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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1673, Mon Nov 6 20:54:26 2006 UTC
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1    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
4            now returns symmetric.
5    
6            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
7    
8            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
9            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
10    
11            * R/Auxiliaries.R (.type.kind): added
12    
13    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
16            running src/CSparse_install.sh
17    
18            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
19    
20    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
23            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
24    
25            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
26    
27            * tests/Class+Meth.R (tstMatrixClass): now assure
28            the (important in method programming) property :
29    
30                    ###>>  Every "Matrix" is either
31                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
32    
33                    (where "*" stands for "Matrix")
34    
35            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
36    
37            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
38            * tests/validObj.R: checks for "comparison"
39    
40            * R/sparseMatrix.R ([): improved indexing for sparse;
41                    trying to keep <symmetric>[ n, n] symmmetric
42    
43            * tests/indexing.R: indexing for logical sparse now ok
44    
45    
46    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * src/Tsparse.c: use xTsparse_validate() , and hence remove
49    
50            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
51    
52    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
55    
56            * tests/simple.R: validObject() checking the above.
57    
58            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
59            replacing both dgCMatrix_validate and lgCM*.
60    
61            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
62            fix dimnames setting in other places.
63            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
64    
65    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
68    
69            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
70            symmetry test, via
71            * R/Auxiliaries.R (.as.dgC.0.factors):
72    
73    2006-11-01  Douglas Bates  <bates@r-project.org>
74    
75            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
76            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
77            <CsparseMatrix>) added
78    
79    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * tests/matprod.R: add a variation of Harri's example
82    
83            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
84            recursive infinitely.
85    
86            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
87    
88            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
89    
90    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
93            matrix if possible; test m+m == 2*m; now test dgRMatrix.
94            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
95            satisfy the above test.
96    
97    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
100    
101            * R/dgCMatrix.R: solve(a, b="missing") based on
102            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
103            RHS = NULL.
104    
105            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
106            add more (needed) [t]crossprod() methods.
107    
108            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
109    
110            * R/Auxiliaries.R (as_CspClass): cleanup
111            (drop0): internal utility for "Csparse_drop(*, 0)"
112            (.bail.out.2): encourage active feedback
113    
114    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dMatrix.R(Compare): new(), then slots [no validity check]
117    
118            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
119            non-valid or 'sorted' case).
120    
121            * R/dsparseMatrix.R: add "chol" method.
122            * R/ddenseMatrix.R: ditto
123    
124            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
125            * NAMESPACE (Ops)
126            * R/diagMatrix.R (diag2T): simple utility used "higher level"
127            coercion; deprecating direct lower level coercions.
128    
129            * R/*.R (seq): use seq_len() and seq_along() where possible.
130    
131    
132    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * DESCRIPTION (Version): 0.9975-5 ready for release
135    
136    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
139    
140    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/AllClass.R (corMatrix): add 'validity' check;
143                    comment out unused "LDL" class definition
144            * NAMESPACE: mention, but do not export "LDL" class
145            * R/corMatrix.R: new (simple), needed for R-devel with
146            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
147              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
148    
149    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
150    
151            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
152            use Rprintf and R's error handling.
153    
154    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
157            * tests/matprod.R: add tests for the bug fixed.
158    
159    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
162            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
163    
164    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
167    
168    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * DESCRIPTION (Version): 0.9975-3
171    
172            * R/diagMatrix.R (bdiag): new function constructing block diagonal
173            (sparse) matrices.
174            * man/bdiag.Rd: docu + examples
175    
176            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
177    
178            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
179            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
180    
181            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
182            that result is sparse or diagonal (and not dense).
183    
184            * man/Subassign-methods.Rd: fix examples
185    
186            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
187            should always return a sparse (and not sometimes a diagonal) matrix.
188    
189    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
192    
193    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * DESCRIPTION (Version): 0.9975-2
196    
197            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
198    
199    2006-10-02  Douglas Bates  <bates@R-project.org>
200    
201            * tests/dg_Matrix.R: Simplify test taking into account new code.
202    
203    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
206    
207            * R/lsTMatrix.R: new files w/ missing methods
208            * R/nsTMatrix.R:  "  'for completeness'
209    
210            * tests/Class+Meth.R: a bit less 'not.ok.classes'
211    
212            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
213    
214    
215    2006-09-28  Douglas Bates  <bates@R-project.org>
216    
217            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
218            included.
219    
220            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
221            Export C-callable functions used in Zt_create in lme4.
222    
223    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * DESCRIPTION (Version): 0.9975-1
226    
227            * tests/simple.R: less checks fail; using NA, found that our
228                    kronecker() is not base-compatible with NA's.
229    
230            * R/dMatrix.R: "Compare" method now implemented for all cases
231    
232            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
233    
234            * man/dtpMatrix-class.Rd: mention length of 'x' slot
235    
236            * src/dtpMatrix.c (dtpMatrix_validate): fix check
237            * src/dspMatrix.c (dspMatrix_validate): ditto
238    
239            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
240              including coercion to [nl]tTMatrix.
241    
242            * R/diagMatrix.R (show): print a header line as for other classes.
243    
244    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/Makefile.win (SUBDIRS): fix typo
247    
248    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
251    
252    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
253    
254            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
255            symmetric and y missing in R code using %*% (cholmod_aat doesn't
256            accept a symmetric matrix).
257            * tests/group-methods.R: Uncomment test of crossprod applied to
258            lsCMatrix objects.
259    
260    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/AllClass.R (symmetricMatrix): add validity method (available
263            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
264    
265            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
266    
267            * tests/indexing.Rout.save:
268            * tests/indexing.R: additions, mainly for 'lsparse'
269    
270            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
271            case.
272    
273            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
274    
275    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
278                    as 'N' (1-letter - Ok?)
279    
280            * tests/group-methods.R: add test for logical + NAs
281    
282            * R/dMatrix.R ("Compare"): fix to work with NA's
283    
284            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
285    
286            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
287                    which is implemented.
288    
289    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/chm_common.c: coerce logical <-> double instead of
292            typecasting;  needed for "l" matrix handling in cholmod.
293    
294            * tests/other-pkgs.R (graph): small extension in "graph" checks.
295    
296            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
297            (Tsp2grNEL): other fixes needed
298    
299    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
302                    Matrices, since "lMatrix", also "lsparseM" can have NA
303            * R/ndenseMatrix.R, etc: new source files
304            * man/nsparseMatrix-classes.Rd, etc: new help files
305            * tests/: adaptions
306            * src/chm_common.c (chm_dense_to_SEXP): and others:
307                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
308            * src/Csparse.c, etc: ditto
309    
310    2006-09-11  Douglas Bates  <bates@R-project.org>
311    
312            * src/Mutils.[ch],init.c inst/include/*.h: Move the
313            alloc_d**Matrix functions to the lme4 package.
314    
315    2006-09-09  Douglas Bates  <bates@R-project.org>
316    
317            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
318            fixed
319    
320    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/lMatrix.R: new
323    
324            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
325    
326            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
327            * man/tcrossprod.Rd: ditto
328    
329    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
332            for exported functions
333            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
334            Remove partitioning algorithms for sparse matrix reordering.  The
335            copyright on the Metis code was problematic and the methods were
336            rarely used.
337            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
338            operations are now done entirely in CHOLMOD code.
339    
340    2006-09-06  Douglas Bates  <bates@R-project.org>
341    
342            * src/Mutils.h: Remove functions that are no longer used.
343    
344    2006-09-04  Douglas Bates  <bates@R-project.org>
345    
346            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
347            * src/DEPS.mkf: update
348    
349    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * created branches/Matrix-for-R-2.3.x;  on trunk: do
352            * DESCRIPTION (Version): 0.9975-0
353            (Depends): R (>= 2.4.0)
354    
355    2006-09-01  Douglas Bates  <bates@R-project.org>
356    
357            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
358    
359    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
362            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
363    
364            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
365    
366    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
369            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
370            * R/dsparseMatrix.R: ditto
371            * R/Csparse.R: ditto
372    
373    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dMatrix.R (Compare): improve availability of "<", etc
376            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
377    
378    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
381            of a 0-index which was used as 1-index (..hmm)
382    
383            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
384    
385            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
386            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
387            (.is.diagonal): ditto
388    
389            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
390    
391            * R/Matrix.R (Matrix): also work for NA data
392    
393    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
396            in all cases.
397    
398    2006-08-27  Douglas Bates  <bates@R-project.org>
399    
400            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
401            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
402    
403    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
406            subclasses of "ddenseMatrix"
407            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
408            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
409            instead of half dozen specialized ones.
410    
411    2006-08-25  Douglas Bates  <bates@R-project.org>
412    
413            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
414            <tillard@cirad.fr> - ordering standard errors to match effects.
415    
416    2006-08-24  Douglas Bates  <bates@R-project.org>
417    
418            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
419            on R_ldl.
420            * R/lCholCMatrix.R,
421            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
422            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
423            * many files in ./R and ./src: Use more general version of
424            dup_mMatrix_as_dgeMatrix to simplify method definitions.
425            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
426            dtpMatrix, dspMatrix and dppMatrix conversions.
427    
428    
429    2006-08-23  Douglas Bates  <bates@R-project.org>
430    
431            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
432            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
433            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
434            dgeMatrix_crossprod (may need to do this in other places).
435            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
436            generic and method for dsCMatrix.  Use CHOLMOD for chol().
437    
438    2006-08-22  Douglas Bates  <bates@R-project.org>
439    
440            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
441            types of classed Matrices, matrices or numeric or logical vectors.
442            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
443            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
444            to Mutils.h (as an inline) and change name to Matrix_check_class;
445            fixes in as_cholmod_factor and chm_factor_to_SEXP.
446            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
447            dsCMatrix_matrix_solve.  Comment out vestigial functions.
448            * src/Csparse.c: use diag_P and uplo_P macros.
449    
450    2006-08-21  Douglas Bates  <bates@R-project.org>
451    
452            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
453            valgrind.
454            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
455            inverses.
456            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
457            -Wall warnings.
458            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
459            Use dup_mMatrix_as_dgeMatrix.
460    
461    2006-08-20  Douglas Bates  <bates@R-project.org>
462    
463            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
464            * tests/sparseQR.R: Added
465            * man/sparseQR-class.Rd: Document methods for qr.* generics
466            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
467    
468    2006-08-19  Douglas Bates  <bates@R-project.org>
469    
470            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
471            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
472            and qr.fitted.
473            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
474            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
475    
476    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
479            the base version has no "..." argument.
480    
481            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
482    
483            * R/Matrix.R: define and
484            * NAMESPACE: export as.numeric() and as.logical() methods.
485                    Let's hope these do not badly slow down something...
486            Finally export the zapsmall() method.
487    
488    2006-08-17  Douglas Bates  <bates@R-project.org>
489    
490            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
491            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
492            * src/dtCMatrix.c :Remove code that is no longer used
493            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
494    
495    2006-08-14  Douglas Bates  <bates@R-project.org>
496    
497            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
498            Csparse_to_logical and Csparse_symmetric_to_general.
499            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
500            coercion methods between CsparseMatrix and TsparseMatrix.
501    
502    2006-08-14  Douglas Bates  <bates@R-project.org>
503    
504            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
505            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
506            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
507            possible.
508    
509    2006-08-12  Douglas Bates  <bates@R-project.org>
510    
511            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
512              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
513              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
514              generalize conversions between TsparseMatrix, CsparseMatrix,
515              denseMatrix and matrix.  Preserve triangularity property and
516              propagate Dimnames in the easy cases.
517    
518    2006-08-10  Douglas Bates  <bates@R-project.org>
519    
520            * src/lmer.c: adjust checks in glmer_init for S4SXP
521            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
522            before S4SXP but for the wrong reasons.
523    
524    2006-08-08  Douglas Bates  <bates@R-project.org>
525    
526            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
527            Later modified to return the upper triangle only.
528            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
529    
530    2006-08-07  Douglas Bates  <bates@R-project.org>
531    
532            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
533            R-level conversion to a sparse symmetric class.
534            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
535            Remove conversion to sparse symmetric classes (now done in C code).
536    
537    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
540            * man/band.Rd:  adapt the \dontshow{} unit test.
541    
542    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * DESCRIPTION (Version): 0.995-14  for CRAN
545    
546            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
547    
548            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
549            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
550    
551            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
552            * R/Tsparse.R (tril, triu, band): methods
553            * R/dgRMatrix.R (tril, ...):    ditto
554            * man/band.Rd:                  ditto
555    
556    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Matrix.R (head, tail): directly use utils:::head.matrix
559                    to be up-to-date automatically.
560    
561    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
564    
565            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
566            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
567            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
568            such that the S4 objects are always created by the current version
569            of R and 'Matrix' class definitions.
570    
571    2006-08-01  Douglas Bates  <bates@R-project.org>
572    
573            * R/lmer.R (LMEoptimize method), tests/lmer.R,
574            inst/external/test3comp.rda: Added warnings for convergence on
575            boundary and test cases.
576    
577            * src/lmer.c (mer_postVar): Modified to return the variances that
578            are marginal to the fixed effects, not conditional on them (which
579            is what the bVar slot contents represent).
580    
581    2006-07-31  Douglas Bates  <bates@R-project.org>
582    
583            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
584            function which calls the C function mer_hat_trace2.
585    
586            * man/ranef.Rd: Include description of "postVar" argument and
587            producing a caterpillar plot.
588    
589    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * NAMESPACE:    change  "correlation" to "corMatrix"
592            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
593            * R/dpoMatrix.R: ditto
594            * R/lmer.R:      ditto
595    
596    2006-07-28  Douglas Bates  <bates@R-project.org>
597    
598            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
599            RZXinv slot's contents into a separate internal function that can
600            be used in mer_hat_trace.
601    
602    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
605            via new smart
606            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
607            utility functions.
608    
609    
610    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Csparse.R (tril, triu, band): do return *triangular* classed
613            matrices when appropriate; band() even symmetric ones.
614            (replCmat): extend to potentially all "CsparseMatrix"
615            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
616            allow subassignment for special sparse matrices.
617    
618            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
619    
620            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
621            argument; in glmer_*(): print only if(verbose).
622    
623            speed-optimize a few places by moving REAL(.) out of loops.
624    
625            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
626    
627    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
630                    since that wrongly triggers also for M[ logi , ]
631    
632            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
633            a symmetric matrix that results in a non-symmetric one.
634            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
635    
636            * R/dMatrix.R: make round(M) work as round(M, 0)
637    
638            * R/dgTMatrix.R (image): coordinate system and axis now use
639            1-based indices, not 0-based ones.
640    
641            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
642            * tests/indexing.R: test it.
643    
644            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
645            * man/isSymmetric-methods.Rd: and document it.
646    
647            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
648            * man/SparseM-conv.Rd: docu them
649    
650            * tests/other-pkgs.R: renamed from tests/graph.R and add example
651                    for 'SparseM' conversions
652    
653    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
654    
655            * R/Matrix.R (head): added head() and tail() methods.
656    
657    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * DESCRIPTION (Version): 0.995-12 released to CRAN
660    
661    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * tests/simple.R: add check for correct dsT -> dgT coercion;
664                    add check for correct printing of symmetric sparse matrices.
665    
666            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
667            for sparse symmetric matrices.
668    
669            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
670            diagonal twice.
671    
672    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
673    
674            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
675            being applied to the x slot (detected by Brian Ripley).
676    
677    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
680    
681            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
682    
683    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * src/lgCMatrix.c (lgCMatrix_diag): new function
686            * R/lgCMatrix.R (diag): for new method
687    
688            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
689                 ==> construction of illegal "*gTMatrix" via new() should
690                 now be much less easy:
691            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
692    
693            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
694                    directly.
695            * man/Matrix.Rd: documents it.
696    
697    2006-07-06  Douglas Bates  <bates@R-project.org>
698    
699            * src/pedigree.c (pedigree_inbreeding): Correction in
700            initialization.  This function is not currently being used and is
701            not fully tested.
702    
703            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
704            Introduced the glmer class.  Added code for mcmcmsamp on glmer
705            objects.  Modified validity check on pedigree objects to account
706            for nonparallel patterns of missingness of parents.
707    
708            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
709            class.
710    
711    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/pMatrix.R: coercion pMatrix -> Tsparse
714    
715    2006-06-12  Douglas Bates  <bates@R-project.org>
716    
717            * DESCRIPTION (Version): 0.995-11 released to CRAN
718    
719            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
720            the output from mcmcsamp.
721    
722    2006-06-10  Douglas Bates  <bates@R-project.org>
723    
724            * R/lmer.R (simulestimate): added C code for calculating the trace
725            of the hat matrix.
726    
727    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
730            classes.
731            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
732    
733    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/dgTMatrix.R (colSums): etc. All four of
736            colSums(), rowSums(), colMeans(), rowMeans() now should work for
737            all "Matrices".
738    
739    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
740    
741            * R/lmer.R (panel.ci): Add a reference line at zero and a
742            background grid to the qqmath plot of ranef.lmer.
743    
744    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
745    
746            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
747            grouping factors to be specified in the formula as (1|foo/bar).
748    
749    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
750    
751            * R/lmer.R (findbars and others): Change check of is.numeric to
752            !is.language to resolve the bug reported by Jacob Wegelin.
753    
754            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
755            code to evaluate inbreeding coefficients without calculating T,
756            based on code in Sargolzaei and Iwaisaki's paper.
757    
758    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
759    
760            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
761            generic and mer methods for isNested and denomDF. This denomDF was
762            an attempt to emulate that in lme but I don't think that makes
763            sense.  Use the trace of the hat matrix instead.
764    
765    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
768            the C code depending on a slot structure that's no longer valid.
769            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
770    
771    
772    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
773    
774            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
775            of lowerTriMatrix generic and methods to tril (also upper to triu)
776            and added a general band extractor.
777    
778    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
779    
780            * R/pedigree.R (pedigree): Replace sire and dam values outside the
781            allowable range with NAs. Added a corresponding check in the
782            validity check for the pedigree class.
783    
784            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
785            crossprod methods now inherits from symmetricMatrix.
786    
787    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
788    
789            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
790            generics lowerTriMatrix and upperTriMatrix along with methods for
791            the Csparse virtual class.  Also added a C function Csparse_band
792            that implements these methods by calling cholmod_band.
793    
794    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
797            erased when it was NULL.  This led to invalid subselections!
798    
799    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
800    
801            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
802            in method for "t" so as not to lose the unit diagonal property.
803    
804    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
805    
806            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
807            and methods.  This is now an option to the ranef method for the
808            mer class.
809    
810            * src/cs_utils.c: Ensure that the nz component is -1 for a
811            compressed column-oriented matrix.  Minor formatting cleanup.
812    
813            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
814            objects.
815    
816    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
819            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
820    
821    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
822    
823            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
824            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
825    
826            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
827            for the dtCMatrix class.
828    
829    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
830    
831            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
832            and methods for it.
833    
834    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
837            arguments, such that M %*% 1:6 now works
838            * Tests/matprod.R: test the above
839    
840    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
841    
842            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
843            the ranef.lmer class.
844    
845            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
846            methods to extract the posterior variances from the bVar slot.
847    
848    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
851            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
852    
853            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
854            * tests/simple: (extended)
855    
856            * R/sparseMatrix.R (isTriangular): now using much improved
857            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
858    
859    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
860    
861            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
862            (problem report from Franklin Parlamis).  This should be done
863            generally.
864    
865    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
866    
867            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
868            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
869            update the plot methods.
870    
871    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
872    
873            * R/lmer.R (resid and ranef methods):  Added methods for the
874            "residuals" and "resid" generic but only for linear mixed model
875            fits.  Changed the ranef method to return a list of data frames so
876            that the plot methods now work.
877    
878    2006-03-16  Douglas Bates  <bates@bates2>
879    
880            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
881            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
882    
883            * DESCRIPTION (Date): New release
884    
885    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
888    
889            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
890            * man/KNex.Rd: and other help files
891            * tests/*.R: several ones needed adaption
892            * inst/doc/Comparisons.Rnw: ditto
893    
894    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
897    
898            * tests/indexing.R: tests for new [<- methods for sparse matrices.
899    
900    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
901    
902            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
903    
904            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
905    
906    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908            * R/dMatrix.R: enable things like  M [ M < 10 ]
909            * R/dgeMatrix.R: implement it
910    
911    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * R/AllClass.R: define "summary.mer" and "*.lmer"
914            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
915            * R/lmer.R (show): now works with summary()
916    
917    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
920            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
921                    support the above
922    
923    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
924    
925            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
926            Use glmFit$prior.weights for weights in a glmm.
927            Allow an option usePQL = FALSE to skip the PQL steps for the
928            Laplace method (and, in time, the AGQ method).
929    
930            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
931            into a separate function internal_mer_Xfactor to be able to call
932            it from internal_bhat.
933    
934    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * tests/Class+Meth.R (tstMatrixClass): function for much better
937            testing; now again of all actual classes.
938    
939            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
940                    use macros and define make_d_matrix_* and make_i_matrix_*
941                    where _i_ is for the ldense routines:
942    
943            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
944            * src/ldense.c (lsyMatrix_as_lgeMatrix):
945    
946            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
947    
948    
949    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
952                    many different kinds of matrices.
953            * R/*.R: quite a few new methods were needed for R CMD check with
954                    new Matrix().  Very good for users playing around.
955    
956    
957    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
958    
959            * src/dgeMatrix.c (dMatrix_validate): new
960            * src/Mutils.c (dense_nonpacked_validate): new
961    
962            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
963    
964    
965    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
966    
967            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
968    
969    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
970    
971            * DESCRIPTION (Version): 0.99-6 released to CRAN
972    
973            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
974            segfault in cases with multiple non-nested grouping factors.
975    
976    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
979                    (Depends): also on 'utils'
980    
981            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
982            * R/diagMatrix.R (Diagonal): constructor and methods for
983            diagonal matrices
984    
985            * R/ltTMatrix.R: new "minimal methods"
986    
987    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
988    
989            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
990            all methods (and help files).
991    
992    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
995                    for case (dimn.  op  no_dimn.)
996    
997    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
998    
999            * DESCRIPTION (Version): 0.99-2  released to CRAN
1000    
1001    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1002    
1003            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1004            by Julian Faraway.
1005    
1006    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * R/Auxiliaries.R (try_as): new utility
1009            * R/sparseMatrix.R: use try_as() in coercion to original class
1010    
1011    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1012    
1013            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1014    
1015    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * R/Auxiliaries.R (dimNamesCheck): added
1018    
1019            * R/Matrix.R (as.array), (as.vector): new
1020    
1021    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1024                    default.
1025            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1026                    "pMatrix" now contains "sparseMatrix"
1027    
1028    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * tests/Class+Meth.R: new tests; t(t(m)) == m
1031    
1032            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1033    
1034            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1035            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1036    
1037            * R/dspMatrix.R: typo in "t" method
1038    
1039    2005-09-18  Douglas Bates  <bates@wisc.edu>
1040    
1041            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1042            * R/Tsparse.R: instead of R/gTMatrix.R
1043            * R/Csparse.R: new
1044            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1045            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1046            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1047                            via cholmod
1048    
1049    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * R/Auxiliaries.R (non0ind): new function using new C code
1052            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1053    
1054    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1055    
1056            * src/chm_common.h: header file required by all C sources that
1057            call CHOLMOD functions.  It defines a cholmod_common structure
1058            called 'c' whose address is passed as the last argument to
1059            (virtually) every CHOLMOD function.
1060    
1061            * src/Pattern.c: Simple example of the use of CHOLMOD.
1062    
1063            * src/init.c: initialize and finalize the cholmod_common structure.
1064    
1065            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1066            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1067    
1068    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * inst/test-tools.R: new file collecting the utility functions used
1071                    in ./tests/*.R
1072    
1073            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1074            * R/Matrix.R (cbind2): methods for NULL and missing
1075    
1076    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1077    
1078            * R/AllClass.R: new "index" class for "[" and "[<-":
1079                    First cut at "symmetricMatrix" and "triangularMatrix"
1080            * R/gTMatrix.R (.ind.prep): new function;
1081                    Logical and character indexing now work too.
1082            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1083            * tests/indexing.R: new, including *.Rout.save
1084            * tests/dgTMatrix.R: new
1085    
1086    2005-08-29  Douglas Bates  <bates@wisc.edu>
1087    
1088            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1089            indicator pos not being updated.  Also enforced upper triangular
1090            for symmetric case.  Need to coerce edges component of elements of
1091            edge list - grr! (Why don't they define their classes cleanly?)
1092    
1093    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095            * R/Matrix.R:  added first "[<-" methods; not yet functional
1096            * R/denseMatrix.R: ditto
1097            * man/Subassign-methods.Rd: new help file for these
1098    
1099    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * DESCRIPTION (Version): 0.98-6
1102    
1103            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1104            matrices.
1105    
1106    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1107    
1108            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1109                    as( <logical>, "matrix")
1110    
1111            * R/pMatrix.R: coercion to "lgTMatrix"
1112    
1113            * R/gTMatrix.R: new virtual class to define "[" methods for.
1114            * man/gTMatrix-class.Rd:
1115            * General slight re-organization of where "[" methods are defined.
1116              more to come.
1117    
1118    2005-08-18  Douglas Bates  <bates@wisc.edu>
1119    
1120            * DESCRIPTION (Version): 0.98-5  released to CRAN
1121    
1122            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1123            * .....
1124    
1125    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1126    
1127            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1128            or glmer objects.
1129    
1130    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1131    
1132            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1133    
1134    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1135    
1136            * R/HBMM.R: finish re-writing R-only code.
1137    
1138    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1139    
1140            * man/externalFormats.Rd: move documentation for writeHB and
1141            writeMM here.
1142    
1143            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1144            (suggested by Paul Roecker).
1145    
1146            * tests/validObj.R (assertError): Comment out test that is failing
1147            after recent changes in r-devel.
1148    
1149    
1150    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1151    
1152            * R/AllClass.R: intermediate virtual class "denseMatrix"
1153            * man/denseMatrix-class.Rd
1154            * NAMESPACE: export it, and also export
1155            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1156    
1157    2005-08-10  Douglas Bates  <bates@wisc.edu>
1158    
1159            * DESCRIPTION (Version): 0.98-3 to CRAN
1160    
1161            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1162            matrix_solve code (which was really, really wrong).
1163    
1164    2005-08-07  Douglas Bates  <bates@wisc.edu>
1165    
1166            * DESCRIPTION (Version): 0.98-2
1167    
1168            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1169    
1170            * R/lmer.R (abbrvNms): new
1171            * R/lmer.R (mcmcsamp): allow transformed parameters
1172            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1173            for the Harwell-Boeing and the MatrixMarket formats.
1174    
1175    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1176    
1177            * man/dtrMatrix-class.Rd: add examples
1178            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1179    
1180            * TODO: note the dtpMatrix (docu) bug
1181    
1182            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1183            in order to ensure that new as.matrix() is used by old functions,
1184            e.g., svd(), qr(), eigen(), dist(),..;
1185                  apply(), also matplot() or pairs().
1186    
1187    
1188    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1191              add comments about 'control' / lmerControl() arguments
1192    
1193    2005-07-27  Douglas Bates  <bates@wisc.edu>
1194    
1195            * man/sleepstudy.Rd: Added the sleep data set.
1196            * DESCRIPTION (Version): 0.98-1  released to CRAN
1197    
1198    2005-07-12  Douglas Bates  <bates@wisc.edu>
1199            * man/sleepstudy.Rd: Added the sleep data set.
1200    
1201            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1202            .Call calls that were producing spurious output.
1203    
1204    2005-07-05  Douglas Bates  <bates@wisc.edu>
1205    
1206            * R/lmer.R (lmer): stored updated variance component estimates in
1207            mer object for the generalized model.  (Bug reported by Renaud
1208            Lancelot).
1209    
1210    2005-07-03  Douglas Bates  <bates@wisc.edu>
1211    
1212            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1213            unidimensional case.
1214    
1215    2005-06-08  Douglas Bates  <bates@wisc.edu>
1216    
1217            * DESCRIPTION (Version): 0.96-1
1218    
1219            * moved  lmer-class' R and C code moved from lme4 to here
1220    
1221    2005-06-04  Douglas Bates  <bates@wisc.edu>
1222    
1223            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1224            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1225    
1226    2005-06-02  Douglas Bates  <bates@wisc.edu>
1227    
1228            * src/Makefile.win: Forgot to update this when Makefile changed.
1229    
1230    2005-05-11  Douglas Bates  <bates@wisc.edu>
1231    
1232            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1233            bug reported by Kurt Hornik and Michael Hahsler.
1234    
1235    2005-05-10  Douglas Bates  <bates@wisc.edu>
1236    
1237            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1238            logical sparse matrices.  These will also be used in the symbolic
1239            analysis for lmer objects.
1240    
1241            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1242            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1243    
1244    2005-05-06  Douglas Bates  <bates@wisc.edu>
1245    
1246            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1247            colMeans, colSums, rowMeans and rowSums.
1248    
1249    2005-04-18  Douglas Bates  <bates@wisc.edu>
1250    
1251            * src/lgCMatrix.[ch]: code for _validate method and stub for
1252            multiplication operation.
1253    
1254            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1255            to dgetrs.
1256    
1257            * src/init.c: Fix cut-and-paste error in definition of
1258            dgeMatrix_matrix_solve
1259    
1260            * src/{many files}: Tighten code by using ALLOC_SLOT.
1261    
1262    2005-04-15  Douglas Bates  <bates@wisc.edu>
1263    
1264            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1265    
1266            * DESCRIPTION: Eliminate import of stats.
1267    
1268    
1269    2005-04-06  Douglas Bates  <bates@wisc.edu>
1270    
1271            * R/AllClass.R : add logical sparse matrix classes
1272    
1273  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1274    
1275          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1276          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1277    
1278  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1279    
1280          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1281    
# Line 29  Line 1301 
1301          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1302            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1303    
1304  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1305    
1306          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1307          * ....          * ....
1308    
1309  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1310    
1311          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1312    
# Line 49  Line 1321 
1321            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1322          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1323    
1324  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1325    
1326          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1327    
1328  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1329    
1330          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1331    
1332  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1333    
1334          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1335          the package.          the package.
# Line 105  Line 1377 
1377    
1378          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1379    
1380  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1381    
1382          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1383          for the geMatrix class.          for the geMatrix class.
1384    
1385  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1386    
1387          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1388    
1389          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1390    
1391  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1392    
1393          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1394          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1395    
1396  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1397    
1398          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1399    
1400  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1401    
1402          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1403          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1404    
1405  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1406    
1407          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1408    
1409          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1410          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1411    
1412  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1413    
1414          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1415          no longer used.          no longer used.
# Line 149  Line 1421 
1421          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1422          Fixes part but not all of #15.          Fixes part but not all of #15.
1423    
1424  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1425    
1426          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1427          scalar grouping factors corrected.          scalar grouping factors corrected.
1428    
1429  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1430    
1431          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1432    
1433  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1434    
1435          * 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
1436          .h file can be included.          .h file can be included.
1437    
1438  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1439    
1440          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1441          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1442    
1443          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1444    
1445  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1446    
1447          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1448    
1449  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1450    
1451          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1452    
1453  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1454    
1455          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1456    
1457  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1458    
1459          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1460    
1461  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1462    
1463          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1464          routines.          routines.
1465    
1466  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1467    
1468          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1469    
1470  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1471    
1472          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1473    

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