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 1234, Tue Mar 21 12:33:28 2006 UTC
# Line 1  Line 1 
1    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
4            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
5            update the plot methods.
6    
7    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/lmer.R (resid and ranef methods):  Added methods for the
10            "residuals" and "resid" generic but only for linear mixed model
11            fits.  Changed the ranef method to return a list of data frames so
12            that the plot methods now work.
13    
14    2006-03-16  Douglas Bates  <bates@bates2>
15    
16            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
17            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
18    
19            * DESCRIPTION (Date): New release
20    
21    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
24    
25            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
26            * man/KNex.Rd: and other help files
27            * tests/*.R: several ones needed adaption
28            * inst/doc/Comparisons.Rnw: dito
29    
30    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
33    
34            * tests/indexing.R: tests for new [<- methods for sparse matrices.
35    
36    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
39    
40            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
41    
42    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dMatrix.R: enable things like  M [ M < 10 ]
45            * R/dgeMatrix.R: implement it
46    
47    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/AllClass.R: define "summary.mer" and "*.lmer"
50            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
51            * R/lmer.R (show): now works with summary()
52    
53    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
56            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
57                    support the above
58    
59    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
60    
61            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
62            Use glmFit$prior.weights for weights in a glmm.
63            Allow an option usePQL = FALSE to skip the PQL steps for the
64            Laplace method (and, in time, the AGQ method).
65    
66            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
67            into a separate function internal_mer_Xfactor to be able to call
68            it from internal_bhat.
69    
70    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * tests/Class+Meth.R (tstMatrixClass): function for much better
73            testing; now again of all actual classes.
74    
75            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
76                    use macros and define make_d_matrix_* and make_i_matrix_*
77                    where _i_ is for the ldense routines:
78    
79            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
80            * src/ldense.c (lsyMatrix_as_lgeMatrix):
81    
82            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
83    
84    
85    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
88                    many different kinds of matrices.
89            * R/*.R: quite a few new methods were needed for R CMD check with
90                    new Matrix().  Very good for users playing around.
91    
92    
93    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/dgeMatrix.c (dMatrix_validate): new
96            * src/Mutils.c (dense_nonpacked_validate): new
97    
98            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
99    
100    
101    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
102    
103            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
104    
105    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
106    
107            * DESCRIPTION (Version): 0.99-6 released to CRAN
108    
109            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
110            segfault in cases with multiple non-nested grouping factors.
111    
112    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
115                    (Depends): also on 'utils'
116    
117            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
118            * R/diagMatrix.R (Diagonal): constructor and methods for
119            diagonal matrices
120    
121            * R/ltTMatrix.R: new "minimal methods"
122    
123    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
126            all methods (and help files).
127    
128    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
131                    for case (dimn.  op  no_dimn.)
132    
133    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
134    
135            * DESCRIPTION (Version): 0.99-2  released to CRAN
136    
137    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
140            by Julian Faraway.
141    
142    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Auxiliaries.R (try_as): new utility
145            * R/sparseMatrix.R: use try_as() in coercion to original class
146    
147    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
150    
151    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/Auxiliaries.R (dimNamesCheck): added
154    
155            * R/Matrix.R (as.array), (as.vector): new
156    
157    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
160                    default.
161            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
162                    "pMatrix" now contains "sparseMatrix"
163    
164    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * tests/Class+Meth.R: new tests; t(t(m)) == m
167    
168            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
169    
170            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
171            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
172    
173            * R/dspMatrix.R: typo in "t" method
174    
175    2005-09-18  Douglas Bates  <bates@wisc.edu>
176    
177            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
178            * R/Tsparse.R: instead of R/gTMatrix.R
179            * R/Csparse.R: new
180            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
181            * src/Tsparse.c: new; many trivial methods calling cholmod_()
182            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
183                            via cholmod
184    
185    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Auxiliaries.R (non0ind): new function using new C code
188            * src/dgCMatrix.c (compressed_non_0_ij): new utility
189    
190    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
191    
192            * src/chm_common.h: header file required by all C sources that
193            call CHOLMOD functions.  It defines a cholmod_common structure
194            called 'c' whose address is passed as the last argument to
195            (virtually) every CHOLMOD function.
196    
197            * src/Pattern.c: Simple example of the use of CHOLMOD.
198    
199            * src/init.c: initialize and finalize the cholmod_common structure.
200    
201            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
202            LDL and CCOLAMD from the U. of Florida sparse matrix library.
203    
204    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * inst/test-tools.R: new file collecting the utility functions used
207                    in ./tests/*.R
208    
209            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
210            * R/Matrix.R (cbind2): methods for NULL and missing
211    
212    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/AllClass.R: new "index" class for "[" and "[<-":
215                    First cut at "symmetricMatrix" and "triangularMatrix"
216            * R/gTMatrix.R (.ind.prep): new function;
217                    Logical and character indexing now work too.
218            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
219            * tests/indexing.R: new, including *.Rout.save
220            * tests/dgTMatrix.R: new
221    
222    2005-08-29  Douglas Bates  <bates@wisc.edu>
223    
224            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
225            indicator pos not being updated.  Also enforced upper triangular
226            for symmetric case.  Need to coerce edges component of elements of
227            edge list - grr! (Why don't they define their classes cleanly?)
228    
229    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/Matrix.R:  added first "[<-" methods; not yet functional
232            * R/denseMatrix.R: dito
233            * man/Subassign-methods.Rd: new help file for these
234    
235    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * DESCRIPTION (Version): 0.98-6
238    
239            * R/denseMatrix.R: new file for "[" fallback methods for all dense
240            matrices.
241    
242    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
245                    as( <logical>, "matrix")
246    
247            * R/pMatrix.R: coercion to "lgTMatrix"
248    
249            * R/gTMatrix.R: new virtual class to define "[" methods for.
250            * man/gTMatrix-class.Rd:
251            * General slight re-organization of where "[" methods are defined.
252              more to come.
253    
254    2005-08-18  Douglas Bates  <bates@wisc.edu>
255    
256            * DESCRIPTION (Version): 0.98-5  released to CRAN
257    
258            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
259            * .....
260    
261    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
262    
263            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
264            or glmer objects.
265    
266    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
269    
270    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
271    
272            * R/HBMM.R: finish re-writing R-only code.
273    
274    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
275    
276            * man/externalFormats.Rd: move documentation for writeHB and
277            writeMM here.
278    
279            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
280            (suggested by Paul Roecker).
281    
282            * tests/validObj.R (assertError): Comment out test that is failing
283            after recent changes in r-devel.
284    
285    
286  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

Legend:
Removed from v.848  
changed lines
  Added in v.1234

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