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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1691, Sun Dec 10 13:54:15 2006 UTC
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1    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
4            to LL before converting to a sparse matrix. (The LDL form can be
5            converted to a sparse matrix but it is implicitly a unit
6            triangular matrix and a diagonal matrix overwritten on the diagonal.)
7    
8    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
9    
10            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
11    
12    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * DESCRIPTION (Version): updated -> release 0.9975-7
15            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
16    
17    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
20    
21    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
24            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
25            is exactly singular.
26    
27    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * DESCRIPTION (Date): updated -> release 0.9975-6
30    
31    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
34            now returns symmetric.
35    
36            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
37    
38            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
39            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
40    
41            * R/Auxiliaries.R (.type.kind): added
42    
43    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
46            running src/CSparse_install.sh
47    
48            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
49    
50    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
53            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
54    
55            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
56    
57            * tests/Class+Meth.R (tstMatrixClass): now assure
58            the (important in method programming) property :
59    
60                    ###>>  Every "Matrix" is either
61                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
62    
63                    (where "*" stands for "Matrix")
64    
65            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
66    
67            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
68            * tests/validObj.R: checks for "comparison"
69    
70            * R/sparseMatrix.R ([): improved indexing for sparse;
71                    trying to keep <symmetric>[ n, n] symmmetric
72    
73            * tests/indexing.R: indexing for logical sparse now ok
74    
75    
76    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * src/Tsparse.c: use xTsparse_validate() , and hence remove
79    
80            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
81    
82    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
85    
86            * tests/simple.R: validObject() checking the above.
87    
88            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
89            replacing both dgCMatrix_validate and lgCM*.
90    
91            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
92            fix dimnames setting in other places.
93            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
94    
95    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
98    
99            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
100            symmetry test, via
101            * R/Auxiliaries.R (.as.dgC.0.factors):
102    
103    2006-11-01  Douglas Bates  <bates@r-project.org>
104    
105            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
106            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
107            <CsparseMatrix>) added
108    
109    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * tests/matprod.R: add a variation of Harri's example
112    
113            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
114            recursive infinitely.
115    
116            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
117    
118            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
119    
120    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
123            matrix if possible; test m+m == 2*m; now test dgRMatrix.
124            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
125            satisfy the above test.
126    
127    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
130    
131            * R/dgCMatrix.R: solve(a, b="missing") based on
132            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
133            RHS = NULL.
134    
135            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
136            add more (needed) [t]crossprod() methods.
137    
138            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
139    
140            * R/Auxiliaries.R (as_CspClass): cleanup
141            (drop0): internal utility for "Csparse_drop(*, 0)"
142            (.bail.out.2): encourage active feedback
143    
144    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/dMatrix.R(Compare): new(), then slots [no validity check]
147    
148            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
149            non-valid or 'sorted' case).
150    
151            * R/dsparseMatrix.R: add "chol" method.
152            * R/ddenseMatrix.R: ditto
153    
154            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
155            * NAMESPACE (Ops)
156            * R/diagMatrix.R (diag2T): simple utility used "higher level"
157            coercion; deprecating direct lower level coercions.
158    
159            * R/*.R (seq): use seq_len() and seq_along() where possible.
160    
161    
162    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * DESCRIPTION (Version): 0.9975-5 ready for release
165    
166    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
167    
168            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
169    
170    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/AllClass.R (corMatrix): add 'validity' check;
173                    comment out unused "LDL" class definition
174            * NAMESPACE: mention, but do not export "LDL" class
175            * R/corMatrix.R: new (simple), needed for R-devel with
176            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
177              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
178    
179    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
180    
181            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
182            use Rprintf and R's error handling.
183    
184    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
187            * tests/matprod.R: add tests for the bug fixed.
188    
189    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
190    
191            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
192            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
193    
194    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
197    
198    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * DESCRIPTION (Version): 0.9975-3
201    
202            * R/diagMatrix.R (bdiag): new function constructing block diagonal
203            (sparse) matrices.
204            * man/bdiag.Rd: docu + examples
205    
206            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
207    
208            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
209            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
210    
211            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
212            that result is sparse or diagonal (and not dense).
213    
214            * man/Subassign-methods.Rd: fix examples
215    
216            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
217            should always return a sparse (and not sometimes a diagonal) matrix.
218    
219    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
222    
223    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * DESCRIPTION (Version): 0.9975-2
226    
227            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
228    
229    2006-10-02  Douglas Bates  <bates@R-project.org>
230    
231            * tests/dg_Matrix.R: Simplify test taking into account new code.
232    
233    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
236    
237            * R/lsTMatrix.R: new files w/ missing methods
238            * R/nsTMatrix.R:  "  'for completeness'
239    
240            * tests/Class+Meth.R: a bit less 'not.ok.classes'
241    
242            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
243    
244    
245    2006-09-28  Douglas Bates  <bates@R-project.org>
246    
247            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
248            included.
249    
250            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
251            Export C-callable functions used in Zt_create in lme4.
252    
253    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * DESCRIPTION (Version): 0.9975-1
256    
257            * tests/simple.R: less checks fail; using NA, found that our
258                    kronecker() is not base-compatible with NA's.
259    
260            * R/dMatrix.R: "Compare" method now implemented for all cases
261    
262            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
263    
264            * man/dtpMatrix-class.Rd: mention length of 'x' slot
265    
266            * src/dtpMatrix.c (dtpMatrix_validate): fix check
267            * src/dspMatrix.c (dspMatrix_validate): ditto
268    
269            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
270              including coercion to [nl]tTMatrix.
271    
272            * R/diagMatrix.R (show): print a header line as for other classes.
273    
274    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * src/Makefile.win (SUBDIRS): fix typo
277    
278    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
281    
282    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
285            symmetric and y missing in R code using %*% (cholmod_aat doesn't
286            accept a symmetric matrix).
287            * tests/group-methods.R: Uncomment test of crossprod applied to
288            lsCMatrix objects.
289    
290    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/AllClass.R (symmetricMatrix): add validity method (available
293            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
294    
295            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
296    
297            * tests/indexing.Rout.save:
298            * tests/indexing.R: additions, mainly for 'lsparse'
299    
300            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
301            case.
302    
303            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
304    
305    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
308                    as 'N' (1-letter - Ok?)
309    
310            * tests/group-methods.R: add test for logical + NAs
311    
312            * R/dMatrix.R ("Compare"): fix to work with NA's
313    
314            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
315    
316            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
317                    which is implemented.
318    
319    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/chm_common.c: coerce logical <-> double instead of
322            typecasting;  needed for "l" matrix handling in cholmod.
323    
324            * tests/other-pkgs.R (graph): small extension in "graph" checks.
325    
326            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
327            (Tsp2grNEL): other fixes needed
328    
329    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
332                    Matrices, since "lMatrix", also "lsparseM" can have NA
333            * R/ndenseMatrix.R, etc: new source files
334            * man/nsparseMatrix-classes.Rd, etc: new help files
335            * tests/: adaptions
336            * src/chm_common.c (chm_dense_to_SEXP): and others:
337                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
338            * src/Csparse.c, etc: ditto
339    
340    2006-09-11  Douglas Bates  <bates@R-project.org>
341    
342            * src/Mutils.[ch],init.c inst/include/*.h: Move the
343            alloc_d**Matrix functions to the lme4 package.
344    
345    2006-09-09  Douglas Bates  <bates@R-project.org>
346    
347            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
348            fixed
349    
350    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/lMatrix.R: new
353    
354            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
355    
356            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
357            * man/tcrossprod.Rd: ditto
358    
359    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
362            for exported functions
363            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
364            Remove partitioning algorithms for sparse matrix reordering.  The
365            copyright on the Metis code was problematic and the methods were
366            rarely used.
367            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
368            operations are now done entirely in CHOLMOD code.
369    
370    2006-09-06  Douglas Bates  <bates@R-project.org>
371    
372            * src/Mutils.h: Remove functions that are no longer used.
373    
374    2006-09-04  Douglas Bates  <bates@R-project.org>
375    
376            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
377            * src/DEPS.mkf: update
378    
379    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * created branches/Matrix-for-R-2.3.x;  on trunk: do
382            * DESCRIPTION (Version): 0.9975-0
383            (Depends): R (>= 2.4.0)
384    
385    2006-09-01  Douglas Bates  <bates@R-project.org>
386    
387            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
388    
389    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
392            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
393    
394            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
395    
396    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
399            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
400            * R/dsparseMatrix.R: ditto
401            * R/Csparse.R: ditto
402    
403    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/dMatrix.R (Compare): improve availability of "<", etc
406            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
407    
408    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
411            of a 0-index which was used as 1-index (..hmm)
412    
413            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
414    
415            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
416            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
417            (.is.diagonal): ditto
418    
419            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
420    
421            * R/Matrix.R (Matrix): also work for NA data
422    
423    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
426            in all cases.
427    
428    2006-08-27  Douglas Bates  <bates@R-project.org>
429    
430            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
431            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
432    
433    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
436            subclasses of "ddenseMatrix"
437            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
438            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
439            instead of half dozen specialized ones.
440    
441    2006-08-25  Douglas Bates  <bates@R-project.org>
442    
443            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
444            <tillard@cirad.fr> - ordering standard errors to match effects.
445    
446    2006-08-24  Douglas Bates  <bates@R-project.org>
447    
448            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
449            on R_ldl.
450            * R/lCholCMatrix.R,
451            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
452            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
453            * many files in ./R and ./src: Use more general version of
454            dup_mMatrix_as_dgeMatrix to simplify method definitions.
455            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
456            dtpMatrix, dspMatrix and dppMatrix conversions.
457    
458    
459    2006-08-23  Douglas Bates  <bates@R-project.org>
460    
461            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
462            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
463            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
464            dgeMatrix_crossprod (may need to do this in other places).
465            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
466            generic and method for dsCMatrix.  Use CHOLMOD for chol().
467    
468    2006-08-22  Douglas Bates  <bates@R-project.org>
469    
470            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
471            types of classed Matrices, matrices or numeric or logical vectors.
472            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
473            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
474            to Mutils.h (as an inline) and change name to Matrix_check_class;
475            fixes in as_cholmod_factor and chm_factor_to_SEXP.
476            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
477            dsCMatrix_matrix_solve.  Comment out vestigial functions.
478            * src/Csparse.c: use diag_P and uplo_P macros.
479    
480    2006-08-21  Douglas Bates  <bates@R-project.org>
481    
482            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
483            valgrind.
484            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
485            inverses.
486            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
487            -Wall warnings.
488            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
489            Use dup_mMatrix_as_dgeMatrix.
490    
491    2006-08-20  Douglas Bates  <bates@R-project.org>
492    
493            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
494            * tests/sparseQR.R: Added
495            * man/sparseQR-class.Rd: Document methods for qr.* generics
496            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
497    
498    2006-08-19  Douglas Bates  <bates@R-project.org>
499    
500            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
501            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
502            and qr.fitted.
503            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
504            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
505    
506    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
509            the base version has no "..." argument.
510    
511            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
512    
513            * R/Matrix.R: define and
514            * NAMESPACE: export as.numeric() and as.logical() methods.
515                    Let's hope these do not badly slow down something...
516            Finally export the zapsmall() method.
517    
518    2006-08-17  Douglas Bates  <bates@R-project.org>
519    
520            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
521            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
522            * src/dtCMatrix.c :Remove code that is no longer used
523            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
524    
525    2006-08-14  Douglas Bates  <bates@R-project.org>
526    
527            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
528            Csparse_to_logical and Csparse_symmetric_to_general.
529            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
530            coercion methods between CsparseMatrix and TsparseMatrix.
531    
532    2006-08-14  Douglas Bates  <bates@R-project.org>
533    
534            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
535            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
536            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
537            possible.
538    
539    2006-08-12  Douglas Bates  <bates@R-project.org>
540    
541            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
542              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
543              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
544              generalize conversions between TsparseMatrix, CsparseMatrix,
545              denseMatrix and matrix.  Preserve triangularity property and
546              propagate Dimnames in the easy cases.
547    
548    2006-08-10  Douglas Bates  <bates@R-project.org>
549    
550            * src/lmer.c: adjust checks in glmer_init for S4SXP
551            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
552            before S4SXP but for the wrong reasons.
553    
554    2006-08-08  Douglas Bates  <bates@R-project.org>
555    
556            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
557            Later modified to return the upper triangle only.
558            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
559    
560    2006-08-07  Douglas Bates  <bates@R-project.org>
561    
562            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
563            R-level conversion to a sparse symmetric class.
564            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
565            Remove conversion to sparse symmetric classes (now done in C code).
566    
567    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
570            * man/band.Rd:  adapt the \dontshow{} unit test.
571    
572    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * DESCRIPTION (Version): 0.995-14  for CRAN
575    
576            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
577    
578            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
579            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
580    
581            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
582            * R/Tsparse.R (tril, triu, band): methods
583            * R/dgRMatrix.R (tril, ...):    ditto
584            * man/band.Rd:                  ditto
585    
586    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/Matrix.R (head, tail): directly use utils:::head.matrix
589                    to be up-to-date automatically.
590    
591    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
594    
595            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
596            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
597            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
598            such that the S4 objects are always created by the current version
599            of R and 'Matrix' class definitions.
600    
601    2006-08-01  Douglas Bates  <bates@R-project.org>
602    
603            * R/lmer.R (LMEoptimize method), tests/lmer.R,
604            inst/external/test3comp.rda: Added warnings for convergence on
605            boundary and test cases.
606    
607            * src/lmer.c (mer_postVar): Modified to return the variances that
608            are marginal to the fixed effects, not conditional on them (which
609            is what the bVar slot contents represent).
610    
611    2006-07-31  Douglas Bates  <bates@R-project.org>
612    
613            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
614            function which calls the C function mer_hat_trace2.
615    
616            * man/ranef.Rd: Include description of "postVar" argument and
617            producing a caterpillar plot.
618    
619    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * NAMESPACE:    change  "correlation" to "corMatrix"
622            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
623            * R/dpoMatrix.R: ditto
624            * R/lmer.R:      ditto
625    
626    2006-07-28  Douglas Bates  <bates@R-project.org>
627    
628            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
629            RZXinv slot's contents into a separate internal function that can
630            be used in mer_hat_trace.
631    
632    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
635            via new smart
636            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
637            utility functions.
638    
639    
640    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/Csparse.R (tril, triu, band): do return *triangular* classed
643            matrices when appropriate; band() even symmetric ones.
644            (replCmat): extend to potentially all "CsparseMatrix"
645            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
646            allow subassignment for special sparse matrices.
647    
648            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
649    
650            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
651            argument; in glmer_*(): print only if(verbose).
652    
653            speed-optimize a few places by moving REAL(.) out of loops.
654    
655            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
656    
657    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
660                    since that wrongly triggers also for M[ logi , ]
661    
662            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
663            a symmetric matrix that results in a non-symmetric one.
664            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
665    
666            * R/dMatrix.R: make round(M) work as round(M, 0)
667    
668            * R/dgTMatrix.R (image): coordinate system and axis now use
669            1-based indices, not 0-based ones.
670    
671            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
672            * tests/indexing.R: test it.
673    
674            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
675            * man/isSymmetric-methods.Rd: and document it.
676    
677            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
678            * man/SparseM-conv.Rd: docu them
679    
680            * tests/other-pkgs.R: renamed from tests/graph.R and add example
681                    for 'SparseM' conversions
682    
683    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
684    
685            * R/Matrix.R (head): added head() and tail() methods.
686    
687    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * DESCRIPTION (Version): 0.995-12 released to CRAN
690    
691    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * tests/simple.R: add check for correct dsT -> dgT coercion;
694                    add check for correct printing of symmetric sparse matrices.
695    
696            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
697            for sparse symmetric matrices.
698    
699            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
700            diagonal twice.
701    
702    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
703    
704            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
705            being applied to the x slot (detected by Brian Ripley).
706    
707    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
710    
711            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
712    
713    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * src/lgCMatrix.c (lgCMatrix_diag): new function
716            * R/lgCMatrix.R (diag): for new method
717    
718            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
719                 ==> construction of illegal "*gTMatrix" via new() should
720                 now be much less easy:
721            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
722    
723            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
724                    directly.
725            * man/Matrix.Rd: documents it.
726    
727    2006-07-06  Douglas Bates  <bates@R-project.org>
728    
729            * src/pedigree.c (pedigree_inbreeding): Correction in
730            initialization.  This function is not currently being used and is
731            not fully tested.
732    
733            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
734            Introduced the glmer class.  Added code for mcmcmsamp on glmer
735            objects.  Modified validity check on pedigree objects to account
736            for nonparallel patterns of missingness of parents.
737    
738            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
739            class.
740    
741    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/pMatrix.R: coercion pMatrix -> Tsparse
744    
745    2006-06-12  Douglas Bates  <bates@R-project.org>
746    
747            * DESCRIPTION (Version): 0.995-11 released to CRAN
748    
749            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
750            the output from mcmcsamp.
751    
752    2006-06-10  Douglas Bates  <bates@R-project.org>
753    
754            * R/lmer.R (simulestimate): added C code for calculating the trace
755            of the hat matrix.
756    
757    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
760            classes.
761            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
762    
763    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/dgTMatrix.R (colSums): etc. All four of
766            colSums(), rowSums(), colMeans(), rowMeans() now should work for
767            all "Matrices".
768    
769    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
770    
771            * R/lmer.R (panel.ci): Add a reference line at zero and a
772            background grid to the qqmath plot of ranef.lmer.
773    
774    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
775    
776            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
777            grouping factors to be specified in the formula as (1|foo/bar).
778    
779    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * R/lmer.R (findbars and others): Change check of is.numeric to
782            !is.language to resolve the bug reported by Jacob Wegelin.
783    
784            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
785            code to evaluate inbreeding coefficients without calculating T,
786            based on code in Sargolzaei and Iwaisaki's paper.
787    
788    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
789    
790            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
791            generic and mer methods for isNested and denomDF. This denomDF was
792            an attempt to emulate that in lme but I don't think that makes
793            sense.  Use the trace of the hat matrix instead.
794    
795    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
798            the C code depending on a slot structure that's no longer valid.
799            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
800    
801    
802    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
803    
804            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
805            of lowerTriMatrix generic and methods to tril (also upper to triu)
806            and added a general band extractor.
807    
808    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
809    
810            * R/pedigree.R (pedigree): Replace sire and dam values outside the
811            allowable range with NAs. Added a corresponding check in the
812            validity check for the pedigree class.
813    
814            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
815            crossprod methods now inherits from symmetricMatrix.
816    
817    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
818    
819            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
820            generics lowerTriMatrix and upperTriMatrix along with methods for
821            the Csparse virtual class.  Also added a C function Csparse_band
822            that implements these methods by calling cholmod_band.
823    
824    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
827            erased when it was NULL.  This led to invalid subselections!
828    
829    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
830    
831            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
832            in method for "t" so as not to lose the unit diagonal property.
833    
834    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
835    
836            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
837            and methods.  This is now an option to the ranef method for the
838            mer class.
839    
840            * src/cs_utils.c: Ensure that the nz component is -1 for a
841            compressed column-oriented matrix.  Minor formatting cleanup.
842    
843            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
844            objects.
845    
846    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
849            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
850    
851    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
852    
853            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
854            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
855    
856            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
857            for the dtCMatrix class.
858    
859    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
860    
861            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
862            and methods for it.
863    
864    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
867            arguments, such that M %*% 1:6 now works
868            * Tests/matprod.R: test the above
869    
870    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
871    
872            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
873            the ranef.lmer class.
874    
875            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
876            methods to extract the posterior variances from the bVar slot.
877    
878    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
881            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
882    
883            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
884            * tests/simple: (extended)
885    
886            * R/sparseMatrix.R (isTriangular): now using much improved
887            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
888    
889    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
890    
891            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
892            (problem report from Franklin Parlamis).  This should be done
893            generally.
894    
895    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
896    
897            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
898            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
899            update the plot methods.
900    
901    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
902    
903            * R/lmer.R (resid and ranef methods):  Added methods for the
904            "residuals" and "resid" generic but only for linear mixed model
905            fits.  Changed the ranef method to return a list of data frames so
906            that the plot methods now work.
907    
908    2006-03-16  Douglas Bates  <bates@bates2>
909    
910            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
911            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
912    
913            * DESCRIPTION (Date): New release
914    
915    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
918    
919            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
920            * man/KNex.Rd: and other help files
921            * tests/*.R: several ones needed adaption
922            * inst/doc/Comparisons.Rnw: ditto
923    
924    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
927    
928            * tests/indexing.R: tests for new [<- methods for sparse matrices.
929    
930    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
933    
934            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
935    
936    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * R/dMatrix.R: enable things like  M [ M < 10 ]
939            * R/dgeMatrix.R: implement it
940    
941    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * R/AllClass.R: define "summary.mer" and "*.lmer"
944            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
945            * R/lmer.R (show): now works with summary()
946    
947    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
948    
949            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
950            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
951                    support the above
952    
953  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
954    
955          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 1123 
1123  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1126          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1127          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1128    
1129  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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