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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1583, Tue Sep 19 08:33:54 2006 UTC
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1    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
4    
5    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
8            symmetric and y missing in R code using %*% (cholmod_aat doesn't
9            accept a symmetric matrix).
10            * tests/group-methods.R: Uncomment test of crossprod applied to
11            lsCMatrix objects.
12    
13    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/AllClass.R (symmetricMatrix): add validity method (available
16            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
17    
18            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
19    
20            * tests/indexing.Rout.save:
21            * tests/indexing.R: additions, mainly for 'lsparse'
22    
23            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
24            case.
25    
26            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
27    
28    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
31                    as 'N' (1-letter - Ok?)
32    
33            * tests/group-methods.R: add test for logical + NAs
34    
35            * R/dMatrix.R ("Compare"): fix to work with NA's
36    
37            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
38    
39            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
40                    which is implemented.
41    
42    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/chm_common.c: coerce logical <-> double instead of
45            typecasting;  needed for "l" matrix handling in cholmod.
46    
47            * tests/other-pkgs.R (graph): small extension in "graph" checks.
48    
49            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
50            (Tsp2grNEL): other fixes needed
51    
52    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
55                    Matrices, since "lMatrix", also "lsparseM" can have NA
56            * R/ndenseMatrix.R, etc: new source files
57            * man/nsparseMatrix-classes.Rd, etc: new help files
58            * tests/: adaptions
59            * src/chm_common.c (chm_dense_to_SEXP): and others:
60                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
61            * src/Csparse.c, etc: ditto
62    
63    2006-09-11  Douglas Bates  <bates@R-project.org>
64    
65            * src/Mutils.[ch],init.c inst/include/*.h: Move the
66            alloc_d**Matrix functions to the lme4 package.
67    
68    2006-09-09  Douglas Bates  <bates@R-project.org>
69    
70            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
71            fixed
72    
73    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/lMatrix.R: new
76    
77            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
78    
79            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
80            * man/tcrossprod.Rd: ditto
81    
82    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
83    
84            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
85            for exported functions
86            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
87            Remove partitioning algorithms for sparse matrix reordering.  The
88            copyright on the Metis code was problematic and the methods were
89            rarely used.
90            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
91            operations are now done entirely in CHOLMOD code.
92    
93    2006-09-06  Douglas Bates  <bates@R-project.org>
94    
95            * src/Mutils.h: Remove functions that are no longer used.
96    
97    2006-09-04  Douglas Bates  <bates@R-project.org>
98    
99            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
100            * src/DEPS.mkf: update
101    
102    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * created branches/Matrix-for-R-2.3.x;  on trunk: do
105            * DESCRIPTION (Version): 0.9975-0
106            (Depends): R (>= 2.4.0)
107    
108    2006-09-01  Douglas Bates  <bates@R-project.org>
109    
110            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
111    
112    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
115            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
116    
117            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
118    
119    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
122            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
123            * R/dsparseMatrix.R: ditto
124            * R/Csparse.R: ditto
125    
126    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/dMatrix.R (Compare): improve availability of "<", etc
129            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
130    
131    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
134            of a 0-index which was used as 1-index (..hmm)
135    
136            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
137    
138            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
139            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
140            (.is.diagonal): ditto
141    
142            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
143    
144            * R/Matrix.R (Matrix): also work for NA data
145    
146    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
149            in all cases.
150    
151    2006-08-27  Douglas Bates  <bates@R-project.org>
152    
153            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
154            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
155    
156    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
159            subclasses of "ddenseMatrix"
160            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
161            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
162            instead of half dozen specialized ones.
163    
164    2006-08-25  Douglas Bates  <bates@R-project.org>
165    
166            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
167            <tillard@cirad.fr> - ordering standard errors to match effects.
168    
169    2006-08-24  Douglas Bates  <bates@R-project.org>
170    
171            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
172            on R_ldl.
173            * R/lCholCMatrix.R,
174            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
175            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
176            * many files in ./R and ./src: Use more general version of
177            dup_mMatrix_as_dgeMatrix to simplify method definitions.
178            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
179            dtpMatrix, dspMatrix and dppMatrix conversions.
180    
181    
182    2006-08-23  Douglas Bates  <bates@R-project.org>
183    
184            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
185            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
186            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
187            dgeMatrix_crossprod (may need to do this in other places).
188            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
189            generic and method for dsCMatrix.  Use CHOLMOD for chol().
190    
191    2006-08-22  Douglas Bates  <bates@R-project.org>
192    
193            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
194            types of classed Matrices, matrices or numeric or logical vectors.
195            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
196            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
197            to Mutils.h (as an inline) and change name to Matrix_check_class;
198            fixes in as_cholmod_factor and chm_factor_to_SEXP.
199            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
200            dsCMatrix_matrix_solve.  Comment out vestigial functions.
201            * src/Csparse.c: use diag_P and uplo_P macros.
202    
203    2006-08-21  Douglas Bates  <bates@R-project.org>
204    
205            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
206            valgrind.
207            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
208            inverses.
209            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
210            -Wall warnings.
211            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
212            Use dup_mMatrix_as_dgeMatrix.
213    
214    2006-08-20  Douglas Bates  <bates@R-project.org>
215    
216            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
217            * tests/sparseQR.R: Added
218            * man/sparseQR-class.Rd: Document methods for qr.* generics
219            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
220    
221    2006-08-19  Douglas Bates  <bates@R-project.org>
222    
223            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
224            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
225            and qr.fitted.
226            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
227            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
228    
229    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
232            the base version has no "..." argument.
233    
234            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
235    
236            * R/Matrix.R: define and
237            * NAMESPACE: export as.numeric() and as.logical() methods.
238                    Let's hope these do not badly slow down something...
239            Finally export the zapsmall() method.
240    
241    2006-08-17  Douglas Bates  <bates@R-project.org>
242    
243            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
244            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
245            * src/dtCMatrix.c :Remove code that is no longer used
246            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
247    
248    2006-08-14  Douglas Bates  <bates@R-project.org>
249    
250            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
251            Csparse_to_logical and Csparse_symmetric_to_general.
252            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
253            coercion methods between CsparseMatrix and TsparseMatrix.
254    
255    2006-08-14  Douglas Bates  <bates@R-project.org>
256    
257            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
258            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
259            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
260            possible.
261    
262    2006-08-12  Douglas Bates  <bates@R-project.org>
263    
264            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
265              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
266              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
267              generalize conversions between TsparseMatrix, CsparseMatrix,
268              denseMatrix and matrix.  Preserve triangularity property and
269              propagate Dimnames in the easy cases.
270    
271    2006-08-10  Douglas Bates  <bates@R-project.org>
272    
273            * src/lmer.c: adjust checks in glmer_init for S4SXP
274            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
275            before S4SXP but for the wrong reasons.
276    
277    2006-08-08  Douglas Bates  <bates@R-project.org>
278    
279            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
280            Later modified to return the upper triangle only.
281            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
282    
283    2006-08-07  Douglas Bates  <bates@R-project.org>
284    
285            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
286            R-level conversion to a sparse symmetric class.
287            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
288            Remove conversion to sparse symmetric classes (now done in C code).
289    
290    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
293            * man/band.Rd:  adapt the \dontshow{} unit test.
294    
295    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * DESCRIPTION (Version): 0.995-14  for CRAN
298    
299            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
300    
301            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
302            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
303    
304            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
305            * R/Tsparse.R (tril, triu, band): methods
306            * R/dgRMatrix.R (tril, ...):    ditto
307            * man/band.Rd:                  ditto
308    
309    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Matrix.R (head, tail): directly use utils:::head.matrix
312                    to be up-to-date automatically.
313    
314    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
317    
318            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
319            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
320            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
321            such that the S4 objects are always created by the current version
322            of R and 'Matrix' class definitions.
323    
324    2006-08-01  Douglas Bates  <bates@R-project.org>
325    
326            * R/lmer.R (LMEoptimize method), tests/lmer.R,
327            inst/external/test3comp.rda: Added warnings for convergence on
328            boundary and test cases.
329    
330            * src/lmer.c (mer_postVar): Modified to return the variances that
331            are marginal to the fixed effects, not conditional on them (which
332            is what the bVar slot contents represent).
333    
334    2006-07-31  Douglas Bates  <bates@R-project.org>
335    
336            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
337            function which calls the C function mer_hat_trace2.
338    
339            * man/ranef.Rd: Include description of "postVar" argument and
340            producing a caterpillar plot.
341    
342    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * NAMESPACE:    change  "correlation" to "corMatrix"
345            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
346            * R/dpoMatrix.R: ditto
347            * R/lmer.R:      ditto
348    
349    2006-07-28  Douglas Bates  <bates@R-project.org>
350    
351            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
352            RZXinv slot's contents into a separate internal function that can
353            be used in mer_hat_trace.
354    
355    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
358            via new smart
359            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
360            utility functions.
361    
362    
363    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/Csparse.R (tril, triu, band): do return *triangular* classed
366            matrices when appropriate; band() even symmetric ones.
367            (replCmat): extend to potentially all "CsparseMatrix"
368            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
369            allow subassignment for special sparse matrices.
370    
371            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
372    
373            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
374            argument; in glmer_*(): print only if(verbose).
375    
376            speed-optimize a few places by moving REAL(.) out of loops.
377    
378            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
379    
380    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
383                    since that wrongly triggers also for M[ logi , ]
384    
385            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
386            a symmetric matrix that results in a non-symmetric one.
387            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
388    
389            * R/dMatrix.R: make round(M) work as round(M, 0)
390    
391            * R/dgTMatrix.R (image): coordinate system and axis now use
392            1-based indices, not 0-based ones.
393    
394            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
395            * tests/indexing.R: test it.
396    
397            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
398            * man/isSymmetric-methods.Rd: and document it.
399    
400            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
401            * man/SparseM-conv.Rd: docu them
402    
403            * tests/other-pkgs.R: renamed from tests/graph.R and add example
404                    for 'SparseM' conversions
405    
406    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
407    
408            * R/Matrix.R (head): added head() and tail() methods.
409    
410    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * DESCRIPTION (Version): 0.995-12 released to CRAN
413    
414    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * tests/simple.R: add check for correct dsT -> dgT coercion;
417                    add check for correct printing of symmetric sparse matrices.
418    
419            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
420            for sparse symmetric matrices.
421    
422            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
423            diagonal twice.
424    
425    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
426    
427            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
428            being applied to the x slot (detected by Brian Ripley).
429    
430    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
433    
434            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
435    
436    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * src/lgCMatrix.c (lgCMatrix_diag): new function
439            * R/lgCMatrix.R (diag): for new method
440    
441            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
442                 ==> construction of illegal "*gTMatrix" via new() should
443                 now be much less easy:
444            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
445    
446            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
447                    directly.
448            * man/Matrix.Rd: documents it.
449    
450    2006-07-06  Douglas Bates  <bates@R-project.org>
451    
452            * src/pedigree.c (pedigree_inbreeding): Correction in
453            initialization.  This function is not currently being used and is
454            not fully tested.
455    
456            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
457            Introduced the glmer class.  Added code for mcmcmsamp on glmer
458            objects.  Modified validity check on pedigree objects to account
459            for nonparallel patterns of missingness of parents.
460    
461            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
462            class.
463    
464    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/pMatrix.R: coercion pMatrix -> Tsparse
467    
468    2006-06-12  Douglas Bates  <bates@R-project.org>
469    
470            * DESCRIPTION (Version): 0.995-11 released to CRAN
471    
472            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
473            the output from mcmcsamp.
474    
475    2006-06-10  Douglas Bates  <bates@R-project.org>
476    
477            * R/lmer.R (simulestimate): added C code for calculating the trace
478            of the hat matrix.
479    
480    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
483            classes.
484            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
485    
486    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/dgTMatrix.R (colSums): etc. All four of
489            colSums(), rowSums(), colMeans(), rowMeans() now should work for
490            all "Matrices".
491    
492    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
493    
494            * R/lmer.R (panel.ci): Add a reference line at zero and a
495            background grid to the qqmath plot of ranef.lmer.
496    
497    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
498    
499            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
500            grouping factors to be specified in the formula as (1|foo/bar).
501    
502    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
503    
504            * R/lmer.R (findbars and others): Change check of is.numeric to
505            !is.language to resolve the bug reported by Jacob Wegelin.
506    
507            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
508            code to evaluate inbreeding coefficients without calculating T,
509            based on code in Sargolzaei and Iwaisaki's paper.
510    
511    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
512    
513            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
514            generic and mer methods for isNested and denomDF. This denomDF was
515            an attempt to emulate that in lme but I don't think that makes
516            sense.  Use the trace of the hat matrix instead.
517    
518    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
521            the C code depending on a slot structure that's no longer valid.
522            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
523    
524    
525    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
526    
527            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
528            of lowerTriMatrix generic and methods to tril (also upper to triu)
529            and added a general band extractor.
530    
531    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
532    
533            * R/pedigree.R (pedigree): Replace sire and dam values outside the
534            allowable range with NAs. Added a corresponding check in the
535            validity check for the pedigree class.
536    
537            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
538            crossprod methods now inherits from symmetricMatrix.
539    
540    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
541    
542            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
543            generics lowerTriMatrix and upperTriMatrix along with methods for
544            the Csparse virtual class.  Also added a C function Csparse_band
545            that implements these methods by calling cholmod_band.
546    
547    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
550            erased when it was NULL.  This led to invalid subselections!
551    
552    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
553    
554            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
555            in method for "t" so as not to lose the unit diagonal property.
556    
557    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
558    
559            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
560            and methods.  This is now an option to the ranef method for the
561            mer class.
562    
563            * src/cs_utils.c: Ensure that the nz component is -1 for a
564            compressed column-oriented matrix.  Minor formatting cleanup.
565    
566            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
567            objects.
568    
569    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
572            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
573    
574    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
575    
576            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
577            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
578    
579            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
580            for the dtCMatrix class.
581    
582    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
583    
584            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
585            and methods for it.
586    
587    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
590            arguments, such that M %*% 1:6 now works
591            * Tests/matprod.R: test the above
592    
593    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
594    
595            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
596            the ranef.lmer class.
597    
598            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
599            methods to extract the posterior variances from the bVar slot.
600    
601    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
604            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
605    
606            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
607            * tests/simple: (extended)
608    
609            * R/sparseMatrix.R (isTriangular): now using much improved
610            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
611    
612    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
613    
614            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
615            (problem report from Franklin Parlamis).  This should be done
616            generally.
617    
618    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
619    
620            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
621            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
622            update the plot methods.
623    
624    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
625    
626            * R/lmer.R (resid and ranef methods):  Added methods for the
627            "residuals" and "resid" generic but only for linear mixed model
628            fits.  Changed the ranef method to return a list of data frames so
629            that the plot methods now work.
630    
631    2006-03-16  Douglas Bates  <bates@bates2>
632    
633            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
634            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
635    
636            * DESCRIPTION (Date): New release
637    
638    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
641    
642            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
643            * man/KNex.Rd: and other help files
644            * tests/*.R: several ones needed adaption
645            * inst/doc/Comparisons.Rnw: ditto
646    
647    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
650    
651            * tests/indexing.R: tests for new [<- methods for sparse matrices.
652    
653    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
656    
657            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
658    
659    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/dMatrix.R: enable things like  M [ M < 10 ]
662            * R/dgeMatrix.R: implement it
663    
664    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/AllClass.R: define "summary.mer" and "*.lmer"
667            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
668            * R/lmer.R (show): now works with summary()
669    
670    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
673            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
674                    support the above
675    
676    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
677    
678            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
679            Use glmFit$prior.weights for weights in a glmm.
680            Allow an option usePQL = FALSE to skip the PQL steps for the
681            Laplace method (and, in time, the AGQ method).
682    
683            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
684            into a separate function internal_mer_Xfactor to be able to call
685            it from internal_bhat.
686    
687    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * tests/Class+Meth.R (tstMatrixClass): function for much better
690            testing; now again of all actual classes.
691    
692            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
693                    use macros and define make_d_matrix_* and make_i_matrix_*
694                    where _i_ is for the ldense routines:
695    
696            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
697            * src/ldense.c (lsyMatrix_as_lgeMatrix):
698    
699            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
700    
701    
702    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
705                    many different kinds of matrices.
706            * R/*.R: quite a few new methods were needed for R CMD check with
707                    new Matrix().  Very good for users playing around.
708    
709    
710    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * src/dgeMatrix.c (dMatrix_validate): new
713            * src/Mutils.c (dense_nonpacked_validate): new
714    
715            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
716    
717    
718    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
719    
720            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
721    
722    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
723    
724            * DESCRIPTION (Version): 0.99-6 released to CRAN
725    
726            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
727            segfault in cases with multiple non-nested grouping factors.
728    
729    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
732                    (Depends): also on 'utils'
733    
734            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
735            * R/diagMatrix.R (Diagonal): constructor and methods for
736            diagonal matrices
737    
738            * R/ltTMatrix.R: new "minimal methods"
739    
740    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
743            all methods (and help files).
744    
745    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
748                    for case (dimn.  op  no_dimn.)
749    
750    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
751    
752            * DESCRIPTION (Version): 0.99-2  released to CRAN
753    
754    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
757            by Julian Faraway.
758    
759    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
760    
761            * R/Auxiliaries.R (try_as): new utility
762            * R/sparseMatrix.R: use try_as() in coercion to original class
763    
764    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
767    
768    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/Auxiliaries.R (dimNamesCheck): added
771    
772            * R/Matrix.R (as.array), (as.vector): new
773    
774    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
777                    default.
778            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
779                    "pMatrix" now contains "sparseMatrix"
780    
781    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * tests/Class+Meth.R: new tests; t(t(m)) == m
784    
785            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
786    
787            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
788            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
789    
790            * R/dspMatrix.R: typo in "t" method
791    
792    2005-09-18  Douglas Bates  <bates@wisc.edu>
793    
794            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
795            * R/Tsparse.R: instead of R/gTMatrix.R
796            * R/Csparse.R: new
797            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
798            * src/Tsparse.c: new; many trivial methods calling cholmod_()
799            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
800                            via cholmod
801    
802    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * R/Auxiliaries.R (non0ind): new function using new C code
805            * src/dgCMatrix.c (compressed_non_0_ij): new utility
806    
807    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
808    
809            * src/chm_common.h: header file required by all C sources that
810            call CHOLMOD functions.  It defines a cholmod_common structure
811            called 'c' whose address is passed as the last argument to
812            (virtually) every CHOLMOD function.
813    
814            * src/Pattern.c: Simple example of the use of CHOLMOD.
815    
816            * src/init.c: initialize and finalize the cholmod_common structure.
817    
818            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
819            LDL and CCOLAMD from the U. of Florida sparse matrix library.
820    
821    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * inst/test-tools.R: new file collecting the utility functions used
824                    in ./tests/*.R
825    
826            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
827            * R/Matrix.R (cbind2): methods for NULL and missing
828    
829    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * R/AllClass.R: new "index" class for "[" and "[<-":
832                    First cut at "symmetricMatrix" and "triangularMatrix"
833            * R/gTMatrix.R (.ind.prep): new function;
834                    Logical and character indexing now work too.
835            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
836            * tests/indexing.R: new, including *.Rout.save
837            * tests/dgTMatrix.R: new
838    
839  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
840    
841          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 846 
846  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
849          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
850          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
851    
852  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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