UTC
# Line 1  Line 1 
1    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
2    
3            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
4            of lowerTriMatrix generic and methods to tril (also upper to triu)
5            and added a general band extractor.
6    
7    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/pedigree.R (pedigree): Replace sire and dam values outside the
10            allowable range with NAs. Added a corresponding check in the
11            validity check for the pedigree class.
12    
13            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
14            crossprod methods now inherits from symmetricMatrix.
15    
16    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
17    
18            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
19            generics lowerTriMatrix and upperTriMatrix along with methods for
20            the Csparse virtual class.  Also added a C function Csparse_band
21            that implements these methods by calling cholmod_band.
22    
23    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
26            erased when it was NULL.  This led to invalid subselections!
27    
28    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
31            in method for "t" so as not to lose the unit diagonal property.
32    
33    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
36            and methods.  This is now an option to the ranef method for the
37            mer class.
38    
39            * src/cs_utils.c: Ensure that the nz component is -1 for a
40            compressed column-oriented matrix.  Minor formatting cleanup.
41    
42            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
43            objects.
44    
45    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
48            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
49    
50    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
53            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
54    
55            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
56            for the dtCMatrix class.
57    
58    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
61            and methods for it.
62    
63    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
66            arguments, such that M %*% 1:6 now works
67            * Tests/matprod.R: test the above
68    
69    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
70    
71            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
72            the ranef.lmer class.
73    
74            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
75            methods to extract the posterior variances from the bVar slot.
76    
77    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
80            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
81    
82            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
83            * tests/simple: (extended)
84    
85            * R/sparseMatrix.R (isTriangular): now using much improved
86            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
87    
88    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
89    
90            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
91            (problem report from Franklin Parlamis).  This should be done
92            generally.
93    
94    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
97            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
98            update the plot methods.
99    
100    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
101    
102            * R/lmer.R (resid and ranef methods):  Added methods for the
103            "residuals" and "resid" generic but only for linear mixed model
104            fits.  Changed the ranef method to return a list of data frames so
105            that the plot methods now work.
106    
107    2006-03-16  Douglas Bates  <bates@bates2>
108    
109            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
110            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
111    
112            * DESCRIPTION (Date): New release
113    
114    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
117    
118            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
119            * man/KNex.Rd: and other help files
120            * tests/*.R: several ones needed adaption
121            * inst/doc/Comparisons.Rnw: dito
122    
123    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
126    
127            * tests/indexing.R: tests for new [<- methods for sparse matrices.
128    
129    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
132    
133            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
134    
135    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/dMatrix.R: enable things like  M [ M < 10 ]
138            * R/dgeMatrix.R: implement it
139    
140    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/AllClass.R: define "summary.mer" and "*.lmer"
143            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
144            * R/lmer.R (show): now works with summary()
145    
146    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
149            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
150                    support the above
151    
152    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
153    
154            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
155            Use glmFit$prior.weights for weights in a glmm.
156            Allow an option usePQL = FALSE to skip the PQL steps for the
157            Laplace method (and, in time, the AGQ method).
158    
159            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
160            into a separate function internal_mer_Xfactor to be able to call
161            it from internal_bhat.
162    
163    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * tests/Class+Meth.R (tstMatrixClass): function for much better
166            testing; now again of all actual classes.
167    
168            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
169                    use macros and define make_d_matrix_* and make_i_matrix_*
170                    where _i_ is for the ldense routines:
171    
172            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
173            * src/ldense.c (lsyMatrix_as_lgeMatrix):
174    
175            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
176    
177    
178    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
181                    many different kinds of matrices.
182            * R/*.R: quite a few new methods were needed for R CMD check with
183                    new Matrix().  Very good for users playing around.
184    
185    
186    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dgeMatrix.c (dMatrix_validate): new
189            * src/Mutils.c (dense_nonpacked_validate): new
190    
191            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
192    
193    
194    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
197    
198    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * DESCRIPTION (Version): 0.99-6 released to CRAN
201    
202            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
203            segfault in cases with multiple non-nested grouping factors.
204    
205    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
208                    (Depends): also on 'utils'
209    
210            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
211            * R/diagMatrix.R (Diagonal): constructor and methods for
212            diagonal matrices
213    
214            * R/ltTMatrix.R: new "minimal methods"
215    
216    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
219            all methods (and help files).
220    
221    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
224                    for case (dimn.  op  no_dimn.)
225    
226    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
227    
228            * DESCRIPTION (Version): 0.99-2  released to CRAN
229    
230    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
231    
232            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
233            by Julian Faraway.
234    
235    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Auxiliaries.R (try_as): new utility
238            * R/sparseMatrix.R: use try_as() in coercion to original class
239    
240    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
243    
244    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Auxiliaries.R (dimNamesCheck): added
247    
248            * R/Matrix.R (as.array), (as.vector): new
249    
250    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
253                    default.
254            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
255                    "pMatrix" now contains "sparseMatrix"
256    
257    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * tests/Class+Meth.R: new tests; t(t(m)) == m
260    
261            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
262    
263            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
264            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
265    
266            * R/dspMatrix.R: typo in "t" method
267    
268    2005-09-18  Douglas Bates  <bates@wisc.edu>
269    
270            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
271            * R/Tsparse.R: instead of R/gTMatrix.R
272            * R/Csparse.R: new
273            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
274            * src/Tsparse.c: new; many trivial methods calling cholmod_()
275            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
276                            via cholmod
277    
278    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/Auxiliaries.R (non0ind): new function using new C code
281            * src/dgCMatrix.c (compressed_non_0_ij): new utility
282    
283    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
284    
285            * src/chm_common.h: header file required by all C sources that
286            call CHOLMOD functions.  It defines a cholmod_common structure
287            called 'c' whose address is passed as the last argument to
288            (virtually) every CHOLMOD function.
289    
290            * src/Pattern.c: Simple example of the use of CHOLMOD.
291    
292            * src/init.c: initialize and finalize the cholmod_common structure.
293    
294            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
295            LDL and CCOLAMD from the U. of Florida sparse matrix library.
296    
297    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * inst/test-tools.R: new file collecting the utility functions used
300                    in ./tests/*.R
301    
302            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
303            * R/Matrix.R (cbind2): methods for NULL and missing
304    
305    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/AllClass.R: new "index" class for "[" and "[<-":
308                    First cut at "symmetricMatrix" and "triangularMatrix"
309            * R/gTMatrix.R (.ind.prep): new function;
310                    Logical and character indexing now work too.
311            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
312            * tests/indexing.R: new, including *.Rout.save
313            * tests/dgTMatrix.R: new
314    
315  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
316    
317          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

Legend:
Removed from v.876  
changed lines
  Added in v.1268

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