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 848, Thu Aug 11 07:41:59 2005 UTC revision 1238, Thu Mar 30 19:56:09 2006 UTC
# Line 1  Line 1 
1    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
4            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
5    
6            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
7            * tests/simple: (extended)
8    
9            * R/sparseMatrix.R (isTriangular): now using much improved
10            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
11    
12    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
15            (problem report from Franklin Parlamis).  This should be done
16            generally.
17    
18    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
21            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
22            update the plot methods.
23    
24    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
25    
26            * R/lmer.R (resid and ranef methods):  Added methods for the
27            "residuals" and "resid" generic but only for linear mixed model
28            fits.  Changed the ranef method to return a list of data frames so
29            that the plot methods now work.
30    
31    2006-03-16  Douglas Bates  <bates@bates2>
32    
33            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
34            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
35    
36            * DESCRIPTION (Date): New release
37    
38    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
41    
42            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
43            * man/KNex.Rd: and other help files
44            * tests/*.R: several ones needed adaption
45            * inst/doc/Comparisons.Rnw: dito
46    
47    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
50    
51            * tests/indexing.R: tests for new [<- methods for sparse matrices.
52    
53    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
56    
57            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
58    
59    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/dMatrix.R: enable things like  M [ M < 10 ]
62            * R/dgeMatrix.R: implement it
63    
64    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/AllClass.R: define "summary.mer" and "*.lmer"
67            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
68            * R/lmer.R (show): now works with summary()
69    
70    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
73            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
74                    support the above
75    
76    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
77    
78            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
79            Use glmFit$prior.weights for weights in a glmm.
80            Allow an option usePQL = FALSE to skip the PQL steps for the
81            Laplace method (and, in time, the AGQ method).
82    
83            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
84            into a separate function internal_mer_Xfactor to be able to call
85            it from internal_bhat.
86    
87    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * tests/Class+Meth.R (tstMatrixClass): function for much better
90            testing; now again of all actual classes.
91    
92            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
93                    use macros and define make_d_matrix_* and make_i_matrix_*
94                    where _i_ is for the ldense routines:
95    
96            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
97            * src/ldense.c (lsyMatrix_as_lgeMatrix):
98    
99            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
100    
101    
102    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
105                    many different kinds of matrices.
106            * R/*.R: quite a few new methods were needed for R CMD check with
107                    new Matrix().  Very good for users playing around.
108    
109    
110    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * src/dgeMatrix.c (dMatrix_validate): new
113            * src/Mutils.c (dense_nonpacked_validate): new
114    
115            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
116    
117    
118    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
121    
122    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
123    
124            * DESCRIPTION (Version): 0.99-6 released to CRAN
125    
126            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
127            segfault in cases with multiple non-nested grouping factors.
128    
129    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
132                    (Depends): also on 'utils'
133    
134            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
135            * R/diagMatrix.R (Diagonal): constructor and methods for
136            diagonal matrices
137    
138            * R/ltTMatrix.R: new "minimal methods"
139    
140    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
143            all methods (and help files).
144    
145    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
148                    for case (dimn.  op  no_dimn.)
149    
150    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * DESCRIPTION (Version): 0.99-2  released to CRAN
153    
154    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
155    
156            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
157            by Julian Faraway.
158    
159    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Auxiliaries.R (try_as): new utility
162            * R/sparseMatrix.R: use try_as() in coercion to original class
163    
164    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
167    
168    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (dimNamesCheck): added
171    
172            * R/Matrix.R (as.array), (as.vector): new
173    
174    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
177                    default.
178            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
179                    "pMatrix" now contains "sparseMatrix"
180    
181    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * tests/Class+Meth.R: new tests; t(t(m)) == m
184    
185            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
186    
187            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
188            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
189    
190            * R/dspMatrix.R: typo in "t" method
191    
192    2005-09-18  Douglas Bates  <bates@wisc.edu>
193    
194            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
195            * R/Tsparse.R: instead of R/gTMatrix.R
196            * R/Csparse.R: new
197            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
198            * src/Tsparse.c: new; many trivial methods calling cholmod_()
199            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
200                            via cholmod
201    
202    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Auxiliaries.R (non0ind): new function using new C code
205            * src/dgCMatrix.c (compressed_non_0_ij): new utility
206    
207    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
208    
209            * src/chm_common.h: header file required by all C sources that
210            call CHOLMOD functions.  It defines a cholmod_common structure
211            called 'c' whose address is passed as the last argument to
212            (virtually) every CHOLMOD function.
213    
214            * src/Pattern.c: Simple example of the use of CHOLMOD.
215    
216            * src/init.c: initialize and finalize the cholmod_common structure.
217    
218            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
219            LDL and CCOLAMD from the U. of Florida sparse matrix library.
220    
221    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * inst/test-tools.R: new file collecting the utility functions used
224                    in ./tests/*.R
225    
226            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
227            * R/Matrix.R (cbind2): methods for NULL and missing
228    
229    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/AllClass.R: new "index" class for "[" and "[<-":
232                    First cut at "symmetricMatrix" and "triangularMatrix"
233            * R/gTMatrix.R (.ind.prep): new function;
234                    Logical and character indexing now work too.
235            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
236            * tests/indexing.R: new, including *.Rout.save
237            * tests/dgTMatrix.R: new
238    
239    2005-08-29  Douglas Bates  <bates@wisc.edu>
240    
241            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
242            indicator pos not being updated.  Also enforced upper triangular
243            for symmetric case.  Need to coerce edges component of elements of
244            edge list - grr! (Why don't they define their classes cleanly?)
245    
246    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R:  added first "[<-" methods; not yet functional
249            * R/denseMatrix.R: dito
250            * man/Subassign-methods.Rd: new help file for these
251    
252    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Version): 0.98-6
255    
256            * R/denseMatrix.R: new file for "[" fallback methods for all dense
257            matrices.
258    
259    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
262                    as( <logical>, "matrix")
263    
264            * R/pMatrix.R: coercion to "lgTMatrix"
265    
266            * R/gTMatrix.R: new virtual class to define "[" methods for.
267            * man/gTMatrix-class.Rd:
268            * General slight re-organization of where "[" methods are defined.
269              more to come.
270    
271    2005-08-18  Douglas Bates  <bates@wisc.edu>
272    
273            * DESCRIPTION (Version): 0.98-5  released to CRAN
274    
275            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
276            * .....
277    
278    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
279    
280            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
281            or glmer objects.
282    
283    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
286    
287    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
288    
289            * R/HBMM.R: finish re-writing R-only code.
290    
291    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
292    
293            * man/externalFormats.Rd: move documentation for writeHB and
294            writeMM here.
295    
296            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
297            (suggested by Paul Roecker).
298    
299            * tests/validObj.R (assertError): Comment out test that is failing
300            after recent changes in r-devel.
301    
302    
303  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

Legend:
Removed from v.848  
changed lines
  Added in v.1238

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