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 392, Tue Dec 14 20:01:16 2004 UTC revision 1352, Mon Aug 7 18:31:12 2006 UTC
# Line 1  Line 1 
1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-08-07  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
4            R-level conversion to a sparse symmetric class.
5            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
6            Remove conversion to sparse symmetric classes (now done in C code).
7    
8    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
11            * man/band.Rd:  adapt the \dontshow{} unit test.
12    
13    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * DESCRIPTION (Version): 0.995-14  for CRAN
16    
17            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
18    
19            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
20            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
21    
22            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
23            * R/Tsparse.R (tril, triu, band): methods
24            * R/dgRMatrix.R (tril, ...):    ditto
25            * man/band.Rd:                  ditto
26    
27    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Matrix.R (head, tail): directly use utils:::head.matrix
30                    to be up-to-date automatically.
31    
32    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
35    
36            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
37            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
38            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
39            such that the S4 objects are always created by the current version
40            of R and 'Matrix' class definitions.
41    
42    2006-08-01  Douglas Bates  <bates@R-project.org>
43    
44            * R/lmer.R (LMEoptimize method), tests/lmer.R,
45            inst/external/test3comp.rda: Added warnings for convergence on
46            boundary and test cases.
47    
48            * src/lmer.c (mer_postVar): Modified to return the variances that
49            are marginal to the fixed effects, not conditional on them (which
50            is what the bVar slot contents represent).
51    
52    2006-07-31  Douglas Bates  <bates@R-project.org>
53    
54            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
55            function which calls the C function mer_hat_trace2.
56    
57            * man/ranef.Rd: Include description of "postVar" argument and
58            producing a caterpillar plot.
59    
60    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * NAMESPACE:    change  "correlation" to "corMatrix"
63            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
64            * R/dpoMatrix.R: ditto
65            * R/lmer.R:      ditto
66    
67    2006-07-28  Douglas Bates  <bates@R-project.org>
68    
69            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
70            RZXinv slot's contents into a separate internal function that can
71            be used in mer_hat_trace.
72    
73    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
76            via new smart
77            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
78            utility functions.
79    
80    
81    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Csparse.R (tril, triu, band): do return *triangular* classed
84            matrices when appropriate; band() even symmetric ones.
85            (replCmat): extend to potentially all "CsparseMatrix"
86            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
87            allow subassignment for special sparse matrices.
88    
89            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
90    
91            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
92            argument; in glmer_*(): print only if(verbose).
93    
94            speed-optimize a few places by moving REAL(.) out of loops.
95    
96            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
97    
98    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
101                    since that wrongly triggers also for M[ logi , ]
102    
103            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
104            a symmetric matrix that results in a non-symmetric one.
105            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
106    
107            * R/dMatrix.R: make round(M) work as round(M, 0)
108    
109            * R/dgTMatrix.R (image): coordinate system and axis now use
110            1-based indices, not 0-based ones.
111    
112            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
113            * tests/indexing.R: test it.
114    
115            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
116            * man/isSymmetric-methods.Rd: and document it.
117    
118            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
119            * man/SparseM-conv.Rd: docu them
120    
121            * tests/other-pkgs.R: renamed from tests/graph.R and add example
122                    for 'SparseM' conversions
123    
124    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
125    
126            * R/Matrix.R (head): added head() and tail() methods.
127    
128    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * DESCRIPTION (Version): 0.995-12 released to CRAN
131    
132    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * tests/simple.R: add check for correct dsT -> dgT coercion;
135                    add check for correct printing of symmetric sparse matrices.
136    
137            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
138            for sparse symmetric matrices.
139    
140            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
141            diagonal twice.
142    
143    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
144    
145            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
146            being applied to the x slot (detected by Brian Ripley).
147    
148    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
151    
152            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
153    
154    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/lgCMatrix.c (lgCMatrix_diag): new function
157            * R/lgCMatrix.R (diag): for new method
158    
159            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
160                 ==> construction of illegal "*gTMatrix" via new() should
161                 now be much less easy:
162            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
163    
164            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
165                    directly.
166            * man/Matrix.Rd: documents it.
167    
168    2006-07-06  Douglas Bates  <bates@R-project.org>
169    
170            * src/pedigree.c (pedigree_inbreeding): Correction in
171            initialization.  This function is not currently being used and is
172            not fully tested.
173    
174            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
175            Introduced the glmer class.  Added code for mcmcmsamp on glmer
176            objects.  Modified validity check on pedigree objects to account
177            for nonparallel patterns of missingness of parents.
178    
179            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
180            class.
181    
182    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/pMatrix.R: coercion pMatrix -> Tsparse
185    
186    2006-06-12  Douglas Bates  <bates@R-project.org>
187    
188            * DESCRIPTION (Version): 0.995-11 released to CRAN
189    
190            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
191            the output from mcmcsamp.
192    
193    2006-06-10  Douglas Bates  <bates@R-project.org>
194    
195            * R/lmer.R (simulestimate): added C code for calculating the trace
196            of the hat matrix.
197    
198    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
201            classes.
202            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
203    
204    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dgTMatrix.R (colSums): etc. All four of
207            colSums(), rowSums(), colMeans(), rowMeans() now should work for
208            all "Matrices".
209    
210    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
211    
212            * R/lmer.R (panel.ci): Add a reference line at zero and a
213            background grid to the qqmath plot of ranef.lmer.
214    
215    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
216    
217            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
218            grouping factors to be specified in the formula as (1|foo/bar).
219    
220    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
221    
222            * R/lmer.R (findbars and others): Change check of is.numeric to
223            !is.language to resolve the bug reported by Jacob Wegelin.
224    
225            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
226            code to evaluate inbreeding coefficients without calculating T,
227            based on code in Sargolzaei and Iwaisaki's paper.
228    
229    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
230    
231            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
232            generic and mer methods for isNested and denomDF. This denomDF was
233            an attempt to emulate that in lme but I don't think that makes
234            sense.  Use the trace of the hat matrix instead.
235    
236    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
239            the C code depending on a slot structure that's no longer valid.
240            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
241    
242    
243    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
244    
245            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
246            of lowerTriMatrix generic and methods to tril (also upper to triu)
247            and added a general band extractor.
248    
249    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
250    
251            * R/pedigree.R (pedigree): Replace sire and dam values outside the
252            allowable range with NAs. Added a corresponding check in the
253            validity check for the pedigree class.
254    
255            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
256            crossprod methods now inherits from symmetricMatrix.
257    
258    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
259    
260            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
261            generics lowerTriMatrix and upperTriMatrix along with methods for
262            the Csparse virtual class.  Also added a C function Csparse_band
263            that implements these methods by calling cholmod_band.
264    
265    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
268            erased when it was NULL.  This led to invalid subselections!
269    
270    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
273            in method for "t" so as not to lose the unit diagonal property.
274    
275    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
276    
277            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
278            and methods.  This is now an option to the ranef method for the
279            mer class.
280    
281            * src/cs_utils.c: Ensure that the nz component is -1 for a
282            compressed column-oriented matrix.  Minor formatting cleanup.
283    
284            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
285            objects.
286    
287    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
290            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
291    
292    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
293    
294            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
295            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
296    
297            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
298            for the dtCMatrix class.
299    
300    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
303            and methods for it.
304    
305    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
308            arguments, such that M %*% 1:6 now works
309            * Tests/matprod.R: test the above
310    
311    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
314            the ranef.lmer class.
315    
316            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
317            methods to extract the posterior variances from the bVar slot.
318    
319    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
322            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
323    
324            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
325            * tests/simple: (extended)
326    
327            * R/sparseMatrix.R (isTriangular): now using much improved
328            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
329    
330    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
333            (problem report from Franklin Parlamis).  This should be done
334            generally.
335    
336    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
339            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
340            update the plot methods.
341    
342    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * R/lmer.R (resid and ranef methods):  Added methods for the
345            "residuals" and "resid" generic but only for linear mixed model
346            fits.  Changed the ranef method to return a list of data frames so
347            that the plot methods now work.
348    
349    2006-03-16  Douglas Bates  <bates@bates2>
350    
351            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
352            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
353    
354            * DESCRIPTION (Date): New release
355    
356    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
359    
360            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
361            * man/KNex.Rd: and other help files
362            * tests/*.R: several ones needed adaption
363            * inst/doc/Comparisons.Rnw: ditto
364    
365    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
368    
369            * tests/indexing.R: tests for new [<- methods for sparse matrices.
370    
371    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
374    
375            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
376    
377    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/dMatrix.R: enable things like  M [ M < 10 ]
380            * R/dgeMatrix.R: implement it
381    
382    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/AllClass.R: define "summary.mer" and "*.lmer"
385            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
386            * R/lmer.R (show): now works with summary()
387    
388    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
391            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
392                    support the above
393    
394    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
395    
396            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
397            Use glmFit$prior.weights for weights in a glmm.
398            Allow an option usePQL = FALSE to skip the PQL steps for the
399            Laplace method (and, in time, the AGQ method).
400    
401            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
402            into a separate function internal_mer_Xfactor to be able to call
403            it from internal_bhat.
404    
405    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * tests/Class+Meth.R (tstMatrixClass): function for much better
408            testing; now again of all actual classes.
409    
410            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
411                    use macros and define make_d_matrix_* and make_i_matrix_*
412                    where _i_ is for the ldense routines:
413    
414            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
415            * src/ldense.c (lsyMatrix_as_lgeMatrix):
416    
417            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
418    
419    
420    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
423                    many different kinds of matrices.
424            * R/*.R: quite a few new methods were needed for R CMD check with
425                    new Matrix().  Very good for users playing around.
426    
427    
428    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * src/dgeMatrix.c (dMatrix_validate): new
431            * src/Mutils.c (dense_nonpacked_validate): new
432    
433            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
434    
435    
436    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
437    
438            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
439    
440    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
441    
442            * DESCRIPTION (Version): 0.99-6 released to CRAN
443    
444            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
445            segfault in cases with multiple non-nested grouping factors.
446    
447    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
450                    (Depends): also on 'utils'
451    
452            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
453            * R/diagMatrix.R (Diagonal): constructor and methods for
454            diagonal matrices
455    
456            * R/ltTMatrix.R: new "minimal methods"
457    
458    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
461            all methods (and help files).
462    
463    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
466                    for case (dimn.  op  no_dimn.)
467    
468    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
469    
470            * DESCRIPTION (Version): 0.99-2  released to CRAN
471    
472    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
473    
474            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
475            by Julian Faraway.
476    
477    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
478    
479            * R/Auxiliaries.R (try_as): new utility
480            * R/sparseMatrix.R: use try_as() in coercion to original class
481    
482    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
485    
486    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/Auxiliaries.R (dimNamesCheck): added
489    
490            * R/Matrix.R (as.array), (as.vector): new
491    
492    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
495                    default.
496            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
497                    "pMatrix" now contains "sparseMatrix"
498    
499    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * tests/Class+Meth.R: new tests; t(t(m)) == m
502    
503            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
504    
505            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
506            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
507    
508            * R/dspMatrix.R: typo in "t" method
509    
510    2005-09-18  Douglas Bates  <bates@wisc.edu>
511    
512            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
513            * R/Tsparse.R: instead of R/gTMatrix.R
514            * R/Csparse.R: new
515            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
516            * src/Tsparse.c: new; many trivial methods calling cholmod_()
517            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
518                            via cholmod
519    
520    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Auxiliaries.R (non0ind): new function using new C code
523            * src/dgCMatrix.c (compressed_non_0_ij): new utility
524    
525    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
526    
527            * src/chm_common.h: header file required by all C sources that
528            call CHOLMOD functions.  It defines a cholmod_common structure
529            called 'c' whose address is passed as the last argument to
530            (virtually) every CHOLMOD function.
531    
532            * src/Pattern.c: Simple example of the use of CHOLMOD.
533    
534            * src/init.c: initialize and finalize the cholmod_common structure.
535    
536            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
537            LDL and CCOLAMD from the U. of Florida sparse matrix library.
538    
539    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * inst/test-tools.R: new file collecting the utility functions used
542                    in ./tests/*.R
543    
544            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
545            * R/Matrix.R (cbind2): methods for NULL and missing
546    
547    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/AllClass.R: new "index" class for "[" and "[<-":
550                    First cut at "symmetricMatrix" and "triangularMatrix"
551            * R/gTMatrix.R (.ind.prep): new function;
552                    Logical and character indexing now work too.
553            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
554            * tests/indexing.R: new, including *.Rout.save
555            * tests/dgTMatrix.R: new
556    
557    2005-08-29  Douglas Bates  <bates@wisc.edu>
558    
559            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
560            indicator pos not being updated.  Also enforced upper triangular
561            for symmetric case.  Need to coerce edges component of elements of
562            edge list - grr! (Why don't they define their classes cleanly?)
563    
564    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/Matrix.R:  added first "[<-" methods; not yet functional
567            * R/denseMatrix.R: ditto
568            * man/Subassign-methods.Rd: new help file for these
569    
570    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * DESCRIPTION (Version): 0.98-6
573    
574            * R/denseMatrix.R: new file for "[" fallback methods for all dense
575            matrices.
576    
577    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
580                    as( <logical>, "matrix")
581    
582            * R/pMatrix.R: coercion to "lgTMatrix"
583    
584            * R/gTMatrix.R: new virtual class to define "[" methods for.
585            * man/gTMatrix-class.Rd:
586            * General slight re-organization of where "[" methods are defined.
587              more to come.
588    
589    2005-08-18  Douglas Bates  <bates@wisc.edu>
590    
591            * DESCRIPTION (Version): 0.98-5  released to CRAN
592    
593            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
594            * .....
595    
596    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
597    
598            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
599            or glmer objects.
600    
601    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
604    
605    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
606    
607            * R/HBMM.R: finish re-writing R-only code.
608    
609    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
610    
611            * man/externalFormats.Rd: move documentation for writeHB and
612            writeMM here.
613    
614            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
615            (suggested by Paul Roecker).
616    
617            * tests/validObj.R (assertError): Comment out test that is failing
618            after recent changes in r-devel.
619    
620    
621    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/AllClass.R: intermediate virtual class "denseMatrix"
624            * man/denseMatrix-class.Rd
625            * NAMESPACE: export it, and also export
626            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
627    
628    2005-08-10  Douglas Bates  <bates@wisc.edu>
629    
630            * DESCRIPTION (Version): 0.98-3 to CRAN
631    
632            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
633            matrix_solve code (which was really, really wrong).
634    
635    2005-08-07  Douglas Bates  <bates@wisc.edu>
636    
637            * DESCRIPTION (Version): 0.98-2
638    
639            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
640    
641            * R/lmer.R (abbrvNms): new
642            * R/lmer.R (mcmcsamp): allow transformed parameters
643            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
644            for the Harwell-Boeing and the MatrixMarket formats.
645    
646    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * man/dtrMatrix-class.Rd: add examples
649            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
650    
651            * TODO: note the dtpMatrix (docu) bug
652    
653            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
654            in order to ensure that new as.matrix() is used by old functions,
655            e.g., svd(), qr(), eigen(), dist(),..;
656                  apply(), also matplot() or pairs().
657    
658    
659    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
662              add comments about 'control' / lmerControl() arguments
663    
664    2005-07-27  Douglas Bates  <bates@wisc.edu>
665    
666            * man/sleepstudy.Rd: Added the sleep data set.
667            * DESCRIPTION (Version): 0.98-1  released to CRAN
668    
669    2005-07-12  Douglas Bates  <bates@wisc.edu>
670            * man/sleepstudy.Rd: Added the sleep data set.
671    
672            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
673            .Call calls that were producing spurious output.
674    
675    2005-07-05  Douglas Bates  <bates@wisc.edu>
676    
677            * R/lmer.R (lmer): stored updated variance component estimates in
678            mer object for the generalized model.  (Bug reported by Renaud
679            Lancelot).
680    
681    2005-07-03  Douglas Bates  <bates@wisc.edu>
682    
683            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
684            unidimensional case.
685    
686    2005-06-08  Douglas Bates  <bates@wisc.edu>
687    
688            * DESCRIPTION (Version): 0.96-1
689    
690            * moved  lmer-class' R and C code moved from lme4 to here
691    
692    2005-06-04  Douglas Bates  <bates@wisc.edu>
693    
694            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
695            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
696    
697    2005-06-02  Douglas Bates  <bates@wisc.edu>
698    
699            * src/Makefile.win: Forgot to update this when Makefile changed.
700    
701    2005-05-11  Douglas Bates  <bates@wisc.edu>
702    
703            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
704            bug reported by Kurt Hornik and Michael Hahsler.
705    
706    2005-05-10  Douglas Bates  <bates@wisc.edu>
707    
708            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
709            logical sparse matrices.  These will also be used in the symbolic
710            analysis for lmer objects.
711    
712            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
713            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
714    
715    2005-05-06  Douglas Bates  <bates@wisc.edu>
716    
717            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
718            colMeans, colSums, rowMeans and rowSums.
719    
720    2005-04-18  Douglas Bates  <bates@wisc.edu>
721    
722            * src/lgCMatrix.[ch]: code for _validate method and stub for
723            multiplication operation.
724    
725            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
726            to dgetrs.
727    
728            * src/init.c: Fix cut-and-paste error in definition of
729            dgeMatrix_matrix_solve
730    
731            * src/{many files}: Tighten code by using ALLOC_SLOT.
732    
733    2005-04-15  Douglas Bates  <bates@wisc.edu>
734    
735            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
736    
737            * DESCRIPTION: Eliminate import of stats.
738    
739    
740    2005-04-06  Douglas Bates  <bates@wisc.edu>
741    
742            * R/AllClass.R : add logical sparse matrix classes
743    
744    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/dgTMatrix.R: add "[" method for triplet matrices
747            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
748    
749    2005-03-31  Douglas Bates  <bates@wisc.edu>
750    
751            * DESCRIPTION (Version): release 0.95-5 to CRAN
752    
753            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
754            * R/sparseMatrix.R: %*%, crossprod()
755            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
756            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
757            * src/lmer.c (lmer_fitted): fix thinko
758    
759    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
760    
761            * R/AllClass.R: add two virtual sparse classes ``on top''
762    
763    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
766                    correspondingly fix examples and tests/ since new()
767                    doesn't work for virtual classes.
768    
769    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/Matrix.R (as.matrix): method and one for unname()
772            * tests/dpoMatrix.R: tests should now be less platform dependent;
773              also run for R 2.1.0; using as.matrix()
774    
775    2005-03-15  Douglas Bates  <bates@wisc.edu>
776    
777            * R/pMatrix.R: "pMatrix" class added
778            * ....
779    
780    2005-03-14  Douglas Bates  <bates@wisc.edu>
781    
782            * R/dtpMatrix.R: Add unpack method and an example.
783    
784            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
785            of general symmetric matrices and associated S4 methods.
786    
787    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
788            +
789    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/dgeMatrix.R (setAs): and many other files: more coercion,
792              crossprod() and "%*%" methods added; tests, too.
793            * tests/matprod.R: new, for testing these
794    
795    2005-03-03  Douglas Bates  <bates@wisc.edu>
796    
797            * src/lmer.c (lmer_fitted): Added.
798    
799    2005-03-02  Douglas Bates  <bates@wisc.edu>
800    
801            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
802    
803    2005-02-28  Douglas Bates  <bates@wisc.edu>
804    
805            * src/*.c,po/,inst/po: Internationalization and localization of
806            the package.
807    
808            * src/ldl.[ch]: Removed these as their contents are referenced in the
809            R_ldl.c file.
810    
811            * src/flame.[ch]: Removed these source files.
812    
813            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
814    
815            * src/LU.[ch],src/init.c: absorb in factorizations
816    
817            * src/Mutils.h: prepare for internationalization
818    
819            * src/cblas.h: move the enum definitions to Mutils.h and remove
820            this file
821    
822    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
825    
826            * R/dtrMatrix.R: fix t() method
827    
828            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
829            * NAMESPACE: export them (and import generics from "methods")
830            * tests/group-methods.R : and test them.
831    
832            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
833            border case
834    
835    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
836    
837            * DESCRIPTION (Version): 0.95-2  released to CRAN
838    
839            * src/dgBCMatrix.c:
840            * src/lmer.c: many changes
841            * ...
842    
843    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * R/Matrix.R: add more sophisticated show() method.
846    
847    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
848    
849            * */* : almost complete reorganization of classes.
850    
851    2005-01-26  Douglas Bates  <bates@wisc.edu>
852    
853            * R/AllGeneric.R: Added matrix exponential generic expm and a method
854            for the geMatrix class.
855    
856    2005-01-24  Douglas Bates  <bates@wisc.edu>
857    
858            * src/Makefile (clean): Remove *.a and *.so
859    
860            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
861    
862    2005-01-23  Douglas Bates  <bates@wisc.edu>
863    
864            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
865            had an effect in cases with more than 2 grouping factors.
866    
867    2005-01-03  Douglas Bates  <bates@wisc.edu>
868    
869            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
870    
871    2004-12-23  Douglas Bates  <bates@wisc.edu>
872    
873            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
874            and R_useDynamicSymbols (suggested by B.D.Ripley).
875    
876    2004-12-14  Douglas Bates  <bates@wisc.edu>
877    
878          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
879    
880          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
881          for tripletMatrix to matrix.          for tripletMatrix to matrix.
882    
883  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
884    
885          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
886          no longer used.          no longer used.
# Line 17  Line 892 
892          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
893          Fixes part but not all of #15.          Fixes part but not all of #15.
894    
895  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
896    
897          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
898          scalar grouping factors corrected.          scalar grouping factors corrected.
899    
900  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
901    
902          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
903    
904  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
905    
906          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
907          .h file can be included.          .h file can be included.
908    
909  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
910    
911          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
912          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
913    
914          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
915    
916  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
917    
918          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
919    
920  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
921    
922          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
923    
924  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
925    
926          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
927    
928  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
929    
930          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
931    
932  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
933    
934          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
935          routines.          routines.
936    
937  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
938    
939          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
940    
941  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
942    
943          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
944    

Legend:
Removed from v.392  
changed lines
  Added in v.1352

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