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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1674, Tue Nov 7 13:29:23 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): updated -> release 0.9975-6
4    
5    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
8            now returns symmetric.
9    
10            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
11    
12            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
13            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
14    
15            * R/Auxiliaries.R (.type.kind): added
16    
17    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
20            running src/CSparse_install.sh
21    
22            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
23    
24    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
27            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
28    
29            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
30    
31            * tests/Class+Meth.R (tstMatrixClass): now assure
32            the (important in method programming) property :
33    
34                    ###>>  Every "Matrix" is either
35                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
36    
37                    (where "*" stands for "Matrix")
38    
39            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
40    
41            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
42            * tests/validObj.R: checks for "comparison"
43    
44            * R/sparseMatrix.R ([): improved indexing for sparse;
45                    trying to keep <symmetric>[ n, n] symmmetric
46    
47            * tests/indexing.R: indexing for logical sparse now ok
48    
49    
50    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * src/Tsparse.c: use xTsparse_validate() , and hence remove
53    
54            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
55    
56    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
59    
60            * tests/simple.R: validObject() checking the above.
61    
62            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
63            replacing both dgCMatrix_validate and lgCM*.
64    
65            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
66            fix dimnames setting in other places.
67            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
68    
69    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
72    
73            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
74            symmetry test, via
75            * R/Auxiliaries.R (.as.dgC.0.factors):
76    
77    2006-11-01  Douglas Bates  <bates@r-project.org>
78    
79            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
80            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
81            <CsparseMatrix>) added
82    
83    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * tests/matprod.R: add a variation of Harri's example
86    
87            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
88            recursive infinitely.
89    
90            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
91    
92            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
93    
94    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
97            matrix if possible; test m+m == 2*m; now test dgRMatrix.
98            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
99            satisfy the above test.
100    
101    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
104    
105            * R/dgCMatrix.R: solve(a, b="missing") based on
106            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
107            RHS = NULL.
108    
109            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
110            add more (needed) [t]crossprod() methods.
111    
112            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
113    
114            * R/Auxiliaries.R (as_CspClass): cleanup
115            (drop0): internal utility for "Csparse_drop(*, 0)"
116            (.bail.out.2): encourage active feedback
117    
118    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/dMatrix.R(Compare): new(), then slots [no validity check]
121    
122            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
123            non-valid or 'sorted' case).
124    
125            * R/dsparseMatrix.R: add "chol" method.
126            * R/ddenseMatrix.R: ditto
127    
128            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
129            * NAMESPACE (Ops)
130            * R/diagMatrix.R (diag2T): simple utility used "higher level"
131            coercion; deprecating direct lower level coercions.
132    
133            * R/*.R (seq): use seq_len() and seq_along() where possible.
134    
135    
136    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * DESCRIPTION (Version): 0.9975-5 ready for release
139    
140    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
141    
142            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
143    
144    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/AllClass.R (corMatrix): add 'validity' check;
147                    comment out unused "LDL" class definition
148            * NAMESPACE: mention, but do not export "LDL" class
149            * R/corMatrix.R: new (simple), needed for R-devel with
150            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
151              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
152    
153    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
156            use Rprintf and R's error handling.
157    
158    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
161            * tests/matprod.R: add tests for the bug fixed.
162    
163    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
166            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
167    
168    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
171    
172    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.9975-3
175    
176            * R/diagMatrix.R (bdiag): new function constructing block diagonal
177            (sparse) matrices.
178            * man/bdiag.Rd: docu + examples
179    
180            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
181    
182            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
183            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
184    
185            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
186            that result is sparse or diagonal (and not dense).
187    
188            * man/Subassign-methods.Rd: fix examples
189    
190            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
191            should always return a sparse (and not sometimes a diagonal) matrix.
192    
193    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
196    
197    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
198    
199            * DESCRIPTION (Version): 0.9975-2
200    
201            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
202    
203    2006-10-02  Douglas Bates  <bates@R-project.org>
204    
205            * tests/dg_Matrix.R: Simplify test taking into account new code.
206    
207    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
210    
211            * R/lsTMatrix.R: new files w/ missing methods
212            * R/nsTMatrix.R:  "  'for completeness'
213    
214            * tests/Class+Meth.R: a bit less 'not.ok.classes'
215    
216            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
217    
218    
219    2006-09-28  Douglas Bates  <bates@R-project.org>
220    
221            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
222            included.
223    
224            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
225            Export C-callable functions used in Zt_create in lme4.
226    
227    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * DESCRIPTION (Version): 0.9975-1
230    
231            * tests/simple.R: less checks fail; using NA, found that our
232                    kronecker() is not base-compatible with NA's.
233    
234            * R/dMatrix.R: "Compare" method now implemented for all cases
235    
236            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
237    
238            * man/dtpMatrix-class.Rd: mention length of 'x' slot
239    
240            * src/dtpMatrix.c (dtpMatrix_validate): fix check
241            * src/dspMatrix.c (dspMatrix_validate): ditto
242    
243            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
244              including coercion to [nl]tTMatrix.
245    
246            * R/diagMatrix.R (show): print a header line as for other classes.
247    
248    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * src/Makefile.win (SUBDIRS): fix typo
251    
252    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
255    
256    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
257    
258            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
259            symmetric and y missing in R code using %*% (cholmod_aat doesn't
260            accept a symmetric matrix).
261            * tests/group-methods.R: Uncomment test of crossprod applied to
262            lsCMatrix objects.
263    
264    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/AllClass.R (symmetricMatrix): add validity method (available
267            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
268    
269            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
270    
271            * tests/indexing.Rout.save:
272            * tests/indexing.R: additions, mainly for 'lsparse'
273    
274            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
275            case.
276    
277            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
278    
279    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
282                    as 'N' (1-letter - Ok?)
283    
284            * tests/group-methods.R: add test for logical + NAs
285    
286            * R/dMatrix.R ("Compare"): fix to work with NA's
287    
288            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
289    
290            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
291                    which is implemented.
292    
293    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * src/chm_common.c: coerce logical <-> double instead of
296            typecasting;  needed for "l" matrix handling in cholmod.
297    
298            * tests/other-pkgs.R (graph): small extension in "graph" checks.
299    
300            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
301            (Tsp2grNEL): other fixes needed
302    
303    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
306                    Matrices, since "lMatrix", also "lsparseM" can have NA
307            * R/ndenseMatrix.R, etc: new source files
308            * man/nsparseMatrix-classes.Rd, etc: new help files
309            * tests/: adaptions
310            * src/chm_common.c (chm_dense_to_SEXP): and others:
311                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
312            * src/Csparse.c, etc: ditto
313    
314    2006-09-11  Douglas Bates  <bates@R-project.org>
315    
316            * src/Mutils.[ch],init.c inst/include/*.h: Move the
317            alloc_d**Matrix functions to the lme4 package.
318    
319    2006-09-09  Douglas Bates  <bates@R-project.org>
320    
321            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
322            fixed
323    
324    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/lMatrix.R: new
327    
328            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
329    
330            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
331            * man/tcrossprod.Rd: ditto
332    
333    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
334    
335            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
336            for exported functions
337            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
338            Remove partitioning algorithms for sparse matrix reordering.  The
339            copyright on the Metis code was problematic and the methods were
340            rarely used.
341            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
342            operations are now done entirely in CHOLMOD code.
343    
344    2006-09-06  Douglas Bates  <bates@R-project.org>
345    
346            * src/Mutils.h: Remove functions that are no longer used.
347    
348    2006-09-04  Douglas Bates  <bates@R-project.org>
349    
350            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
351            * src/DEPS.mkf: update
352    
353    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * created branches/Matrix-for-R-2.3.x;  on trunk: do
356            * DESCRIPTION (Version): 0.9975-0
357            (Depends): R (>= 2.4.0)
358    
359    2006-09-01  Douglas Bates  <bates@R-project.org>
360    
361            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
362    
363    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
366            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
367    
368            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
369    
370    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
373            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
374            * R/dsparseMatrix.R: ditto
375            * R/Csparse.R: ditto
376    
377    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/dMatrix.R (Compare): improve availability of "<", etc
380            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
381    
382    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
385            of a 0-index which was used as 1-index (..hmm)
386    
387            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
388    
389            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
390            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
391            (.is.diagonal): ditto
392    
393            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
394    
395            * R/Matrix.R (Matrix): also work for NA data
396    
397    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
400            in all cases.
401    
402    2006-08-27  Douglas Bates  <bates@R-project.org>
403    
404            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
405            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
406    
407    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
410            subclasses of "ddenseMatrix"
411            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
412            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
413            instead of half dozen specialized ones.
414    
415    2006-08-25  Douglas Bates  <bates@R-project.org>
416    
417            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
418            <tillard@cirad.fr> - ordering standard errors to match effects.
419    
420    2006-08-24  Douglas Bates  <bates@R-project.org>
421    
422            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
423            on R_ldl.
424            * R/lCholCMatrix.R,
425            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
426            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
427            * many files in ./R and ./src: Use more general version of
428            dup_mMatrix_as_dgeMatrix to simplify method definitions.
429            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
430            dtpMatrix, dspMatrix and dppMatrix conversions.
431    
432    
433    2006-08-23  Douglas Bates  <bates@R-project.org>
434    
435            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
436            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
437            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
438            dgeMatrix_crossprod (may need to do this in other places).
439            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
440            generic and method for dsCMatrix.  Use CHOLMOD for chol().
441    
442    2006-08-22  Douglas Bates  <bates@R-project.org>
443    
444            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
445            types of classed Matrices, matrices or numeric or logical vectors.
446            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
447            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
448            to Mutils.h (as an inline) and change name to Matrix_check_class;
449            fixes in as_cholmod_factor and chm_factor_to_SEXP.
450            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
451            dsCMatrix_matrix_solve.  Comment out vestigial functions.
452            * src/Csparse.c: use diag_P and uplo_P macros.
453    
454    2006-08-21  Douglas Bates  <bates@R-project.org>
455    
456            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
457            valgrind.
458            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
459            inverses.
460            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
461            -Wall warnings.
462            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
463            Use dup_mMatrix_as_dgeMatrix.
464    
465    2006-08-20  Douglas Bates  <bates@R-project.org>
466    
467            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
468            * tests/sparseQR.R: Added
469            * man/sparseQR-class.Rd: Document methods for qr.* generics
470            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
471    
472    2006-08-19  Douglas Bates  <bates@R-project.org>
473    
474            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
475            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
476            and qr.fitted.
477            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
478            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
479    
480    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
483            the base version has no "..." argument.
484    
485            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
486    
487            * R/Matrix.R: define and
488            * NAMESPACE: export as.numeric() and as.logical() methods.
489                    Let's hope these do not badly slow down something...
490            Finally export the zapsmall() method.
491    
492    2006-08-17  Douglas Bates  <bates@R-project.org>
493    
494            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
495            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
496            * src/dtCMatrix.c :Remove code that is no longer used
497            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
498    
499    2006-08-14  Douglas Bates  <bates@R-project.org>
500    
501            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
502            Csparse_to_logical and Csparse_symmetric_to_general.
503            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
504            coercion methods between CsparseMatrix and TsparseMatrix.
505    
506    2006-08-14  Douglas Bates  <bates@R-project.org>
507    
508            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
509            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
510            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
511            possible.
512    
513    2006-08-12  Douglas Bates  <bates@R-project.org>
514    
515            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
516              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
517              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
518              generalize conversions between TsparseMatrix, CsparseMatrix,
519              denseMatrix and matrix.  Preserve triangularity property and
520              propagate Dimnames in the easy cases.
521    
522    2006-08-10  Douglas Bates  <bates@R-project.org>
523    
524            * src/lmer.c: adjust checks in glmer_init for S4SXP
525            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
526            before S4SXP but for the wrong reasons.
527    
528    2006-08-08  Douglas Bates  <bates@R-project.org>
529    
530            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
531            Later modified to return the upper triangle only.
532            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
533    
534    2006-08-07  Douglas Bates  <bates@R-project.org>
535    
536            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
537            R-level conversion to a sparse symmetric class.
538            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
539            Remove conversion to sparse symmetric classes (now done in C code).
540    
541    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
544            * man/band.Rd:  adapt the \dontshow{} unit test.
545    
546    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * DESCRIPTION (Version): 0.995-14  for CRAN
549    
550            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
551    
552            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
553            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
554    
555            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
556            * R/Tsparse.R (tril, triu, band): methods
557            * R/dgRMatrix.R (tril, ...):    ditto
558            * man/band.Rd:                  ditto
559    
560    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/Matrix.R (head, tail): directly use utils:::head.matrix
563                    to be up-to-date automatically.
564    
565    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
568    
569            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
570            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
571            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
572            such that the S4 objects are always created by the current version
573            of R and 'Matrix' class definitions.
574    
575    2006-08-01  Douglas Bates  <bates@R-project.org>
576    
577            * R/lmer.R (LMEoptimize method), tests/lmer.R,
578            inst/external/test3comp.rda: Added warnings for convergence on
579            boundary and test cases.
580    
581            * src/lmer.c (mer_postVar): Modified to return the variances that
582            are marginal to the fixed effects, not conditional on them (which
583            is what the bVar slot contents represent).
584    
585    2006-07-31  Douglas Bates  <bates@R-project.org>
586    
587            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
588            function which calls the C function mer_hat_trace2.
589    
590            * man/ranef.Rd: Include description of "postVar" argument and
591            producing a caterpillar plot.
592    
593    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * NAMESPACE:    change  "correlation" to "corMatrix"
596            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
597            * R/dpoMatrix.R: ditto
598            * R/lmer.R:      ditto
599    
600    2006-07-28  Douglas Bates  <bates@R-project.org>
601    
602            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
603            RZXinv slot's contents into a separate internal function that can
604            be used in mer_hat_trace.
605    
606    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
609            via new smart
610            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
611            utility functions.
612    
613    
614    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Csparse.R (tril, triu, band): do return *triangular* classed
617            matrices when appropriate; band() even symmetric ones.
618            (replCmat): extend to potentially all "CsparseMatrix"
619            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
620            allow subassignment for special sparse matrices.
621    
622            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
623    
624            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
625            argument; in glmer_*(): print only if(verbose).
626    
627            speed-optimize a few places by moving REAL(.) out of loops.
628    
629            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
630    
631    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
634                    since that wrongly triggers also for M[ logi , ]
635    
636            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
637            a symmetric matrix that results in a non-symmetric one.
638            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
639    
640            * R/dMatrix.R: make round(M) work as round(M, 0)
641    
642            * R/dgTMatrix.R (image): coordinate system and axis now use
643            1-based indices, not 0-based ones.
644    
645            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
646            * tests/indexing.R: test it.
647    
648            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
649            * man/isSymmetric-methods.Rd: and document it.
650    
651            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
652            * man/SparseM-conv.Rd: docu them
653    
654            * tests/other-pkgs.R: renamed from tests/graph.R and add example
655                    for 'SparseM' conversions
656    
657    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
658    
659            * R/Matrix.R (head): added head() and tail() methods.
660    
661    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * DESCRIPTION (Version): 0.995-12 released to CRAN
664    
665    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * tests/simple.R: add check for correct dsT -> dgT coercion;
668                    add check for correct printing of symmetric sparse matrices.
669    
670            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
671            for sparse symmetric matrices.
672    
673            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
674            diagonal twice.
675    
676    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
677    
678            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
679            being applied to the x slot (detected by Brian Ripley).
680    
681    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
684    
685            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
686    
687    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * src/lgCMatrix.c (lgCMatrix_diag): new function
690            * R/lgCMatrix.R (diag): for new method
691    
692            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
693                 ==> construction of illegal "*gTMatrix" via new() should
694                 now be much less easy:
695            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
696    
697            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
698                    directly.
699            * man/Matrix.Rd: documents it.
700    
701    2006-07-06  Douglas Bates  <bates@R-project.org>
702    
703            * src/pedigree.c (pedigree_inbreeding): Correction in
704            initialization.  This function is not currently being used and is
705            not fully tested.
706    
707            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
708            Introduced the glmer class.  Added code for mcmcmsamp on glmer
709            objects.  Modified validity check on pedigree objects to account
710            for nonparallel patterns of missingness of parents.
711    
712            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
713            class.
714    
715    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/pMatrix.R: coercion pMatrix -> Tsparse
718    
719    2006-06-12  Douglas Bates  <bates@R-project.org>
720    
721            * DESCRIPTION (Version): 0.995-11 released to CRAN
722    
723            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
724            the output from mcmcsamp.
725    
726    2006-06-10  Douglas Bates  <bates@R-project.org>
727    
728            * R/lmer.R (simulestimate): added C code for calculating the trace
729            of the hat matrix.
730    
731    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
734            classes.
735            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
736    
737    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/dgTMatrix.R (colSums): etc. All four of
740            colSums(), rowSums(), colMeans(), rowMeans() now should work for
741            all "Matrices".
742    
743    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
744    
745            * R/lmer.R (panel.ci): Add a reference line at zero and a
746            background grid to the qqmath plot of ranef.lmer.
747    
748    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
749    
750            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
751            grouping factors to be specified in the formula as (1|foo/bar).
752    
753    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
754    
755            * R/lmer.R (findbars and others): Change check of is.numeric to
756            !is.language to resolve the bug reported by Jacob Wegelin.
757    
758            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
759            code to evaluate inbreeding coefficients without calculating T,
760            based on code in Sargolzaei and Iwaisaki's paper.
761    
762    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
763    
764            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
765            generic and mer methods for isNested and denomDF. This denomDF was
766            an attempt to emulate that in lme but I don't think that makes
767            sense.  Use the trace of the hat matrix instead.
768    
769    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
772            the C code depending on a slot structure that's no longer valid.
773            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
774    
775    
776    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
777    
778            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
779            of lowerTriMatrix generic and methods to tril (also upper to triu)
780            and added a general band extractor.
781    
782    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
783    
784            * R/pedigree.R (pedigree): Replace sire and dam values outside the
785            allowable range with NAs. Added a corresponding check in the
786            validity check for the pedigree class.
787    
788            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
789            crossprod methods now inherits from symmetricMatrix.
790    
791    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
792    
793            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
794            generics lowerTriMatrix and upperTriMatrix along with methods for
795            the Csparse virtual class.  Also added a C function Csparse_band
796            that implements these methods by calling cholmod_band.
797    
798    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
801            erased when it was NULL.  This led to invalid subselections!
802    
803    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
804    
805            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
806            in method for "t" so as not to lose the unit diagonal property.
807    
808    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
809    
810            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
811            and methods.  This is now an option to the ranef method for the
812            mer class.
813    
814            * src/cs_utils.c: Ensure that the nz component is -1 for a
815            compressed column-oriented matrix.  Minor formatting cleanup.
816    
817            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
818            objects.
819    
820    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
823            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
824    
825    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
826    
827            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
828            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
829    
830            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
831            for the dtCMatrix class.
832    
833    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
834    
835            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
836            and methods for it.
837    
838    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
841            arguments, such that M %*% 1:6 now works
842            * Tests/matprod.R: test the above
843    
844    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
845    
846            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
847            the ranef.lmer class.
848    
849            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
850            methods to extract the posterior variances from the bVar slot.
851    
852    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
855            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
856    
857            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
858            * tests/simple: (extended)
859    
860            * R/sparseMatrix.R (isTriangular): now using much improved
861            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
862    
863    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
864    
865            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
866            (problem report from Franklin Parlamis).  This should be done
867            generally.
868    
869    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
870    
871            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
872            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
873            update the plot methods.
874    
875    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
876    
877            * R/lmer.R (resid and ranef methods):  Added methods for the
878            "residuals" and "resid" generic but only for linear mixed model
879            fits.  Changed the ranef method to return a list of data frames so
880            that the plot methods now work.
881    
882    2006-03-16  Douglas Bates  <bates@bates2>
883    
884            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
885            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
886    
887            * DESCRIPTION (Date): New release
888    
889    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
892    
893            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
894            * man/KNex.Rd: and other help files
895            * tests/*.R: several ones needed adaption
896            * inst/doc/Comparisons.Rnw: ditto
897    
898    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
900            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
901    
902            * tests/indexing.R: tests for new [<- methods for sparse matrices.
903    
904    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
907    
908            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
909    
910    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * R/dMatrix.R: enable things like  M [ M < 10 ]
913            * R/dgeMatrix.R: implement it
914    
915    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/AllClass.R: define "summary.mer" and "*.lmer"
918            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
919            * R/lmer.R (show): now works with summary()
920    
921    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
922    
923            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
924            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
925                    support the above
926    
927    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
928    
929            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
930            Use glmFit$prior.weights for weights in a glmm.
931            Allow an option usePQL = FALSE to skip the PQL steps for the
932            Laplace method (and, in time, the AGQ method).
933    
934            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
935            into a separate function internal_mer_Xfactor to be able to call
936            it from internal_bhat.
937    
938    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * tests/Class+Meth.R (tstMatrixClass): function for much better
941            testing; now again of all actual classes.
942    
943            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
944                    use macros and define make_d_matrix_* and make_i_matrix_*
945                    where _i_ is for the ldense routines:
946    
947            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
948            * src/ldense.c (lsyMatrix_as_lgeMatrix):
949    
950            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
951    
952    
953    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
956                    many different kinds of matrices.
957            * R/*.R: quite a few new methods were needed for R CMD check with
958                    new Matrix().  Very good for users playing around.
959    
960    
961    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * src/dgeMatrix.c (dMatrix_validate): new
964            * src/Mutils.c (dense_nonpacked_validate): new
965    
966            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
967    
968    
969    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
970    
971            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
972    
973    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
974    
975            * DESCRIPTION (Version): 0.99-6 released to CRAN
976    
977            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
978            segfault in cases with multiple non-nested grouping factors.
979    
980    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
983                    (Depends): also on 'utils'
984    
985            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
986            * R/diagMatrix.R (Diagonal): constructor and methods for
987            diagonal matrices
988    
989            * R/ltTMatrix.R: new "minimal methods"
990    
991    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
994            all methods (and help files).
995    
996    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
999                    for case (dimn.  op  no_dimn.)
1000    
1001    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1002    
1003            * DESCRIPTION (Version): 0.99-2  released to CRAN
1004    
1005    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1006    
1007            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1008            by Julian Faraway.
1009    
1010    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * R/Auxiliaries.R (try_as): new utility
1013            * R/sparseMatrix.R: use try_as() in coercion to original class
1014    
1015    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1018    
1019    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/Auxiliaries.R (dimNamesCheck): added
1022    
1023            * R/Matrix.R (as.array), (as.vector): new
1024    
1025    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1028                    default.
1029            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1030                    "pMatrix" now contains "sparseMatrix"
1031    
1032    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * tests/Class+Meth.R: new tests; t(t(m)) == m
1035    
1036            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1037    
1038            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1039            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1040    
1041            * R/dspMatrix.R: typo in "t" method
1042    
1043    2005-09-18  Douglas Bates  <bates@wisc.edu>
1044    
1045            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1046            * R/Tsparse.R: instead of R/gTMatrix.R
1047            * R/Csparse.R: new
1048            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1049            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1050            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1051                            via cholmod
1052    
1053    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1054    
1055            * R/Auxiliaries.R (non0ind): new function using new C code
1056            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1057    
1058    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1059    
1060            * src/chm_common.h: header file required by all C sources that
1061            call CHOLMOD functions.  It defines a cholmod_common structure
1062            called 'c' whose address is passed as the last argument to
1063            (virtually) every CHOLMOD function.
1064    
1065            * src/Pattern.c: Simple example of the use of CHOLMOD.
1066    
1067            * src/init.c: initialize and finalize the cholmod_common structure.
1068    
1069            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1070            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1071    
1072    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * inst/test-tools.R: new file collecting the utility functions used
1075                    in ./tests/*.R
1076    
1077            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1078            * R/Matrix.R (cbind2): methods for NULL and missing
1079    
1080    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1081    
1082            * R/AllClass.R: new "index" class for "[" and "[<-":
1083                    First cut at "symmetricMatrix" and "triangularMatrix"
1084            * R/gTMatrix.R (.ind.prep): new function;
1085                    Logical and character indexing now work too.
1086            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1087            * tests/indexing.R: new, including *.Rout.save
1088            * tests/dgTMatrix.R: new
1089    
1090    2005-08-29  Douglas Bates  <bates@wisc.edu>
1091    
1092            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1093            indicator pos not being updated.  Also enforced upper triangular
1094            for symmetric case.  Need to coerce edges component of elements of
1095            edge list - grr! (Why don't they define their classes cleanly?)
1096    
1097    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * R/Matrix.R:  added first "[<-" methods; not yet functional
1100            * R/denseMatrix.R: ditto
1101            * man/Subassign-methods.Rd: new help file for these
1102    
1103    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1104    
1105            * DESCRIPTION (Version): 0.98-6
1106    
1107            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1108            matrices.
1109    
1110    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1111    
1112            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1113                    as( <logical>, "matrix")
1114    
1115            * R/pMatrix.R: coercion to "lgTMatrix"
1116    
1117            * R/gTMatrix.R: new virtual class to define "[" methods for.
1118            * man/gTMatrix-class.Rd:
1119            * General slight re-organization of where "[" methods are defined.
1120              more to come.
1121    
1122    2005-08-18  Douglas Bates  <bates@wisc.edu>
1123    
1124            * DESCRIPTION (Version): 0.98-5  released to CRAN
1125    
1126            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1127            * .....
1128    
1129    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1130    
1131            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1132            or glmer objects.
1133    
1134    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1137    
1138    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1139    
1140            * R/HBMM.R: finish re-writing R-only code.
1141    
1142    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1143    
1144            * man/externalFormats.Rd: move documentation for writeHB and
1145            writeMM here.
1146    
1147            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1148            (suggested by Paul Roecker).
1149    
1150            * tests/validObj.R (assertError): Comment out test that is failing
1151            after recent changes in r-devel.
1152    
1153    
1154    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1155    
1156            * R/AllClass.R: intermediate virtual class "denseMatrix"
1157            * man/denseMatrix-class.Rd
1158            * NAMESPACE: export it, and also export
1159            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1160    
1161    2005-08-10  Douglas Bates  <bates@wisc.edu>
1162    
1163            * DESCRIPTION (Version): 0.98-3 to CRAN
1164    
1165            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1166            matrix_solve code (which was really, really wrong).
1167    
1168    2005-08-07  Douglas Bates  <bates@wisc.edu>
1169    
1170            * DESCRIPTION (Version): 0.98-2
1171    
1172            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1173    
1174            * R/lmer.R (abbrvNms): new
1175            * R/lmer.R (mcmcsamp): allow transformed parameters
1176            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1177            for the Harwell-Boeing and the MatrixMarket formats.
1178    
1179    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * man/dtrMatrix-class.Rd: add examples
1182            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1183    
1184            * TODO: note the dtpMatrix (docu) bug
1185    
1186            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1187            in order to ensure that new as.matrix() is used by old functions,
1188            e.g., svd(), qr(), eigen(), dist(),..;
1189                  apply(), also matplot() or pairs().
1190    
1191    
1192    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1195              add comments about 'control' / lmerControl() arguments
1196    
1197    2005-07-27  Douglas Bates  <bates@wisc.edu>
1198    
1199            * man/sleepstudy.Rd: Added the sleep data set.
1200            * DESCRIPTION (Version): 0.98-1  released to CRAN
1201    
1202    2005-07-12  Douglas Bates  <bates@wisc.edu>
1203            * man/sleepstudy.Rd: Added the sleep data set.
1204    
1205            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1206            .Call calls that were producing spurious output.
1207    
1208    2005-07-05  Douglas Bates  <bates@wisc.edu>
1209    
1210            * R/lmer.R (lmer): stored updated variance component estimates in
1211            mer object for the generalized model.  (Bug reported by Renaud
1212            Lancelot).
1213    
1214    2005-07-03  Douglas Bates  <bates@wisc.edu>
1215    
1216            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1217            unidimensional case.
1218    
1219    2005-06-08  Douglas Bates  <bates@wisc.edu>
1220    
1221            * DESCRIPTION (Version): 0.96-1
1222    
1223            * moved  lmer-class' R and C code moved from lme4 to here
1224    
1225    2005-06-04  Douglas Bates  <bates@wisc.edu>
1226    
1227            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1228            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1229    
1230    2005-06-02  Douglas Bates  <bates@wisc.edu>
1231    
1232            * src/Makefile.win: Forgot to update this when Makefile changed.
1233    
1234    2005-05-11  Douglas Bates  <bates@wisc.edu>
1235    
1236            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1237            bug reported by Kurt Hornik and Michael Hahsler.
1238    
1239    2005-05-10  Douglas Bates  <bates@wisc.edu>
1240    
1241            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1242            logical sparse matrices.  These will also be used in the symbolic
1243            analysis for lmer objects.
1244    
1245            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1246            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1247    
1248    2005-05-06  Douglas Bates  <bates@wisc.edu>
1249    
1250            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1251            colMeans, colSums, rowMeans and rowSums.
1252    
1253    2005-04-18  Douglas Bates  <bates@wisc.edu>
1254    
1255            * src/lgCMatrix.[ch]: code for _validate method and stub for
1256            multiplication operation.
1257    
1258            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1259            to dgetrs.
1260    
1261            * src/init.c: Fix cut-and-paste error in definition of
1262            dgeMatrix_matrix_solve
1263    
1264            * src/{many files}: Tighten code by using ALLOC_SLOT.
1265    
1266    2005-04-15  Douglas Bates  <bates@wisc.edu>
1267    
1268            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1269    
1270            * DESCRIPTION: Eliminate import of stats.
1271    
1272    
1273    2005-04-06  Douglas Bates  <bates@wisc.edu>
1274    
1275            * R/AllClass.R : add logical sparse matrix classes
1276    
1277    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1278    
1279            * R/dgTMatrix.R: add "[" method for triplet matrices
1280            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1281    
1282    2005-03-31  Douglas Bates  <bates@wisc.edu>
1283    
1284            * DESCRIPTION (Version): release 0.95-5 to CRAN
1285    
1286            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1287            * R/sparseMatrix.R: %*%, crossprod()
1288            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1289            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1290            * src/lmer.c (lmer_fitted): fix thinko
1291    
1292    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1293    
1294            * R/AllClass.R: add two virtual sparse classes ``on top''
1295    
1296    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1297    
1298            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1299                    correspondingly fix examples and tests/ since new()
1300                    doesn't work for virtual classes.
1301    
1302    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * R/Matrix.R (as.matrix): method and one for unname()
1305            * tests/dpoMatrix.R: tests should now be less platform dependent;
1306              also run for R 2.1.0; using as.matrix()
1307    
1308    2005-03-15  Douglas Bates  <bates@wisc.edu>
1309    
1310            * R/pMatrix.R: "pMatrix" class added
1311            * ....
1312    
1313    2005-03-14  Douglas Bates  <bates@wisc.edu>
1314    
1315            * R/dtpMatrix.R: Add unpack method and an example.
1316    
1317            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1318            of general symmetric matrices and associated S4 methods.
1319    
1320    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1321            +
1322    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1323    
1324            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1325              crossprod() and "%*%" methods added; tests, too.
1326            * tests/matprod.R: new, for testing these
1327    
1328    2005-03-03  Douglas Bates  <bates@wisc.edu>
1329    
1330            * src/lmer.c (lmer_fitted): Added.
1331    
1332    2005-03-02  Douglas Bates  <bates@wisc.edu>
1333    
1334            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1335    
1336    2005-02-28  Douglas Bates  <bates@wisc.edu>
1337    
1338            * src/*.c,po/,inst/po: Internationalization and localization of
1339            the package.
1340    
1341            * src/ldl.[ch]: Removed these as their contents are referenced in the
1342            R_ldl.c file.
1343    
1344            * src/flame.[ch]: Removed these source files.
1345    
1346            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1347    
1348            * src/LU.[ch],src/init.c: absorb in factorizations
1349    
1350            * src/Mutils.h: prepare for internationalization
1351    
1352            * src/cblas.h: move the enum definitions to Mutils.h and remove
1353            this file
1354    
1355    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1356    
1357            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1358    
1359            * R/dtrMatrix.R: fix t() method
1360    
1361            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1362            * NAMESPACE: export them (and import generics from "methods")
1363            * tests/group-methods.R : and test them.
1364    
1365            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1366            border case
1367    
1368    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1369    
1370            * DESCRIPTION (Version): 0.95-2  released to CRAN
1371    
1372            * src/dgBCMatrix.c:
1373            * src/lmer.c: many changes
1374            * ...
1375    
1376    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1377    
1378            * R/Matrix.R: add more sophisticated show() method.
1379    
1380    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1381    
1382            * */* : almost complete reorganization of classes.
1383    
1384    2005-01-26  Douglas Bates  <bates@wisc.edu>
1385    
1386            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1387            for the geMatrix class.
1388    
1389    2005-01-24  Douglas Bates  <bates@wisc.edu>
1390    
1391            * src/Makefile (clean): Remove *.a and *.so
1392    
1393            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1394    
1395    2005-01-23  Douglas Bates  <bates@wisc.edu>
1396    
1397            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1398            had an effect in cases with more than 2 grouping factors.
1399    
1400    2005-01-03  Douglas Bates  <bates@wisc.edu>
1401    
1402            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1403    
1404    2004-12-23  Douglas Bates  <bates@wisc.edu>
1405    
1406            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1407            and R_useDynamicSymbols (suggested by B.D.Ripley).
1408    
1409    2004-12-14  Douglas Bates  <bates@wisc.edu>
1410    
1411          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1412    
1413          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1414          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1415    
1416  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1417    
1418          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1419          no longer used.          no longer used.
# Line 17  Line 1425 
1425          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1426          Fixes part but not all of #15.          Fixes part but not all of #15.
1427    
1428  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1429    
1430          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1431          scalar grouping factors corrected.          scalar grouping factors corrected.
1432    
1433  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1434    
1435          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1436    
1437  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1438    
1439          * 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
1440          .h file can be included.          .h file can be included.
1441    
1442  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1443    
1444          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1445          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1446    
1447          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1448    
1449  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1450    
1451          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1452    
1453  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1454    
1455          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1456    
1457  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1458    
1459          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1460    
1461  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1462    
1463          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1464    
1465  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1466    
1467          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1468          routines.          routines.
1469    
1470  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1471    
1472          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1473    
1474  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1475    
1476          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1477    

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