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 1571, Sat Sep 16 21:03:12 2006 UTC
# Line 1  Line 1 
1    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/group-methods.R: add test for logical + NAs
4    
5            * R/dMatrix.R ("Compare"): fix to work with NA's
6    
7            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
8    
9            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
10                    which is implemented.
11    
12    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * src/chm_common.c: coerce logical <-> double instead of
15            typecasting;  needed for "l" matrix handling in cholmod.
16    
17            * tests/other-pkgs.R (graph): small extension in "graph" checks.
18    
19            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
20            (Tsp2grNEL): other fixes needed
21    
22    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
25                    Matrices, since "lMatrix", also "lsparseM" can have NA
26            * R/ndenseMatrix.R, etc: new source files
27            * man/nsparseMatrix-classes.Rd, etc: new help files
28            * tests/: adaptions
29            * src/chm_common.c (chm_dense_to_SEXP): and others:
30                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
31            * src/Csparse.c, etc: dito
32    
33    2006-09-11  Douglas Bates  <bates@R-project.org>
34    
35            * src/Mutils.[ch],init.c inst/include/*.h: Move the
36            alloc_d**Matrix functions to the lme4 package.
37    
38    2006-09-09  Douglas Bates  <bates@R-project.org>
39    
40            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
41            fixed
42    
43    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/lMatrix.R: new
46    
47            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
48    
49            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
50            * man/tcrossprod.Rd: dito
51    
52    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
55            for exported functions
56            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
57            Remove partitioning algorithms for sparse matrix reordering.  The
58            copyright on the Metis code was problematic and the methods were
59            rarely used.
60            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
61            operations are now done entirely in CHOLMOD code.
62    
63    2006-09-06  Douglas Bates  <bates@R-project.org>
64    
65            * src/Mutils.h: Remove functions that are no longer used.
66    
67    2006-09-04  Douglas Bates  <bates@R-project.org>
68    
69            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
70            * src/DEPS.mkf: update
71    
72    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * created branches/Matrix-for-R-2.3.x;  on trunk: do
75            * DESCRIPTION (Version): 0.9975-0
76            (Depends): R (>= 2.4.0)
77    
78    2006-09-01  Douglas Bates  <bates@R-project.org>
79    
80            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
81    
82    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
85            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
86    
87            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
88    
89    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
92            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
93            * R/dsparseMatrix.R: dito
94            * R/Csparse.R: dito
95    
96    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dMatrix.R (Compare): improve availability of "<", etc
99            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
100    
101    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
104            of a 0-index which was used as 1-index (..hmm)
105    
106            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
107    
108            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
109            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
110            (.is.diagonal): dito
111    
112            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
113    
114            * R/Matrix.R (Matrix): also work for NA data
115    
116    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
119            in all cases.
120    
121    2006-08-27  Douglas Bates  <bates@R-project.org>
122    
123            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
124            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
125    
126    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
129            subclasses of "ddenseMatrix"
130            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
131            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
132            instead of half dozen specialized ones.
133    
134    2006-08-25  Douglas Bates  <bates@R-project.org>
135    
136            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
137            <tillard@cirad.fr> - ordering standard errors to match effects.
138    
139    2006-08-24  Douglas Bates  <bates@R-project.org>
140    
141            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
142            on R_ldl.
143            * R/lCholCMatrix.R,
144            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
145            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
146            * many files in ./R and ./src: Use more general version of
147            dup_mMatrix_as_dgeMatrix to simplify method definitions.
148            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
149            dtpMatrix, dspMatrix and dppMatrix conversions.
150    
151    
152    2006-08-23  Douglas Bates  <bates@R-project.org>
153    
154            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
155            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
156            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
157            dgeMatrix_crossprod (may need to do this in other places).
158            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
159            generic and method for dsCMatrix.  Use CHOLMOD for chol().
160    
161    2006-08-22  Douglas Bates  <bates@R-project.org>
162    
163            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
164            types of classed Matrices, matrices or numeric or logical vectors.
165            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
166            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
167            to Mutils.h (as an inline) and change name to Matrix_check_class;
168            fixes in as_cholmod_factor and chm_factor_to_SEXP.
169            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
170            dsCMatrix_matrix_solve.  Comment out vestigial functions.
171            * src/Csparse.c: use diag_P and uplo_P macros.
172    
173    2006-08-21  Douglas Bates  <bates@R-project.org>
174    
175            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
176            valgrind.
177            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
178            inverses.
179            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
180            -Wall warnings.
181            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
182            Use dup_mMatrix_as_dgeMatrix.
183    
184    2006-08-20  Douglas Bates  <bates@R-project.org>
185    
186            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
187            * tests/sparseQR.R: Added
188            * man/sparseQR-class.Rd: Document methods for qr.* generics
189            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
190    
191    2006-08-19  Douglas Bates  <bates@R-project.org>
192    
193            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
194            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
195            and qr.fitted.
196            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
197            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
198    
199    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
202            the base version has no "..." argument.
203    
204            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
205    
206            * R/Matrix.R: define and
207            * NAMESPACE: export as.numeric() and as.logical() methods.
208                    Let's hope these do not badly slow down something...
209            Finally export the zapsmall() method.
210    
211    2006-08-17  Douglas Bates  <bates@R-project.org>
212    
213            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
214            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
215            * src/dtCMatrix.c :Remove code that is no longer used
216            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
217    
218    2006-08-14  Douglas Bates  <bates@R-project.org>
219    
220            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
221            Csparse_to_logical and Csparse_symmetric_to_general.
222            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
223            coercion methods between CsparseMatrix and TsparseMatrix.
224    
225    2006-08-14  Douglas Bates  <bates@R-project.org>
226    
227            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
228            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
229            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
230            possible.
231    
232    2006-08-12  Douglas Bates  <bates@R-project.org>
233    
234            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
235              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
236              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
237              generalize conversions between TsparseMatrix, CsparseMatrix,
238              denseMatrix and matrix.  Preserve triangularity property and
239              propagate Dimnames in the easy cases.
240    
241    2006-08-10  Douglas Bates  <bates@R-project.org>
242    
243            * src/lmer.c: adjust checks in glmer_init for S4SXP
244            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
245            before S4SXP but for the wrong reasons.
246    
247    2006-08-08  Douglas Bates  <bates@R-project.org>
248    
249            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
250            Later modified to return the upper triangle only.
251            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
252    
253    2006-08-07  Douglas Bates  <bates@R-project.org>
254    
255            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
256            R-level conversion to a sparse symmetric class.
257            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
258            Remove conversion to sparse symmetric classes (now done in C code).
259    
260    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
263            * man/band.Rd:  adapt the \dontshow{} unit test.
264    
265    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * DESCRIPTION (Version): 0.995-14  for CRAN
268    
269            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
270    
271            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
272            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
273    
274            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
275            * R/Tsparse.R (tril, triu, band): methods
276            * R/dgRMatrix.R (tril, ...):    ditto
277            * man/band.Rd:                  ditto
278    
279    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Matrix.R (head, tail): directly use utils:::head.matrix
282                    to be up-to-date automatically.
283    
284    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
287    
288            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
289            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
290            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
291            such that the S4 objects are always created by the current version
292            of R and 'Matrix' class definitions.
293    
294    2006-08-01  Douglas Bates  <bates@R-project.org>
295    
296            * R/lmer.R (LMEoptimize method), tests/lmer.R,
297            inst/external/test3comp.rda: Added warnings for convergence on
298            boundary and test cases.
299    
300            * src/lmer.c (mer_postVar): Modified to return the variances that
301            are marginal to the fixed effects, not conditional on them (which
302            is what the bVar slot contents represent).
303    
304    2006-07-31  Douglas Bates  <bates@R-project.org>
305    
306            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
307            function which calls the C function mer_hat_trace2.
308    
309            * man/ranef.Rd: Include description of "postVar" argument and
310            producing a caterpillar plot.
311    
312    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * NAMESPACE:    change  "correlation" to "corMatrix"
315            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
316            * R/dpoMatrix.R: ditto
317            * R/lmer.R:      ditto
318    
319    2006-07-28  Douglas Bates  <bates@R-project.org>
320    
321            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
322            RZXinv slot's contents into a separate internal function that can
323            be used in mer_hat_trace.
324    
325    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
328            via new smart
329            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
330            utility functions.
331    
332    
333    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Csparse.R (tril, triu, band): do return *triangular* classed
336            matrices when appropriate; band() even symmetric ones.
337            (replCmat): extend to potentially all "CsparseMatrix"
338            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
339            allow subassignment for special sparse matrices.
340    
341            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
342    
343            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
344            argument; in glmer_*(): print only if(verbose).
345    
346            speed-optimize a few places by moving REAL(.) out of loops.
347    
348            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
349    
350    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
353                    since that wrongly triggers also for M[ logi , ]
354    
355            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
356            a symmetric matrix that results in a non-symmetric one.
357            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
358    
359            * R/dMatrix.R: make round(M) work as round(M, 0)
360    
361            * R/dgTMatrix.R (image): coordinate system and axis now use
362            1-based indices, not 0-based ones.
363    
364            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
365            * tests/indexing.R: test it.
366    
367            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
368            * man/isSymmetric-methods.Rd: and document it.
369    
370            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
371            * man/SparseM-conv.Rd: docu them
372    
373            * tests/other-pkgs.R: renamed from tests/graph.R and add example
374                    for 'SparseM' conversions
375    
376    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
377    
378            * R/Matrix.R (head): added head() and tail() methods.
379    
380    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * DESCRIPTION (Version): 0.995-12 released to CRAN
383    
384    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * tests/simple.R: add check for correct dsT -> dgT coercion;
387                    add check for correct printing of symmetric sparse matrices.
388    
389            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
390            for sparse symmetric matrices.
391    
392            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
393            diagonal twice.
394    
395    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
396    
397            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
398            being applied to the x slot (detected by Brian Ripley).
399    
400    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
403    
404            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
405    
406    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * src/lgCMatrix.c (lgCMatrix_diag): new function
409            * R/lgCMatrix.R (diag): for new method
410    
411            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
412                 ==> construction of illegal "*gTMatrix" via new() should
413                 now be much less easy:
414            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
415    
416            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
417                    directly.
418            * man/Matrix.Rd: documents it.
419    
420    2006-07-06  Douglas Bates  <bates@R-project.org>
421    
422            * src/pedigree.c (pedigree_inbreeding): Correction in
423            initialization.  This function is not currently being used and is
424            not fully tested.
425    
426            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
427            Introduced the glmer class.  Added code for mcmcmsamp on glmer
428            objects.  Modified validity check on pedigree objects to account
429            for nonparallel patterns of missingness of parents.
430    
431            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
432            class.
433    
434    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/pMatrix.R: coercion pMatrix -> Tsparse
437    
438    2006-06-12  Douglas Bates  <bates@R-project.org>
439    
440            * DESCRIPTION (Version): 0.995-11 released to CRAN
441    
442            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
443            the output from mcmcsamp.
444    
445    2006-06-10  Douglas Bates  <bates@R-project.org>
446    
447            * R/lmer.R (simulestimate): added C code for calculating the trace
448            of the hat matrix.
449    
450    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
453            classes.
454            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
455    
456    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/dgTMatrix.R (colSums): etc. All four of
459            colSums(), rowSums(), colMeans(), rowMeans() now should work for
460            all "Matrices".
461    
462    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
463    
464            * R/lmer.R (panel.ci): Add a reference line at zero and a
465            background grid to the qqmath plot of ranef.lmer.
466    
467    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
468    
469            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
470            grouping factors to be specified in the formula as (1|foo/bar).
471    
472    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
473    
474            * R/lmer.R (findbars and others): Change check of is.numeric to
475            !is.language to resolve the bug reported by Jacob Wegelin.
476    
477            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
478            code to evaluate inbreeding coefficients without calculating T,
479            based on code in Sargolzaei and Iwaisaki's paper.
480    
481    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
482    
483            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
484            generic and mer methods for isNested and denomDF. This denomDF was
485            an attempt to emulate that in lme but I don't think that makes
486            sense.  Use the trace of the hat matrix instead.
487    
488    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
491            the C code depending on a slot structure that's no longer valid.
492            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
493    
494    
495    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
496    
497            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
498            of lowerTriMatrix generic and methods to tril (also upper to triu)
499            and added a general band extractor.
500    
501    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * R/pedigree.R (pedigree): Replace sire and dam values outside the
504            allowable range with NAs. Added a corresponding check in the
505            validity check for the pedigree class.
506    
507            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
508            crossprod methods now inherits from symmetricMatrix.
509    
510    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
511    
512            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
513            generics lowerTriMatrix and upperTriMatrix along with methods for
514            the Csparse virtual class.  Also added a C function Csparse_band
515            that implements these methods by calling cholmod_band.
516    
517    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
520            erased when it was NULL.  This led to invalid subselections!
521    
522    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
525            in method for "t" so as not to lose the unit diagonal property.
526    
527    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
528    
529            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
530            and methods.  This is now an option to the ranef method for the
531            mer class.
532    
533            * src/cs_utils.c: Ensure that the nz component is -1 for a
534            compressed column-oriented matrix.  Minor formatting cleanup.
535    
536            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
537            objects.
538    
539    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
542            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
543    
544    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
545    
546            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
547            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
548    
549            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
550            for the dtCMatrix class.
551    
552    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
553    
554            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
555            and methods for it.
556    
557    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
560            arguments, such that M %*% 1:6 now works
561            * Tests/matprod.R: test the above
562    
563    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
564    
565            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
566            the ranef.lmer class.
567    
568            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
569            methods to extract the posterior variances from the bVar slot.
570    
571    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
574            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
575    
576            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
577            * tests/simple: (extended)
578    
579            * R/sparseMatrix.R (isTriangular): now using much improved
580            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
581    
582    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
583    
584            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
585            (problem report from Franklin Parlamis).  This should be done
586            generally.
587    
588    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
589    
590            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
591            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
592            update the plot methods.
593    
594    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
595    
596            * R/lmer.R (resid and ranef methods):  Added methods for the
597            "residuals" and "resid" generic but only for linear mixed model
598            fits.  Changed the ranef method to return a list of data frames so
599            that the plot methods now work.
600    
601    2006-03-16  Douglas Bates  <bates@bates2>
602    
603            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
604            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
605    
606            * DESCRIPTION (Date): New release
607    
608    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
611    
612            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
613            * man/KNex.Rd: and other help files
614            * tests/*.R: several ones needed adaption
615            * inst/doc/Comparisons.Rnw: ditto
616    
617    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
620    
621            * tests/indexing.R: tests for new [<- methods for sparse matrices.
622    
623    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
626    
627            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
628    
629    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/dMatrix.R: enable things like  M [ M < 10 ]
632            * R/dgeMatrix.R: implement it
633    
634    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/AllClass.R: define "summary.mer" and "*.lmer"
637            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
638            * R/lmer.R (show): now works with summary()
639    
640    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
643            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
644                    support the above
645    
646    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
649            Use glmFit$prior.weights for weights in a glmm.
650            Allow an option usePQL = FALSE to skip the PQL steps for the
651            Laplace method (and, in time, the AGQ method).
652    
653            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
654            into a separate function internal_mer_Xfactor to be able to call
655            it from internal_bhat.
656    
657    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * tests/Class+Meth.R (tstMatrixClass): function for much better
660            testing; now again of all actual classes.
661    
662            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
663                    use macros and define make_d_matrix_* and make_i_matrix_*
664                    where _i_ is for the ldense routines:
665    
666            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
667            * src/ldense.c (lsyMatrix_as_lgeMatrix):
668    
669            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
670    
671    
672    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
675                    many different kinds of matrices.
676            * R/*.R: quite a few new methods were needed for R CMD check with
677                    new Matrix().  Very good for users playing around.
678    
679    
680    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * src/dgeMatrix.c (dMatrix_validate): new
683            * src/Mutils.c (dense_nonpacked_validate): new
684    
685            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
686    
687    
688    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
689    
690            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
691    
692    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
693    
694            * DESCRIPTION (Version): 0.99-6 released to CRAN
695    
696            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
697            segfault in cases with multiple non-nested grouping factors.
698    
699    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
702                    (Depends): also on 'utils'
703    
704            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
705            * R/diagMatrix.R (Diagonal): constructor and methods for
706            diagonal matrices
707    
708            * R/ltTMatrix.R: new "minimal methods"
709    
710    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
713            all methods (and help files).
714    
715    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
718                    for case (dimn.  op  no_dimn.)
719    
720    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
721    
722            * DESCRIPTION (Version): 0.99-2  released to CRAN
723    
724    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
725    
726            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
727            by Julian Faraway.
728    
729    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/Auxiliaries.R (try_as): new utility
732            * R/sparseMatrix.R: use try_as() in coercion to original class
733    
734    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
737    
738    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/Auxiliaries.R (dimNamesCheck): added
741    
742            * R/Matrix.R (as.array), (as.vector): new
743    
744    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
747                    default.
748            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
749                    "pMatrix" now contains "sparseMatrix"
750    
751    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * tests/Class+Meth.R: new tests; t(t(m)) == m
754    
755            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
756    
757            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
758            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
759    
760            * R/dspMatrix.R: typo in "t" method
761    
762    2005-09-18  Douglas Bates  <bates@wisc.edu>
763    
764            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
765            * R/Tsparse.R: instead of R/gTMatrix.R
766            * R/Csparse.R: new
767            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
768            * src/Tsparse.c: new; many trivial methods calling cholmod_()
769            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
770                            via cholmod
771    
772    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/Auxiliaries.R (non0ind): new function using new C code
775            * src/dgCMatrix.c (compressed_non_0_ij): new utility
776    
777    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
778    
779            * src/chm_common.h: header file required by all C sources that
780            call CHOLMOD functions.  It defines a cholmod_common structure
781            called 'c' whose address is passed as the last argument to
782            (virtually) every CHOLMOD function.
783    
784            * src/Pattern.c: Simple example of the use of CHOLMOD.
785    
786            * src/init.c: initialize and finalize the cholmod_common structure.
787    
788            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
789            LDL and CCOLAMD from the U. of Florida sparse matrix library.
790    
791    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * inst/test-tools.R: new file collecting the utility functions used
794                    in ./tests/*.R
795    
796            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
797            * R/Matrix.R (cbind2): methods for NULL and missing
798    
799    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/AllClass.R: new "index" class for "[" and "[<-":
802                    First cut at "symmetricMatrix" and "triangularMatrix"
803            * R/gTMatrix.R (.ind.prep): new function;
804                    Logical and character indexing now work too.
805            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
806            * tests/indexing.R: new, including *.Rout.save
807            * tests/dgTMatrix.R: new
808    
809    2005-08-29  Douglas Bates  <bates@wisc.edu>
810    
811            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
812            indicator pos not being updated.  Also enforced upper triangular
813            for symmetric case.  Need to coerce edges component of elements of
814            edge list - grr! (Why don't they define their classes cleanly?)
815    
816    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/Matrix.R:  added first "[<-" methods; not yet functional
819            * R/denseMatrix.R: ditto
820            * man/Subassign-methods.Rd: new help file for these
821    
822    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * DESCRIPTION (Version): 0.98-6
825    
826            * R/denseMatrix.R: new file for "[" fallback methods for all dense
827            matrices.
828    
829    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
832                    as( <logical>, "matrix")
833    
834            * R/pMatrix.R: coercion to "lgTMatrix"
835    
836            * R/gTMatrix.R: new virtual class to define "[" methods for.
837            * man/gTMatrix-class.Rd:
838            * General slight re-organization of where "[" methods are defined.
839              more to come.
840    
841    2005-08-18  Douglas Bates  <bates@wisc.edu>
842    
843            * DESCRIPTION (Version): 0.98-5  released to CRAN
844    
845            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
846            * .....
847    
848    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
849    
850            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
851            or glmer objects.
852    
853    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
856    
857    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
858    
859            * R/HBMM.R: finish re-writing R-only code.
860    
861    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
862    
863            * man/externalFormats.Rd: move documentation for writeHB and
864            writeMM here.
865    
866            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
867            (suggested by Paul Roecker).
868    
869            * tests/validObj.R (assertError): Comment out test that is failing
870            after recent changes in r-devel.
871    
872    
873  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

Legend:
Removed from v.848  
changed lines
  Added in v.1571

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