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 350, Tue Nov 23 15:39:45 2004 UTC revision 1665, Fri Nov 3 23:18:07 2006 UTC
# Line 1  Line 1 
1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
4            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
5    
6            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
7    
8            * tests/Class+Meth.R (tstMatrixClass): now assure
9            the (important in method programming) property :
10    
11                    ###>>  Every "Matrix" is either
12                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
13    
14                    (where "*" stands for "Matrix")
15    
16            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
17    
18            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
19            * tests/validObj.R: checks for "comparison"
20    
21            * R/sparseMatrix.R ([): improved indexing for sparse;
22                    trying to keep <symmetric>[ n, n] symmmetric
23    
24            * tests/indexing.R: indexing for logical sparse now ok
25    
26    
27    
28    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * src/Tsparse.c: use xTsparse_validate() , and hence remove
31    
32            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
33    
34    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
37    
38            * tests/simple.R: validObject() checking the above.
39    
40            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
41            replacing both dgCMatrix_validate and lgCM*.
42    
43            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
44            fix dimnames setting in other places.
45            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
46    
47    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
50    
51            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
52            symmetry test, via
53            * R/Auxiliaries.R (.as.dgC.0.factors):
54    
55    2006-11-01  Douglas Bates  <bates@r-project.org>
56    
57            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
58            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
59            <CsparseMatrix>) added
60    
61    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * tests/matprod.R: add a variation of Harri's example
64    
65            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
66            recursive infinitely.
67    
68            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
69    
70            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
71    
72    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
75            matrix if possible; test m+m == 2*m; now test dgRMatrix.
76            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
77            satisfy the above test.
78    
79    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
82    
83            * R/dgCMatrix.R: solve(a, b="missing") based on
84            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
85            RHS = NULL.
86    
87            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
88            add more (needed) [t]crossprod() methods.
89    
90            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
91    
92            * R/Auxiliaries.R (as_CspClass): cleanup
93            (drop0): internal utility for "Csparse_drop(*, 0)"
94            (.bail.out.2): encourage active feedback
95    
96    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dMatrix.R(Compare): new(), then slots [no validity check]
99    
100            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
101            non-valid or 'sorted' case).
102    
103            * R/dsparseMatrix.R: add "chol" method.
104            * R/ddenseMatrix.R: ditto
105    
106            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
107            * NAMESPACE (Ops)
108            * R/diagMatrix.R (diag2T): simple utility used "higher level"
109            coercion; deprecating direct lower level coercions.
110    
111            * R/*.R (seq): use seq_len() and seq_along() where possible.
112    
113    
114    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.9975-5 ready for release
117    
118    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
121    
122    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/AllClass.R (corMatrix): add 'validity' check;
125                    comment out unused "LDL" class definition
126            * NAMESPACE: mention, but do not export "LDL" class
127            * R/corMatrix.R: new (simple), needed for R-devel with
128            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
129              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
130    
131    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
134            use Rprintf and R's error handling.
135    
136    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
139            * tests/matprod.R: add tests for the bug fixed.
140    
141    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
144            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
145    
146    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
147    
148            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
149    
150    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Version): 0.9975-3
153    
154            * R/diagMatrix.R (bdiag): new function constructing block diagonal
155            (sparse) matrices.
156            * man/bdiag.Rd: docu + examples
157    
158            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
159    
160            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
161            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
162    
163            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
164            that result is sparse or diagonal (and not dense).
165    
166            * man/Subassign-methods.Rd: fix examples
167    
168            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
169            should always return a sparse (and not sometimes a diagonal) matrix.
170    
171    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
174    
175    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
176    
177            * DESCRIPTION (Version): 0.9975-2
178    
179            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
180    
181    2006-10-02  Douglas Bates  <bates@R-project.org>
182    
183            * tests/dg_Matrix.R: Simplify test taking into account new code.
184    
185    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
188    
189            * R/lsTMatrix.R: new files w/ missing methods
190            * R/nsTMatrix.R:  "  'for completeness'
191    
192            * tests/Class+Meth.R: a bit less 'not.ok.classes'
193    
194            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
195    
196    
197    2006-09-28  Douglas Bates  <bates@R-project.org>
198    
199            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
200            included.
201    
202            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
203            Export C-callable functions used in Zt_create in lme4.
204    
205    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * DESCRIPTION (Version): 0.9975-1
208    
209            * tests/simple.R: less checks fail; using NA, found that our
210                    kronecker() is not base-compatible with NA's.
211    
212            * R/dMatrix.R: "Compare" method now implemented for all cases
213    
214            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
215    
216            * man/dtpMatrix-class.Rd: mention length of 'x' slot
217    
218            * src/dtpMatrix.c (dtpMatrix_validate): fix check
219            * src/dspMatrix.c (dspMatrix_validate): ditto
220    
221            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
222              including coercion to [nl]tTMatrix.
223    
224            * R/diagMatrix.R (show): print a header line as for other classes.
225    
226    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * src/Makefile.win (SUBDIRS): fix typo
229    
230    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
233    
234    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
235    
236            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
237            symmetric and y missing in R code using %*% (cholmod_aat doesn't
238            accept a symmetric matrix).
239            * tests/group-methods.R: Uncomment test of crossprod applied to
240            lsCMatrix objects.
241    
242    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/AllClass.R (symmetricMatrix): add validity method (available
245            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
246    
247            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
248    
249            * tests/indexing.Rout.save:
250            * tests/indexing.R: additions, mainly for 'lsparse'
251    
252            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
253            case.
254    
255            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
256    
257    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
260                    as 'N' (1-letter - Ok?)
261    
262            * tests/group-methods.R: add test for logical + NAs
263    
264            * R/dMatrix.R ("Compare"): fix to work with NA's
265    
266            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
267    
268            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
269                    which is implemented.
270    
271    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * src/chm_common.c: coerce logical <-> double instead of
274            typecasting;  needed for "l" matrix handling in cholmod.
275    
276            * tests/other-pkgs.R (graph): small extension in "graph" checks.
277    
278            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
279            (Tsp2grNEL): other fixes needed
280    
281    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
284                    Matrices, since "lMatrix", also "lsparseM" can have NA
285            * R/ndenseMatrix.R, etc: new source files
286            * man/nsparseMatrix-classes.Rd, etc: new help files
287            * tests/: adaptions
288            * src/chm_common.c (chm_dense_to_SEXP): and others:
289                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
290            * src/Csparse.c, etc: ditto
291    
292    2006-09-11  Douglas Bates  <bates@R-project.org>
293    
294            * src/Mutils.[ch],init.c inst/include/*.h: Move the
295            alloc_d**Matrix functions to the lme4 package.
296    
297    2006-09-09  Douglas Bates  <bates@R-project.org>
298    
299            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
300            fixed
301    
302    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/lMatrix.R: new
305    
306            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
307    
308            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
309            * man/tcrossprod.Rd: ditto
310    
311    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
314            for exported functions
315            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
316            Remove partitioning algorithms for sparse matrix reordering.  The
317            copyright on the Metis code was problematic and the methods were
318            rarely used.
319            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
320            operations are now done entirely in CHOLMOD code.
321    
322    2006-09-06  Douglas Bates  <bates@R-project.org>
323    
324            * src/Mutils.h: Remove functions that are no longer used.
325    
326    2006-09-04  Douglas Bates  <bates@R-project.org>
327    
328            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
329            * src/DEPS.mkf: update
330    
331    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * created branches/Matrix-for-R-2.3.x;  on trunk: do
334            * DESCRIPTION (Version): 0.9975-0
335            (Depends): R (>= 2.4.0)
336    
337    2006-09-01  Douglas Bates  <bates@R-project.org>
338    
339            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
340    
341    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
344            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
345    
346            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
347    
348    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
351            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
352            * R/dsparseMatrix.R: ditto
353            * R/Csparse.R: ditto
354    
355    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/dMatrix.R (Compare): improve availability of "<", etc
358            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
359    
360    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
363            of a 0-index which was used as 1-index (..hmm)
364    
365            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
366    
367            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
368            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
369            (.is.diagonal): ditto
370    
371            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
372    
373            * R/Matrix.R (Matrix): also work for NA data
374    
375    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
378            in all cases.
379    
380    2006-08-27  Douglas Bates  <bates@R-project.org>
381    
382            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
383            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
384    
385    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
388            subclasses of "ddenseMatrix"
389            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
390            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
391            instead of half dozen specialized ones.
392    
393    2006-08-25  Douglas Bates  <bates@R-project.org>
394    
395            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
396            <tillard@cirad.fr> - ordering standard errors to match effects.
397    
398    2006-08-24  Douglas Bates  <bates@R-project.org>
399    
400            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
401            on R_ldl.
402            * R/lCholCMatrix.R,
403            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
404            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
405            * many files in ./R and ./src: Use more general version of
406            dup_mMatrix_as_dgeMatrix to simplify method definitions.
407            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
408            dtpMatrix, dspMatrix and dppMatrix conversions.
409    
410    
411    2006-08-23  Douglas Bates  <bates@R-project.org>
412    
413            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
414            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
415            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
416            dgeMatrix_crossprod (may need to do this in other places).
417            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
418            generic and method for dsCMatrix.  Use CHOLMOD for chol().
419    
420    2006-08-22  Douglas Bates  <bates@R-project.org>
421    
422            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
423            types of classed Matrices, matrices or numeric or logical vectors.
424            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
425            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
426            to Mutils.h (as an inline) and change name to Matrix_check_class;
427            fixes in as_cholmod_factor and chm_factor_to_SEXP.
428            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
429            dsCMatrix_matrix_solve.  Comment out vestigial functions.
430            * src/Csparse.c: use diag_P and uplo_P macros.
431    
432    2006-08-21  Douglas Bates  <bates@R-project.org>
433    
434            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
435            valgrind.
436            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
437            inverses.
438            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
439            -Wall warnings.
440            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
441            Use dup_mMatrix_as_dgeMatrix.
442    
443    2006-08-20  Douglas Bates  <bates@R-project.org>
444    
445            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
446            * tests/sparseQR.R: Added
447            * man/sparseQR-class.Rd: Document methods for qr.* generics
448            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
449    
450    2006-08-19  Douglas Bates  <bates@R-project.org>
451    
452            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
453            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
454            and qr.fitted.
455            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
456            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
457    
458    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
461            the base version has no "..." argument.
462    
463            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
464    
465            * R/Matrix.R: define and
466            * NAMESPACE: export as.numeric() and as.logical() methods.
467                    Let's hope these do not badly slow down something...
468            Finally export the zapsmall() method.
469    
470    2006-08-17  Douglas Bates  <bates@R-project.org>
471    
472            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
473            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
474            * src/dtCMatrix.c :Remove code that is no longer used
475            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
476    
477    2006-08-14  Douglas Bates  <bates@R-project.org>
478    
479            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
480            Csparse_to_logical and Csparse_symmetric_to_general.
481            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
482            coercion methods between CsparseMatrix and TsparseMatrix.
483    
484    2006-08-14  Douglas Bates  <bates@R-project.org>
485    
486            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
487            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
488            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
489            possible.
490    
491    2006-08-12  Douglas Bates  <bates@R-project.org>
492    
493            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
494              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
495              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
496              generalize conversions between TsparseMatrix, CsparseMatrix,
497              denseMatrix and matrix.  Preserve triangularity property and
498              propagate Dimnames in the easy cases.
499    
500    2006-08-10  Douglas Bates  <bates@R-project.org>
501    
502            * src/lmer.c: adjust checks in glmer_init for S4SXP
503            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
504            before S4SXP but for the wrong reasons.
505    
506    2006-08-08  Douglas Bates  <bates@R-project.org>
507    
508            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
509            Later modified to return the upper triangle only.
510            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
511    
512    2006-08-07  Douglas Bates  <bates@R-project.org>
513    
514            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
515            R-level conversion to a sparse symmetric class.
516            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
517            Remove conversion to sparse symmetric classes (now done in C code).
518    
519    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
522            * man/band.Rd:  adapt the \dontshow{} unit test.
523    
524    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * DESCRIPTION (Version): 0.995-14  for CRAN
527    
528            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
529    
530            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
531            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
532    
533            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
534            * R/Tsparse.R (tril, triu, band): methods
535            * R/dgRMatrix.R (tril, ...):    ditto
536            * man/band.Rd:                  ditto
537    
538    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/Matrix.R (head, tail): directly use utils:::head.matrix
541                    to be up-to-date automatically.
542    
543    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
546    
547            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
548            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
549            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
550            such that the S4 objects are always created by the current version
551            of R and 'Matrix' class definitions.
552    
553    2006-08-01  Douglas Bates  <bates@R-project.org>
554    
555            * R/lmer.R (LMEoptimize method), tests/lmer.R,
556            inst/external/test3comp.rda: Added warnings for convergence on
557            boundary and test cases.
558    
559            * src/lmer.c (mer_postVar): Modified to return the variances that
560            are marginal to the fixed effects, not conditional on them (which
561            is what the bVar slot contents represent).
562    
563    2006-07-31  Douglas Bates  <bates@R-project.org>
564    
565            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
566            function which calls the C function mer_hat_trace2.
567    
568            * man/ranef.Rd: Include description of "postVar" argument and
569            producing a caterpillar plot.
570    
571    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * NAMESPACE:    change  "correlation" to "corMatrix"
574            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
575            * R/dpoMatrix.R: ditto
576            * R/lmer.R:      ditto
577    
578    2006-07-28  Douglas Bates  <bates@R-project.org>
579    
580            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
581            RZXinv slot's contents into a separate internal function that can
582            be used in mer_hat_trace.
583    
584    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
587            via new smart
588            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
589            utility functions.
590    
591    
592    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Csparse.R (tril, triu, band): do return *triangular* classed
595            matrices when appropriate; band() even symmetric ones.
596            (replCmat): extend to potentially all "CsparseMatrix"
597            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
598            allow subassignment for special sparse matrices.
599    
600            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
601    
602            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
603            argument; in glmer_*(): print only if(verbose).
604    
605            speed-optimize a few places by moving REAL(.) out of loops.
606    
607            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
608    
609    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
612                    since that wrongly triggers also for M[ logi , ]
613    
614            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
615            a symmetric matrix that results in a non-symmetric one.
616            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
617    
618            * R/dMatrix.R: make round(M) work as round(M, 0)
619    
620            * R/dgTMatrix.R (image): coordinate system and axis now use
621            1-based indices, not 0-based ones.
622    
623            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
624            * tests/indexing.R: test it.
625    
626            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
627            * man/isSymmetric-methods.Rd: and document it.
628    
629            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
630            * man/SparseM-conv.Rd: docu them
631    
632            * tests/other-pkgs.R: renamed from tests/graph.R and add example
633                    for 'SparseM' conversions
634    
635    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
636    
637            * R/Matrix.R (head): added head() and tail() methods.
638    
639    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * DESCRIPTION (Version): 0.995-12 released to CRAN
642    
643    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * tests/simple.R: add check for correct dsT -> dgT coercion;
646                    add check for correct printing of symmetric sparse matrices.
647    
648            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
649            for sparse symmetric matrices.
650    
651            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
652            diagonal twice.
653    
654    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
655    
656            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
657            being applied to the x slot (detected by Brian Ripley).
658    
659    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
662    
663            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
664    
665    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * src/lgCMatrix.c (lgCMatrix_diag): new function
668            * R/lgCMatrix.R (diag): for new method
669    
670            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
671                 ==> construction of illegal "*gTMatrix" via new() should
672                 now be much less easy:
673            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
674    
675            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
676                    directly.
677            * man/Matrix.Rd: documents it.
678    
679    2006-07-06  Douglas Bates  <bates@R-project.org>
680    
681            * src/pedigree.c (pedigree_inbreeding): Correction in
682            initialization.  This function is not currently being used and is
683            not fully tested.
684    
685            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
686            Introduced the glmer class.  Added code for mcmcmsamp on glmer
687            objects.  Modified validity check on pedigree objects to account
688            for nonparallel patterns of missingness of parents.
689    
690            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
691            class.
692    
693    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/pMatrix.R: coercion pMatrix -> Tsparse
696    
697    2006-06-12  Douglas Bates  <bates@R-project.org>
698    
699            * DESCRIPTION (Version): 0.995-11 released to CRAN
700    
701            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
702            the output from mcmcsamp.
703    
704    2006-06-10  Douglas Bates  <bates@R-project.org>
705    
706            * R/lmer.R (simulestimate): added C code for calculating the trace
707            of the hat matrix.
708    
709    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
712            classes.
713            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
714    
715    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/dgTMatrix.R (colSums): etc. All four of
718            colSums(), rowSums(), colMeans(), rowMeans() now should work for
719            all "Matrices".
720    
721    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
722    
723            * R/lmer.R (panel.ci): Add a reference line at zero and a
724            background grid to the qqmath plot of ranef.lmer.
725    
726    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
727    
728            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
729            grouping factors to be specified in the formula as (1|foo/bar).
730    
731    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
732    
733            * R/lmer.R (findbars and others): Change check of is.numeric to
734            !is.language to resolve the bug reported by Jacob Wegelin.
735    
736            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
737            code to evaluate inbreeding coefficients without calculating T,
738            based on code in Sargolzaei and Iwaisaki's paper.
739    
740    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
741    
742            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
743            generic and mer methods for isNested and denomDF. This denomDF was
744            an attempt to emulate that in lme but I don't think that makes
745            sense.  Use the trace of the hat matrix instead.
746    
747    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
750            the C code depending on a slot structure that's no longer valid.
751            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
752    
753    
754    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
755    
756            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
757            of lowerTriMatrix generic and methods to tril (also upper to triu)
758            and added a general band extractor.
759    
760    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
761    
762            * R/pedigree.R (pedigree): Replace sire and dam values outside the
763            allowable range with NAs. Added a corresponding check in the
764            validity check for the pedigree class.
765    
766            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
767            crossprod methods now inherits from symmetricMatrix.
768    
769    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
770    
771            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
772            generics lowerTriMatrix and upperTriMatrix along with methods for
773            the Csparse virtual class.  Also added a C function Csparse_band
774            that implements these methods by calling cholmod_band.
775    
776    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
779            erased when it was NULL.  This led to invalid subselections!
780    
781    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
782    
783            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
784            in method for "t" so as not to lose the unit diagonal property.
785    
786    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
787    
788            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
789            and methods.  This is now an option to the ranef method for the
790            mer class.
791    
792            * src/cs_utils.c: Ensure that the nz component is -1 for a
793            compressed column-oriented matrix.  Minor formatting cleanup.
794    
795            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
796            objects.
797    
798    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
801            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
802    
803    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
804    
805            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
806            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
807    
808            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
809            for the dtCMatrix class.
810    
811    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
812    
813            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
814            and methods for it.
815    
816    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
819            arguments, such that M %*% 1:6 now works
820            * Tests/matprod.R: test the above
821    
822    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
823    
824            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
825            the ranef.lmer class.
826    
827            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
828            methods to extract the posterior variances from the bVar slot.
829    
830    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
833            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
834    
835            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
836            * tests/simple: (extended)
837    
838            * R/sparseMatrix.R (isTriangular): now using much improved
839            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
840    
841    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
842    
843            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
844            (problem report from Franklin Parlamis).  This should be done
845            generally.
846    
847    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
848    
849            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
850            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
851            update the plot methods.
852    
853    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
854    
855            * R/lmer.R (resid and ranef methods):  Added methods for the
856            "residuals" and "resid" generic but only for linear mixed model
857            fits.  Changed the ranef method to return a list of data frames so
858            that the plot methods now work.
859    
860    2006-03-16  Douglas Bates  <bates@bates2>
861    
862            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
863            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
864    
865            * DESCRIPTION (Date): New release
866    
867    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
870    
871            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
872            * man/KNex.Rd: and other help files
873            * tests/*.R: several ones needed adaption
874            * inst/doc/Comparisons.Rnw: ditto
875    
876    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
879    
880            * tests/indexing.R: tests for new [<- methods for sparse matrices.
881    
882    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
885    
886            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
887    
888    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
889    
890            * R/dMatrix.R: enable things like  M [ M < 10 ]
891            * R/dgeMatrix.R: implement it
892    
893    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
894    
895            * R/AllClass.R: define "summary.mer" and "*.lmer"
896            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
897            * R/lmer.R (show): now works with summary()
898    
899    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
902            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
903                    support the above
904    
905    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
906    
907            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
908            Use glmFit$prior.weights for weights in a glmm.
909            Allow an option usePQL = FALSE to skip the PQL steps for the
910            Laplace method (and, in time, the AGQ method).
911    
912            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
913            into a separate function internal_mer_Xfactor to be able to call
914            it from internal_bhat.
915    
916    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
917    
918            * tests/Class+Meth.R (tstMatrixClass): function for much better
919            testing; now again of all actual classes.
920    
921            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
922                    use macros and define make_d_matrix_* and make_i_matrix_*
923                    where _i_ is for the ldense routines:
924    
925            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
926            * src/ldense.c (lsyMatrix_as_lgeMatrix):
927    
928            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
929    
930    
931    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
934                    many different kinds of matrices.
935            * R/*.R: quite a few new methods were needed for R CMD check with
936                    new Matrix().  Very good for users playing around.
937    
938    
939    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * src/dgeMatrix.c (dMatrix_validate): new
942            * src/Mutils.c (dense_nonpacked_validate): new
943    
944            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
945    
946    
947    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
948    
949            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
950    
951    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
952    
953            * DESCRIPTION (Version): 0.99-6 released to CRAN
954    
955            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
956            segfault in cases with multiple non-nested grouping factors.
957    
958    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
961                    (Depends): also on 'utils'
962    
963            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
964            * R/diagMatrix.R (Diagonal): constructor and methods for
965            diagonal matrices
966    
967            * R/ltTMatrix.R: new "minimal methods"
968    
969    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
972            all methods (and help files).
973    
974    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
977                    for case (dimn.  op  no_dimn.)
978    
979    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
980    
981            * DESCRIPTION (Version): 0.99-2  released to CRAN
982    
983    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
984    
985            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
986            by Julian Faraway.
987    
988    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * R/Auxiliaries.R (try_as): new utility
991            * R/sparseMatrix.R: use try_as() in coercion to original class
992    
993    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
996    
997    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * R/Auxiliaries.R (dimNamesCheck): added
1000    
1001            * R/Matrix.R (as.array), (as.vector): new
1002    
1003    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1006                    default.
1007            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1008                    "pMatrix" now contains "sparseMatrix"
1009    
1010    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * tests/Class+Meth.R: new tests; t(t(m)) == m
1013    
1014            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1015    
1016            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1017            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1018    
1019            * R/dspMatrix.R: typo in "t" method
1020    
1021    2005-09-18  Douglas Bates  <bates@wisc.edu>
1022    
1023            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1024            * R/Tsparse.R: instead of R/gTMatrix.R
1025            * R/Csparse.R: new
1026            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1027            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1028            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1029                            via cholmod
1030    
1031    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/Auxiliaries.R (non0ind): new function using new C code
1034            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1035    
1036    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1037    
1038            * src/chm_common.h: header file required by all C sources that
1039            call CHOLMOD functions.  It defines a cholmod_common structure
1040            called 'c' whose address is passed as the last argument to
1041            (virtually) every CHOLMOD function.
1042    
1043            * src/Pattern.c: Simple example of the use of CHOLMOD.
1044    
1045            * src/init.c: initialize and finalize the cholmod_common structure.
1046    
1047            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1048            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1049    
1050    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * inst/test-tools.R: new file collecting the utility functions used
1053                    in ./tests/*.R
1054    
1055            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1056            * R/Matrix.R (cbind2): methods for NULL and missing
1057    
1058    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1059    
1060            * R/AllClass.R: new "index" class for "[" and "[<-":
1061                    First cut at "symmetricMatrix" and "triangularMatrix"
1062            * R/gTMatrix.R (.ind.prep): new function;
1063                    Logical and character indexing now work too.
1064            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1065            * tests/indexing.R: new, including *.Rout.save
1066            * tests/dgTMatrix.R: new
1067    
1068    2005-08-29  Douglas Bates  <bates@wisc.edu>
1069    
1070            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1071            indicator pos not being updated.  Also enforced upper triangular
1072            for symmetric case.  Need to coerce edges component of elements of
1073            edge list - grr! (Why don't they define their classes cleanly?)
1074    
1075    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/Matrix.R:  added first "[<-" methods; not yet functional
1078            * R/denseMatrix.R: ditto
1079            * man/Subassign-methods.Rd: new help file for these
1080    
1081    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1082    
1083            * DESCRIPTION (Version): 0.98-6
1084    
1085            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1086            matrices.
1087    
1088    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1091                    as( <logical>, "matrix")
1092    
1093            * R/pMatrix.R: coercion to "lgTMatrix"
1094    
1095            * R/gTMatrix.R: new virtual class to define "[" methods for.
1096            * man/gTMatrix-class.Rd:
1097            * General slight re-organization of where "[" methods are defined.
1098              more to come.
1099    
1100    2005-08-18  Douglas Bates  <bates@wisc.edu>
1101    
1102            * DESCRIPTION (Version): 0.98-5  released to CRAN
1103    
1104            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1105            * .....
1106    
1107    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1108    
1109            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1110            or glmer objects.
1111    
1112    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1115    
1116    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1117    
1118            * R/HBMM.R: finish re-writing R-only code.
1119    
1120    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1121    
1122            * man/externalFormats.Rd: move documentation for writeHB and
1123            writeMM here.
1124    
1125            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1126            (suggested by Paul Roecker).
1127    
1128            * tests/validObj.R (assertError): Comment out test that is failing
1129            after recent changes in r-devel.
1130    
1131    
1132    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1133    
1134            * R/AllClass.R: intermediate virtual class "denseMatrix"
1135            * man/denseMatrix-class.Rd
1136            * NAMESPACE: export it, and also export
1137            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1138    
1139    2005-08-10  Douglas Bates  <bates@wisc.edu>
1140    
1141            * DESCRIPTION (Version): 0.98-3 to CRAN
1142    
1143            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1144            matrix_solve code (which was really, really wrong).
1145    
1146    2005-08-07  Douglas Bates  <bates@wisc.edu>
1147    
1148            * DESCRIPTION (Version): 0.98-2
1149    
1150            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1151    
1152            * R/lmer.R (abbrvNms): new
1153            * R/lmer.R (mcmcsamp): allow transformed parameters
1154            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1155            for the Harwell-Boeing and the MatrixMarket formats.
1156    
1157    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1158    
1159            * man/dtrMatrix-class.Rd: add examples
1160            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1161    
1162            * TODO: note the dtpMatrix (docu) bug
1163    
1164            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1165            in order to ensure that new as.matrix() is used by old functions,
1166            e.g., svd(), qr(), eigen(), dist(),..;
1167                  apply(), also matplot() or pairs().
1168    
1169    
1170    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1173              add comments about 'control' / lmerControl() arguments
1174    
1175    2005-07-27  Douglas Bates  <bates@wisc.edu>
1176    
1177            * man/sleepstudy.Rd: Added the sleep data set.
1178            * DESCRIPTION (Version): 0.98-1  released to CRAN
1179    
1180    2005-07-12  Douglas Bates  <bates@wisc.edu>
1181            * man/sleepstudy.Rd: Added the sleep data set.
1182    
1183            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1184            .Call calls that were producing spurious output.
1185    
1186    2005-07-05  Douglas Bates  <bates@wisc.edu>
1187    
1188            * R/lmer.R (lmer): stored updated variance component estimates in
1189            mer object for the generalized model.  (Bug reported by Renaud
1190            Lancelot).
1191    
1192    2005-07-03  Douglas Bates  <bates@wisc.edu>
1193    
1194            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1195            unidimensional case.
1196    
1197    2005-06-08  Douglas Bates  <bates@wisc.edu>
1198    
1199            * DESCRIPTION (Version): 0.96-1
1200    
1201            * moved  lmer-class' R and C code moved from lme4 to here
1202    
1203    2005-06-04  Douglas Bates  <bates@wisc.edu>
1204    
1205            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1206            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1207    
1208    2005-06-02  Douglas Bates  <bates@wisc.edu>
1209    
1210            * src/Makefile.win: Forgot to update this when Makefile changed.
1211    
1212    2005-05-11  Douglas Bates  <bates@wisc.edu>
1213    
1214            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1215            bug reported by Kurt Hornik and Michael Hahsler.
1216    
1217    2005-05-10  Douglas Bates  <bates@wisc.edu>
1218    
1219            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1220            logical sparse matrices.  These will also be used in the symbolic
1221            analysis for lmer objects.
1222    
1223            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1224            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1225    
1226    2005-05-06  Douglas Bates  <bates@wisc.edu>
1227    
1228            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1229            colMeans, colSums, rowMeans and rowSums.
1230    
1231    2005-04-18  Douglas Bates  <bates@wisc.edu>
1232    
1233            * src/lgCMatrix.[ch]: code for _validate method and stub for
1234            multiplication operation.
1235    
1236            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1237            to dgetrs.
1238    
1239            * src/init.c: Fix cut-and-paste error in definition of
1240            dgeMatrix_matrix_solve
1241    
1242            * src/{many files}: Tighten code by using ALLOC_SLOT.
1243    
1244    2005-04-15  Douglas Bates  <bates@wisc.edu>
1245    
1246            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1247    
1248            * DESCRIPTION: Eliminate import of stats.
1249    
1250    
1251    2005-04-06  Douglas Bates  <bates@wisc.edu>
1252    
1253            * R/AllClass.R : add logical sparse matrix classes
1254    
1255    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1256    
1257            * R/dgTMatrix.R: add "[" method for triplet matrices
1258            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1259    
1260    2005-03-31  Douglas Bates  <bates@wisc.edu>
1261    
1262            * DESCRIPTION (Version): release 0.95-5 to CRAN
1263    
1264            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1265            * R/sparseMatrix.R: %*%, crossprod()
1266            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1267            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1268            * src/lmer.c (lmer_fitted): fix thinko
1269    
1270    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1271    
1272            * R/AllClass.R: add two virtual sparse classes ``on top''
1273    
1274    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1275    
1276            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1277                    correspondingly fix examples and tests/ since new()
1278                    doesn't work for virtual classes.
1279    
1280    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * R/Matrix.R (as.matrix): method and one for unname()
1283            * tests/dpoMatrix.R: tests should now be less platform dependent;
1284              also run for R 2.1.0; using as.matrix()
1285    
1286    2005-03-15  Douglas Bates  <bates@wisc.edu>
1287    
1288            * R/pMatrix.R: "pMatrix" class added
1289            * ....
1290    
1291    2005-03-14  Douglas Bates  <bates@wisc.edu>
1292    
1293            * R/dtpMatrix.R: Add unpack method and an example.
1294    
1295            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1296            of general symmetric matrices and associated S4 methods.
1297    
1298    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1299            +
1300    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1303              crossprod() and "%*%" methods added; tests, too.
1304            * tests/matprod.R: new, for testing these
1305    
1306    2005-03-03  Douglas Bates  <bates@wisc.edu>
1307    
1308            * src/lmer.c (lmer_fitted): Added.
1309    
1310    2005-03-02  Douglas Bates  <bates@wisc.edu>
1311    
1312            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1313    
1314    2005-02-28  Douglas Bates  <bates@wisc.edu>
1315    
1316            * src/*.c,po/,inst/po: Internationalization and localization of
1317            the package.
1318    
1319            * src/ldl.[ch]: Removed these as their contents are referenced in the
1320            R_ldl.c file.
1321    
1322            * src/flame.[ch]: Removed these source files.
1323    
1324            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1325    
1326            * src/LU.[ch],src/init.c: absorb in factorizations
1327    
1328            * src/Mutils.h: prepare for internationalization
1329    
1330            * src/cblas.h: move the enum definitions to Mutils.h and remove
1331            this file
1332    
1333    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1334    
1335            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1336    
1337            * R/dtrMatrix.R: fix t() method
1338    
1339            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1340            * NAMESPACE: export them (and import generics from "methods")
1341            * tests/group-methods.R : and test them.
1342    
1343            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1344            border case
1345    
1346    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1347    
1348            * DESCRIPTION (Version): 0.95-2  released to CRAN
1349    
1350            * src/dgBCMatrix.c:
1351            * src/lmer.c: many changes
1352            * ...
1353    
1354    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1355    
1356            * R/Matrix.R: add more sophisticated show() method.
1357    
1358    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1359    
1360            * */* : almost complete reorganization of classes.
1361    
1362    2005-01-26  Douglas Bates  <bates@wisc.edu>
1363    
1364            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1365            for the geMatrix class.
1366    
1367    2005-01-24  Douglas Bates  <bates@wisc.edu>
1368    
1369            * src/Makefile (clean): Remove *.a and *.so
1370    
1371            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1372    
1373    2005-01-23  Douglas Bates  <bates@wisc.edu>
1374    
1375            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1376            had an effect in cases with more than 2 grouping factors.
1377    
1378    2005-01-03  Douglas Bates  <bates@wisc.edu>
1379    
1380            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1381    
1382    2004-12-23  Douglas Bates  <bates@wisc.edu>
1383    
1384            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1385            and R_useDynamicSymbols (suggested by B.D.Ripley).
1386    
1387    2004-12-14  Douglas Bates  <bates@wisc.edu>
1388    
1389            * R/sscMatrix.R: Add determinant methods
1390    
1391            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1392            for tripletMatrix to matrix.
1393    
1394    2004-12-13  Douglas Bates  <bates@wisc.edu>
1395    
1396            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1397            no longer used.
1398    
1399            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1400            with dynamic allocation of scratch arrays.
1401    
1402            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1403            for multivariate random effects with multiple grouping factors.
1404            Fixes part but not all of #15.
1405    
1406    2004-12-03  Douglas Bates  <bates@wisc.edu>
1407    
1408            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1409            scalar grouping factors corrected.
1410    
1411    2004-11-29  Douglas Bates  <bates@wisc.edu>
1412    
1413            * src/bCrosstab.c: remove diag_update which is no longer used
1414    
1415    2004-11-16  Douglas Bates  <bates@wisc.edu>
1416    
1417          * 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
1418          .h file can be included.          .h file can be included.
1419    
1420  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1421    
1422          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1423          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1424    
1425          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1426    
1427  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1428    
1429          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1430    
1431  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1432    
1433          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1434    
1435  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1436    
1437          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1438    
1439  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1440    
1441          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1442    
1443  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1444    
1445          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1446          routines.          routines.
1447    
1448  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1449    
1450          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1451    
1452  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1453    
1454          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1455    

Legend:
Removed from v.350  
changed lines
  Added in v.1665

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