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revision 1268, Wed May 17 17:42:09 2006 UTC revision 1682, Fri Dec 1 18:42:40 2006 UTC
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1    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
4    
5    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
8            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
9            is exactly singular.
10    
11    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * DESCRIPTION (Date): updated -> release 0.9975-6
14    
15    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
18            now returns symmetric.
19    
20            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
21    
22            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
23            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
24    
25            * R/Auxiliaries.R (.type.kind): added
26    
27    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
30            running src/CSparse_install.sh
31    
32            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
33    
34    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
37            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
38    
39            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
40    
41            * tests/Class+Meth.R (tstMatrixClass): now assure
42            the (important in method programming) property :
43    
44                    ###>>  Every "Matrix" is either
45                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
46    
47                    (where "*" stands for "Matrix")
48    
49            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
50    
51            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
52            * tests/validObj.R: checks for "comparison"
53    
54            * R/sparseMatrix.R ([): improved indexing for sparse;
55                    trying to keep <symmetric>[ n, n] symmmetric
56    
57            * tests/indexing.R: indexing for logical sparse now ok
58    
59    
60    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/Tsparse.c: use xTsparse_validate() , and hence remove
63    
64            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
65    
66    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
69    
70            * tests/simple.R: validObject() checking the above.
71    
72            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
73            replacing both dgCMatrix_validate and lgCM*.
74    
75            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
76            fix dimnames setting in other places.
77            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
78    
79    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
82    
83            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
84            symmetry test, via
85            * R/Auxiliaries.R (.as.dgC.0.factors):
86    
87    2006-11-01  Douglas Bates  <bates@r-project.org>
88    
89            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
90            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
91            <CsparseMatrix>) added
92    
93    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * tests/matprod.R: add a variation of Harri's example
96    
97            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
98            recursive infinitely.
99    
100            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
101    
102            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
103    
104    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
107            matrix if possible; test m+m == 2*m; now test dgRMatrix.
108            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
109            satisfy the above test.
110    
111    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
114    
115            * R/dgCMatrix.R: solve(a, b="missing") based on
116            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
117            RHS = NULL.
118    
119            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
120            add more (needed) [t]crossprod() methods.
121    
122            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
123    
124            * R/Auxiliaries.R (as_CspClass): cleanup
125            (drop0): internal utility for "Csparse_drop(*, 0)"
126            (.bail.out.2): encourage active feedback
127    
128    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dMatrix.R(Compare): new(), then slots [no validity check]
131    
132            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
133            non-valid or 'sorted' case).
134    
135            * R/dsparseMatrix.R: add "chol" method.
136            * R/ddenseMatrix.R: ditto
137    
138            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
139            * NAMESPACE (Ops)
140            * R/diagMatrix.R (diag2T): simple utility used "higher level"
141            coercion; deprecating direct lower level coercions.
142    
143            * R/*.R (seq): use seq_len() and seq_along() where possible.
144    
145    
146    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * DESCRIPTION (Version): 0.9975-5 ready for release
149    
150    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
153    
154    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/AllClass.R (corMatrix): add 'validity' check;
157                    comment out unused "LDL" class definition
158            * NAMESPACE: mention, but do not export "LDL" class
159            * R/corMatrix.R: new (simple), needed for R-devel with
160            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
161              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
162    
163    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
166            use Rprintf and R's error handling.
167    
168    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
171            * tests/matprod.R: add tests for the bug fixed.
172    
173    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
176            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
177    
178    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
179    
180            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
181    
182    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version): 0.9975-3
185    
186            * R/diagMatrix.R (bdiag): new function constructing block diagonal
187            (sparse) matrices.
188            * man/bdiag.Rd: docu + examples
189    
190            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
191    
192            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
193            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
194    
195            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
196            that result is sparse or diagonal (and not dense).
197    
198            * man/Subassign-methods.Rd: fix examples
199    
200            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
201            should always return a sparse (and not sometimes a diagonal) matrix.
202    
203    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
206    
207    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * DESCRIPTION (Version): 0.9975-2
210    
211            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
212    
213    2006-10-02  Douglas Bates  <bates@R-project.org>
214    
215            * tests/dg_Matrix.R: Simplify test taking into account new code.
216    
217    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
220    
221            * R/lsTMatrix.R: new files w/ missing methods
222            * R/nsTMatrix.R:  "  'for completeness'
223    
224            * tests/Class+Meth.R: a bit less 'not.ok.classes'
225    
226            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
227    
228    
229    2006-09-28  Douglas Bates  <bates@R-project.org>
230    
231            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
232            included.
233    
234            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
235            Export C-callable functions used in Zt_create in lme4.
236    
237    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * DESCRIPTION (Version): 0.9975-1
240    
241            * tests/simple.R: less checks fail; using NA, found that our
242                    kronecker() is not base-compatible with NA's.
243    
244            * R/dMatrix.R: "Compare" method now implemented for all cases
245    
246            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
247    
248            * man/dtpMatrix-class.Rd: mention length of 'x' slot
249    
250            * src/dtpMatrix.c (dtpMatrix_validate): fix check
251            * src/dspMatrix.c (dspMatrix_validate): ditto
252    
253            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
254              including coercion to [nl]tTMatrix.
255    
256            * R/diagMatrix.R (show): print a header line as for other classes.
257    
258    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * src/Makefile.win (SUBDIRS): fix typo
261    
262    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
265    
266    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
267    
268            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
269            symmetric and y missing in R code using %*% (cholmod_aat doesn't
270            accept a symmetric matrix).
271            * tests/group-methods.R: Uncomment test of crossprod applied to
272            lsCMatrix objects.
273    
274    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/AllClass.R (symmetricMatrix): add validity method (available
277            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
278    
279            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
280    
281            * tests/indexing.Rout.save:
282            * tests/indexing.R: additions, mainly for 'lsparse'
283    
284            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
285            case.
286    
287            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
288    
289    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
292                    as 'N' (1-letter - Ok?)
293    
294            * tests/group-methods.R: add test for logical + NAs
295    
296            * R/dMatrix.R ("Compare"): fix to work with NA's
297    
298            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
299    
300            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
301                    which is implemented.
302    
303    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * src/chm_common.c: coerce logical <-> double instead of
306            typecasting;  needed for "l" matrix handling in cholmod.
307    
308            * tests/other-pkgs.R (graph): small extension in "graph" checks.
309    
310            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
311            (Tsp2grNEL): other fixes needed
312    
313    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
316                    Matrices, since "lMatrix", also "lsparseM" can have NA
317            * R/ndenseMatrix.R, etc: new source files
318            * man/nsparseMatrix-classes.Rd, etc: new help files
319            * tests/: adaptions
320            * src/chm_common.c (chm_dense_to_SEXP): and others:
321                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
322            * src/Csparse.c, etc: ditto
323    
324    2006-09-11  Douglas Bates  <bates@R-project.org>
325    
326            * src/Mutils.[ch],init.c inst/include/*.h: Move the
327            alloc_d**Matrix functions to the lme4 package.
328    
329    2006-09-09  Douglas Bates  <bates@R-project.org>
330    
331            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
332            fixed
333    
334    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/lMatrix.R: new
337    
338            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
339    
340            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
341            * man/tcrossprod.Rd: ditto
342    
343    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
344    
345            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
346            for exported functions
347            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
348            Remove partitioning algorithms for sparse matrix reordering.  The
349            copyright on the Metis code was problematic and the methods were
350            rarely used.
351            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
352            operations are now done entirely in CHOLMOD code.
353    
354    2006-09-06  Douglas Bates  <bates@R-project.org>
355    
356            * src/Mutils.h: Remove functions that are no longer used.
357    
358    2006-09-04  Douglas Bates  <bates@R-project.org>
359    
360            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
361            * src/DEPS.mkf: update
362    
363    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * created branches/Matrix-for-R-2.3.x;  on trunk: do
366            * DESCRIPTION (Version): 0.9975-0
367            (Depends): R (>= 2.4.0)
368    
369    2006-09-01  Douglas Bates  <bates@R-project.org>
370    
371            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
372    
373    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
376            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
377    
378            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
379    
380    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
383            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
384            * R/dsparseMatrix.R: ditto
385            * R/Csparse.R: ditto
386    
387    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dMatrix.R (Compare): improve availability of "<", etc
390            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
391    
392    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
395            of a 0-index which was used as 1-index (..hmm)
396    
397            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
398    
399            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
400            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
401            (.is.diagonal): ditto
402    
403            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
404    
405            * R/Matrix.R (Matrix): also work for NA data
406    
407    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
410            in all cases.
411    
412    2006-08-27  Douglas Bates  <bates@R-project.org>
413    
414            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
415            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
416    
417    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
420            subclasses of "ddenseMatrix"
421            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
422            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
423            instead of half dozen specialized ones.
424    
425    2006-08-25  Douglas Bates  <bates@R-project.org>
426    
427            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
428            <tillard@cirad.fr> - ordering standard errors to match effects.
429    
430    2006-08-24  Douglas Bates  <bates@R-project.org>
431    
432            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
433            on R_ldl.
434            * R/lCholCMatrix.R,
435            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
436            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
437            * many files in ./R and ./src: Use more general version of
438            dup_mMatrix_as_dgeMatrix to simplify method definitions.
439            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
440            dtpMatrix, dspMatrix and dppMatrix conversions.
441    
442    
443    2006-08-23  Douglas Bates  <bates@R-project.org>
444    
445            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
446            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
447            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
448            dgeMatrix_crossprod (may need to do this in other places).
449            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
450            generic and method for dsCMatrix.  Use CHOLMOD for chol().
451    
452    2006-08-22  Douglas Bates  <bates@R-project.org>
453    
454            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
455            types of classed Matrices, matrices or numeric or logical vectors.
456            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
457            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
458            to Mutils.h (as an inline) and change name to Matrix_check_class;
459            fixes in as_cholmod_factor and chm_factor_to_SEXP.
460            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
461            dsCMatrix_matrix_solve.  Comment out vestigial functions.
462            * src/Csparse.c: use diag_P and uplo_P macros.
463    
464    2006-08-21  Douglas Bates  <bates@R-project.org>
465    
466            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
467            valgrind.
468            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
469            inverses.
470            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
471            -Wall warnings.
472            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
473            Use dup_mMatrix_as_dgeMatrix.
474    
475    2006-08-20  Douglas Bates  <bates@R-project.org>
476    
477            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
478            * tests/sparseQR.R: Added
479            * man/sparseQR-class.Rd: Document methods for qr.* generics
480            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
481    
482    2006-08-19  Douglas Bates  <bates@R-project.org>
483    
484            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
485            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
486            and qr.fitted.
487            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
488            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
489    
490    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
493            the base version has no "..." argument.
494    
495            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
496    
497            * R/Matrix.R: define and
498            * NAMESPACE: export as.numeric() and as.logical() methods.
499                    Let's hope these do not badly slow down something...
500            Finally export the zapsmall() method.
501    
502    2006-08-17  Douglas Bates  <bates@R-project.org>
503    
504            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
505            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
506            * src/dtCMatrix.c :Remove code that is no longer used
507            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
508    
509    2006-08-14  Douglas Bates  <bates@R-project.org>
510    
511            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
512            Csparse_to_logical and Csparse_symmetric_to_general.
513            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
514            coercion methods between CsparseMatrix and TsparseMatrix.
515    
516    2006-08-14  Douglas Bates  <bates@R-project.org>
517    
518            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
519            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
520            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
521            possible.
522    
523    2006-08-12  Douglas Bates  <bates@R-project.org>
524    
525            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
526              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
527              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
528              generalize conversions between TsparseMatrix, CsparseMatrix,
529              denseMatrix and matrix.  Preserve triangularity property and
530              propagate Dimnames in the easy cases.
531    
532    2006-08-10  Douglas Bates  <bates@R-project.org>
533    
534            * src/lmer.c: adjust checks in glmer_init for S4SXP
535            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
536            before S4SXP but for the wrong reasons.
537    
538    2006-08-08  Douglas Bates  <bates@R-project.org>
539    
540            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
541            Later modified to return the upper triangle only.
542            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
543    
544    2006-08-07  Douglas Bates  <bates@R-project.org>
545    
546            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
547            R-level conversion to a sparse symmetric class.
548            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
549            Remove conversion to sparse symmetric classes (now done in C code).
550    
551    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
554            * man/band.Rd:  adapt the \dontshow{} unit test.
555    
556    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * DESCRIPTION (Version): 0.995-14  for CRAN
559    
560            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
561    
562            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
563            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
564    
565            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
566            * R/Tsparse.R (tril, triu, band): methods
567            * R/dgRMatrix.R (tril, ...):    ditto
568            * man/band.Rd:                  ditto
569    
570    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * R/Matrix.R (head, tail): directly use utils:::head.matrix
573                    to be up-to-date automatically.
574    
575    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
578    
579            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
580            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
581            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
582            such that the S4 objects are always created by the current version
583            of R and 'Matrix' class definitions.
584    
585    2006-08-01  Douglas Bates  <bates@R-project.org>
586    
587            * R/lmer.R (LMEoptimize method), tests/lmer.R,
588            inst/external/test3comp.rda: Added warnings for convergence on
589            boundary and test cases.
590    
591            * src/lmer.c (mer_postVar): Modified to return the variances that
592            are marginal to the fixed effects, not conditional on them (which
593            is what the bVar slot contents represent).
594    
595    2006-07-31  Douglas Bates  <bates@R-project.org>
596    
597            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
598            function which calls the C function mer_hat_trace2.
599    
600            * man/ranef.Rd: Include description of "postVar" argument and
601            producing a caterpillar plot.
602    
603    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * NAMESPACE:    change  "correlation" to "corMatrix"
606            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
607            * R/dpoMatrix.R: ditto
608            * R/lmer.R:      ditto
609    
610    2006-07-28  Douglas Bates  <bates@R-project.org>
611    
612            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
613            RZXinv slot's contents into a separate internal function that can
614            be used in mer_hat_trace.
615    
616    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
619            via new smart
620            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
621            utility functions.
622    
623    
624    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Csparse.R (tril, triu, band): do return *triangular* classed
627            matrices when appropriate; band() even symmetric ones.
628            (replCmat): extend to potentially all "CsparseMatrix"
629            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
630            allow subassignment for special sparse matrices.
631    
632            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
633    
634            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
635            argument; in glmer_*(): print only if(verbose).
636    
637            speed-optimize a few places by moving REAL(.) out of loops.
638    
639            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
640    
641    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
644                    since that wrongly triggers also for M[ logi , ]
645    
646            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
647            a symmetric matrix that results in a non-symmetric one.
648            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
649    
650            * R/dMatrix.R: make round(M) work as round(M, 0)
651    
652            * R/dgTMatrix.R (image): coordinate system and axis now use
653            1-based indices, not 0-based ones.
654    
655            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
656            * tests/indexing.R: test it.
657    
658            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
659            * man/isSymmetric-methods.Rd: and document it.
660    
661            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
662            * man/SparseM-conv.Rd: docu them
663    
664            * tests/other-pkgs.R: renamed from tests/graph.R and add example
665                    for 'SparseM' conversions
666    
667    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
668    
669            * R/Matrix.R (head): added head() and tail() methods.
670    
671    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * DESCRIPTION (Version): 0.995-12 released to CRAN
674    
675    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * tests/simple.R: add check for correct dsT -> dgT coercion;
678                    add check for correct printing of symmetric sparse matrices.
679    
680            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
681            for sparse symmetric matrices.
682    
683            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
684            diagonal twice.
685    
686    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
687    
688            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
689            being applied to the x slot (detected by Brian Ripley).
690    
691    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
694    
695            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
696    
697    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * src/lgCMatrix.c (lgCMatrix_diag): new function
700            * R/lgCMatrix.R (diag): for new method
701    
702            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
703                 ==> construction of illegal "*gTMatrix" via new() should
704                 now be much less easy:
705            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
706    
707            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
708                    directly.
709            * man/Matrix.Rd: documents it.
710    
711    2006-07-06  Douglas Bates  <bates@R-project.org>
712    
713            * src/pedigree.c (pedigree_inbreeding): Correction in
714            initialization.  This function is not currently being used and is
715            not fully tested.
716    
717            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
718            Introduced the glmer class.  Added code for mcmcmsamp on glmer
719            objects.  Modified validity check on pedigree objects to account
720            for nonparallel patterns of missingness of parents.
721    
722            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
723            class.
724    
725    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/pMatrix.R: coercion pMatrix -> Tsparse
728    
729    2006-06-12  Douglas Bates  <bates@R-project.org>
730    
731            * DESCRIPTION (Version): 0.995-11 released to CRAN
732    
733            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
734            the output from mcmcsamp.
735    
736    2006-06-10  Douglas Bates  <bates@R-project.org>
737    
738            * R/lmer.R (simulestimate): added C code for calculating the trace
739            of the hat matrix.
740    
741    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
744            classes.
745            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
746    
747    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/dgTMatrix.R (colSums): etc. All four of
750            colSums(), rowSums(), colMeans(), rowMeans() now should work for
751            all "Matrices".
752    
753    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
754    
755            * R/lmer.R (panel.ci): Add a reference line at zero and a
756            background grid to the qqmath plot of ranef.lmer.
757    
758    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
759    
760            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
761            grouping factors to be specified in the formula as (1|foo/bar).
762    
763    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
764    
765            * R/lmer.R (findbars and others): Change check of is.numeric to
766            !is.language to resolve the bug reported by Jacob Wegelin.
767    
768            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
769            code to evaluate inbreeding coefficients without calculating T,
770            based on code in Sargolzaei and Iwaisaki's paper.
771    
772    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
773    
774            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
775            generic and mer methods for isNested and denomDF. This denomDF was
776            an attempt to emulate that in lme but I don't think that makes
777            sense.  Use the trace of the hat matrix instead.
778    
779    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
782            the C code depending on a slot structure that's no longer valid.
783            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
784    
785    
786  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
787    
788          *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name          *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
# Line 118  Line 903 
903          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
904          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
905          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
906          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
907    
908  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
# Line 322  Line 1107 
1107  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1108    
1109          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1110          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1111          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1112    
1113  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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