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 1265, Mon May 15 22:36:59 2006 UTC
# Line 1  Line 1 
1    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
4            generics lowerTriMatrix and upperTriMatrix along with methods for
5            the Csparse virtual class.  Also added a C function Csparse_band
6            that implements these methods by calling cholmod_band.
7    
8    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
11            erased when it was NULL.  This led to invalid subselections!
12    
13    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
16            in method for "t" so as not to lose the unit diagonal property.
17    
18    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
21            and methods.  This is now an option to the ranef method for the
22            mer class.
23    
24            * src/cs_utils.c: Ensure that the nz component is -1 for a
25            compressed column-oriented matrix.  Minor formatting cleanup.
26    
27            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
28            objects.
29    
30    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
33            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
34    
35    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
38            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
39    
40            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
41            for the dtCMatrix class.
42    
43    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
46            and methods for it.
47    
48    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
51            arguments, such that M %*% 1:6 now works
52            * Tests/matprod.R: test the above
53    
54    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
57            the ranef.lmer class.
58    
59            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
60            methods to extract the posterior variances from the bVar slot.
61    
62    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
65            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
66    
67            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
68            * tests/simple: (extended)
69    
70            * R/sparseMatrix.R (isTriangular): now using much improved
71            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
72    
73    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
76            (problem report from Franklin Parlamis).  This should be done
77            generally.
78    
79    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
82            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
83            update the plot methods.
84    
85    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/lmer.R (resid and ranef methods):  Added methods for the
88            "residuals" and "resid" generic but only for linear mixed model
89            fits.  Changed the ranef method to return a list of data frames so
90            that the plot methods now work.
91    
92    2006-03-16  Douglas Bates  <bates@bates2>
93    
94            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
95            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
96    
97            * DESCRIPTION (Date): New release
98    
99    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
102    
103            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
104            * man/KNex.Rd: and other help files
105            * tests/*.R: several ones needed adaption
106            * inst/doc/Comparisons.Rnw: dito
107    
108    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
111    
112            * tests/indexing.R: tests for new [<- methods for sparse matrices.
113    
114    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
117    
118            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
119    
120    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/dMatrix.R: enable things like  M [ M < 10 ]
123            * R/dgeMatrix.R: implement it
124    
125    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R: define "summary.mer" and "*.lmer"
128            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
129            * R/lmer.R (show): now works with summary()
130    
131    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
134            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
135                    support the above
136    
137    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
140            Use glmFit$prior.weights for weights in a glmm.
141            Allow an option usePQL = FALSE to skip the PQL steps for the
142            Laplace method (and, in time, the AGQ method).
143    
144            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
145            into a separate function internal_mer_Xfactor to be able to call
146            it from internal_bhat.
147    
148    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * tests/Class+Meth.R (tstMatrixClass): function for much better
151            testing; now again of all actual classes.
152    
153            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
154                    use macros and define make_d_matrix_* and make_i_matrix_*
155                    where _i_ is for the ldense routines:
156    
157            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
158            * src/ldense.c (lsyMatrix_as_lgeMatrix):
159    
160            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
161    
162    
163    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
166                    many different kinds of matrices.
167            * R/*.R: quite a few new methods were needed for R CMD check with
168                    new Matrix().  Very good for users playing around.
169    
170    
171    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * src/dgeMatrix.c (dMatrix_validate): new
174            * src/Mutils.c (dense_nonpacked_validate): new
175    
176            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
177    
178    
179    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
180    
181            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
182    
183    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
184    
185            * DESCRIPTION (Version): 0.99-6 released to CRAN
186    
187            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
188            segfault in cases with multiple non-nested grouping factors.
189    
190    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
193                    (Depends): also on 'utils'
194    
195            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
196            * R/diagMatrix.R (Diagonal): constructor and methods for
197            diagonal matrices
198    
199            * R/ltTMatrix.R: new "minimal methods"
200    
201    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
204            all methods (and help files).
205    
206    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
209                    for case (dimn.  op  no_dimn.)
210    
211    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
212    
213            * DESCRIPTION (Version): 0.99-2  released to CRAN
214    
215    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
216    
217            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
218            by Julian Faraway.
219    
220    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/Auxiliaries.R (try_as): new utility
223            * R/sparseMatrix.R: use try_as() in coercion to original class
224    
225    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
228    
229    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/Auxiliaries.R (dimNamesCheck): added
232    
233            * R/Matrix.R (as.array), (as.vector): new
234    
235    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
238                    default.
239            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
240                    "pMatrix" now contains "sparseMatrix"
241    
242    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * tests/Class+Meth.R: new tests; t(t(m)) == m
245    
246            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
247    
248            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
249            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
250    
251            * R/dspMatrix.R: typo in "t" method
252    
253    2005-09-18  Douglas Bates  <bates@wisc.edu>
254    
255            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
256            * R/Tsparse.R: instead of R/gTMatrix.R
257            * R/Csparse.R: new
258            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
259            * src/Tsparse.c: new; many trivial methods calling cholmod_()
260            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
261                            via cholmod
262    
263    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Auxiliaries.R (non0ind): new function using new C code
266            * src/dgCMatrix.c (compressed_non_0_ij): new utility
267    
268    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
269    
270            * src/chm_common.h: header file required by all C sources that
271            call CHOLMOD functions.  It defines a cholmod_common structure
272            called 'c' whose address is passed as the last argument to
273            (virtually) every CHOLMOD function.
274    
275            * src/Pattern.c: Simple example of the use of CHOLMOD.
276    
277            * src/init.c: initialize and finalize the cholmod_common structure.
278    
279            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
280            LDL and CCOLAMD from the U. of Florida sparse matrix library.
281    
282    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * inst/test-tools.R: new file collecting the utility functions used
285                    in ./tests/*.R
286    
287            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
288            * R/Matrix.R (cbind2): methods for NULL and missing
289    
290    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/AllClass.R: new "index" class for "[" and "[<-":
293                    First cut at "symmetricMatrix" and "triangularMatrix"
294            * R/gTMatrix.R (.ind.prep): new function;
295                    Logical and character indexing now work too.
296            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
297            * tests/indexing.R: new, including *.Rout.save
298            * tests/dgTMatrix.R: new
299    
300  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
301    
302          * 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.1265

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