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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1707, Thu Dec 21 08:03:05 2006 UTC
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1    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/bind.R: a few more cases
4            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
5    
6            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
7            * R/ddenseMatrix.R (cbind2/rbind2)
8            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
9            * tests/indexing.R
10            * tests/indexing.Rout.save: updated
11    
12    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
15            * tests/indexing.R
16    
17    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
20            align with proper position of "0", i.e., right for integers.
21            argument 'align' by default is "fancy".
22    
23    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
26            * R/Csparse.R: and fix "Compare" for more cases.
27            * tests/Class+Meth.R: test some of these (m == m, m != m)
28    
29    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/lsparseMatrix.R: all() and any() methods
32            * R/ldenseMatrix.R:      ditto
33            * NAMESPACE, R/Matrix.R: ditto
34    
35            * man/all-methods.Rd: document them minimally
36    
37            * tests/simple.R: add a few examples for these
38    
39    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Tsparse.R ([): fix long standing typo in symmetric case
42            * man/dsCMatrix-class.Rd: add example exhibiting the above case
43    
44    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
45    
46            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
47            to LL before converting to a sparse matrix. (The LDL form can be
48            converted to a sparse matrix but it is implicitly a unit
49            triangular matrix and a diagonal matrix overwritten on the diagonal.)
50    
51    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
54    
55    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * DESCRIPTION (Version): updated -> release 0.9975-7
58            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
59    
60    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
63    
64    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
67            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
68            is exactly singular.
69    
70    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Date): updated -> release 0.9975-6
73    
74    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
77            now returns symmetric.
78    
79            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
80    
81            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
82            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
83    
84            * R/Auxiliaries.R (.type.kind): added
85    
86    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
89            running src/CSparse_install.sh
90    
91            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
92    
93    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
96            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
97    
98            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
99    
100            * tests/Class+Meth.R (tstMatrixClass): now assure
101            the (important in method programming) property :
102    
103                    ###>>  Every "Matrix" is either
104                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
105    
106                    (where "*" stands for "Matrix")
107    
108            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
109    
110            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
111            * tests/validObj.R: checks for "comparison"
112    
113            * R/sparseMatrix.R ([): improved indexing for sparse;
114                    trying to keep <symmetric>[ n, n] symmmetric
115    
116            * tests/indexing.R: indexing for logical sparse now ok
117    
118    
119    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * src/Tsparse.c: use xTsparse_validate() , and hence remove
122    
123            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
124    
125    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
128    
129            * tests/simple.R: validObject() checking the above.
130    
131            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
132            replacing both dgCMatrix_validate and lgCM*.
133    
134            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
135            fix dimnames setting in other places.
136            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
137    
138    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
141    
142            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
143            symmetry test, via
144            * R/Auxiliaries.R (.as.dgC.0.factors):
145    
146    2006-11-01  Douglas Bates  <bates@r-project.org>
147    
148            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
149            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
150            <CsparseMatrix>) added
151    
152    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * tests/matprod.R: add a variation of Harri's example
155    
156            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
157            recursive infinitely.
158    
159            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
160    
161            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
162    
163    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
166            matrix if possible; test m+m == 2*m; now test dgRMatrix.
167            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
168            satisfy the above test.
169    
170    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
173    
174            * R/dgCMatrix.R: solve(a, b="missing") based on
175            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
176            RHS = NULL.
177    
178            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
179            add more (needed) [t]crossprod() methods.
180    
181            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
182    
183            * R/Auxiliaries.R (as_CspClass): cleanup
184            (drop0): internal utility for "Csparse_drop(*, 0)"
185            (.bail.out.2): encourage active feedback
186    
187    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/dMatrix.R(Compare): new(), then slots [no validity check]
190    
191            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
192            non-valid or 'sorted' case).
193    
194            * R/dsparseMatrix.R: add "chol" method.
195            * R/ddenseMatrix.R: ditto
196    
197            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
198            * NAMESPACE (Ops)
199            * R/diagMatrix.R (diag2T): simple utility used "higher level"
200            coercion; deprecating direct lower level coercions.
201    
202            * R/*.R (seq): use seq_len() and seq_along() where possible.
203    
204    
205    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * DESCRIPTION (Version): 0.9975-5 ready for release
208    
209    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
210    
211            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
212    
213    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/AllClass.R (corMatrix): add 'validity' check;
216                    comment out unused "LDL" class definition
217            * NAMESPACE: mention, but do not export "LDL" class
218            * R/corMatrix.R: new (simple), needed for R-devel with
219            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
220              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
221    
222    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
225            use Rprintf and R's error handling.
226    
227    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
230            * tests/matprod.R: add tests for the bug fixed.
231    
232    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
235            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
236    
237    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
240    
241    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION (Version): 0.9975-3
244    
245            * R/diagMatrix.R (bdiag): new function constructing block diagonal
246            (sparse) matrices.
247            * man/bdiag.Rd: docu + examples
248    
249            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
250    
251            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
252            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
253    
254            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
255            that result is sparse or diagonal (and not dense).
256    
257            * man/Subassign-methods.Rd: fix examples
258    
259            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
260            should always return a sparse (and not sometimes a diagonal) matrix.
261    
262    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
265    
266    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
267    
268            * DESCRIPTION (Version): 0.9975-2
269    
270            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
271    
272    2006-10-02  Douglas Bates  <bates@R-project.org>
273    
274            * tests/dg_Matrix.R: Simplify test taking into account new code.
275    
276    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
279    
280            * R/lsTMatrix.R: new files w/ missing methods
281            * R/nsTMatrix.R:  "  'for completeness'
282    
283            * tests/Class+Meth.R: a bit less 'not.ok.classes'
284    
285            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
286    
287    
288    2006-09-28  Douglas Bates  <bates@R-project.org>
289    
290            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
291            included.
292    
293            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
294            Export C-callable functions used in Zt_create in lme4.
295    
296    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * DESCRIPTION (Version): 0.9975-1
299    
300            * tests/simple.R: less checks fail; using NA, found that our
301                    kronecker() is not base-compatible with NA's.
302    
303            * R/dMatrix.R: "Compare" method now implemented for all cases
304    
305            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
306    
307            * man/dtpMatrix-class.Rd: mention length of 'x' slot
308    
309            * src/dtpMatrix.c (dtpMatrix_validate): fix check
310            * src/dspMatrix.c (dspMatrix_validate): ditto
311    
312            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
313              including coercion to [nl]tTMatrix.
314    
315            * R/diagMatrix.R (show): print a header line as for other classes.
316    
317    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * src/Makefile.win (SUBDIRS): fix typo
320    
321    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
324    
325    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
326    
327            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
328            symmetric and y missing in R code using %*% (cholmod_aat doesn't
329            accept a symmetric matrix).
330            * tests/group-methods.R: Uncomment test of crossprod applied to
331            lsCMatrix objects.
332    
333    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/AllClass.R (symmetricMatrix): add validity method (available
336            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
337    
338            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
339    
340            * tests/indexing.Rout.save:
341            * tests/indexing.R: additions, mainly for 'lsparse'
342    
343            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
344            case.
345    
346            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
347    
348    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
351                    as 'N' (1-letter - Ok?)
352    
353            * tests/group-methods.R: add test for logical + NAs
354    
355            * R/dMatrix.R ("Compare"): fix to work with NA's
356    
357            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
358    
359            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
360                    which is implemented.
361    
362    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * src/chm_common.c: coerce logical <-> double instead of
365            typecasting;  needed for "l" matrix handling in cholmod.
366    
367            * tests/other-pkgs.R (graph): small extension in "graph" checks.
368    
369            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
370            (Tsp2grNEL): other fixes needed
371    
372    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
375                    Matrices, since "lMatrix", also "lsparseM" can have NA
376            * R/ndenseMatrix.R, etc: new source files
377            * man/nsparseMatrix-classes.Rd, etc: new help files
378            * tests/: adaptions
379            * src/chm_common.c (chm_dense_to_SEXP): and others:
380                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
381            * src/Csparse.c, etc: ditto
382    
383    2006-09-11  Douglas Bates  <bates@R-project.org>
384    
385            * src/Mutils.[ch],init.c inst/include/*.h: Move the
386            alloc_d**Matrix functions to the lme4 package.
387    
388    2006-09-09  Douglas Bates  <bates@R-project.org>
389    
390            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
391            fixed
392    
393    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/lMatrix.R: new
396    
397            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
398    
399            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
400            * man/tcrossprod.Rd: ditto
401    
402    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
403    
404            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
405            for exported functions
406            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
407            Remove partitioning algorithms for sparse matrix reordering.  The
408            copyright on the Metis code was problematic and the methods were
409            rarely used.
410            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
411            operations are now done entirely in CHOLMOD code.
412    
413    2006-09-06  Douglas Bates  <bates@R-project.org>
414    
415            * src/Mutils.h: Remove functions that are no longer used.
416    
417    2006-09-04  Douglas Bates  <bates@R-project.org>
418    
419            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
420            * src/DEPS.mkf: update
421    
422    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * created branches/Matrix-for-R-2.3.x;  on trunk: do
425            * DESCRIPTION (Version): 0.9975-0
426            (Depends): R (>= 2.4.0)
427    
428    2006-09-01  Douglas Bates  <bates@R-project.org>
429    
430            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
431    
432    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
435            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
436    
437            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
438    
439    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
442            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
443            * R/dsparseMatrix.R: ditto
444            * R/Csparse.R: ditto
445    
446    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/dMatrix.R (Compare): improve availability of "<", etc
449            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
450    
451    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
454            of a 0-index which was used as 1-index (..hmm)
455    
456            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
457    
458            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
459            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
460            (.is.diagonal): ditto
461    
462            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
463    
464            * R/Matrix.R (Matrix): also work for NA data
465    
466    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
469            in all cases.
470    
471    2006-08-27  Douglas Bates  <bates@R-project.org>
472    
473            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
474            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
475    
476    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
479            subclasses of "ddenseMatrix"
480            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
481            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
482            instead of half dozen specialized ones.
483    
484    2006-08-25  Douglas Bates  <bates@R-project.org>
485    
486            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
487            <tillard@cirad.fr> - ordering standard errors to match effects.
488    
489    2006-08-24  Douglas Bates  <bates@R-project.org>
490    
491            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
492            on R_ldl.
493            * R/lCholCMatrix.R,
494            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
495            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
496            * many files in ./R and ./src: Use more general version of
497            dup_mMatrix_as_dgeMatrix to simplify method definitions.
498            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
499            dtpMatrix, dspMatrix and dppMatrix conversions.
500    
501    
502    2006-08-23  Douglas Bates  <bates@R-project.org>
503    
504            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
505            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
506            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
507            dgeMatrix_crossprod (may need to do this in other places).
508            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
509            generic and method for dsCMatrix.  Use CHOLMOD for chol().
510    
511    2006-08-22  Douglas Bates  <bates@R-project.org>
512    
513            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
514            types of classed Matrices, matrices or numeric or logical vectors.
515            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
516            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
517            to Mutils.h (as an inline) and change name to Matrix_check_class;
518            fixes in as_cholmod_factor and chm_factor_to_SEXP.
519            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
520            dsCMatrix_matrix_solve.  Comment out vestigial functions.
521            * src/Csparse.c: use diag_P and uplo_P macros.
522    
523    2006-08-21  Douglas Bates  <bates@R-project.org>
524    
525            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
526            valgrind.
527            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
528            inverses.
529            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
530            -Wall warnings.
531            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
532            Use dup_mMatrix_as_dgeMatrix.
533    
534    2006-08-20  Douglas Bates  <bates@R-project.org>
535    
536            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
537            * tests/sparseQR.R: Added
538            * man/sparseQR-class.Rd: Document methods for qr.* generics
539            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
540    
541    2006-08-19  Douglas Bates  <bates@R-project.org>
542    
543            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
544            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
545            and qr.fitted.
546            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
547            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
548    
549    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
552            the base version has no "..." argument.
553    
554            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
555    
556            * R/Matrix.R: define and
557            * NAMESPACE: export as.numeric() and as.logical() methods.
558                    Let's hope these do not badly slow down something...
559            Finally export the zapsmall() method.
560    
561    2006-08-17  Douglas Bates  <bates@R-project.org>
562    
563            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
564            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
565            * src/dtCMatrix.c :Remove code that is no longer used
566            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
567    
568    2006-08-14  Douglas Bates  <bates@R-project.org>
569    
570            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
571            Csparse_to_logical and Csparse_symmetric_to_general.
572            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
573            coercion methods between CsparseMatrix and TsparseMatrix.
574    
575    2006-08-14  Douglas Bates  <bates@R-project.org>
576    
577            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
578            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
579            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
580            possible.
581    
582    2006-08-12  Douglas Bates  <bates@R-project.org>
583    
584            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
585              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
586              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
587              generalize conversions between TsparseMatrix, CsparseMatrix,
588              denseMatrix and matrix.  Preserve triangularity property and
589              propagate Dimnames in the easy cases.
590    
591    2006-08-10  Douglas Bates  <bates@R-project.org>
592    
593            * src/lmer.c: adjust checks in glmer_init for S4SXP
594            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
595            before S4SXP but for the wrong reasons.
596    
597    2006-08-08  Douglas Bates  <bates@R-project.org>
598    
599            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
600            Later modified to return the upper triangle only.
601            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
602    
603    2006-08-07  Douglas Bates  <bates@R-project.org>
604    
605            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
606            R-level conversion to a sparse symmetric class.
607            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
608            Remove conversion to sparse symmetric classes (now done in C code).
609    
610    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
613            * man/band.Rd:  adapt the \dontshow{} unit test.
614    
615    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * DESCRIPTION (Version): 0.995-14  for CRAN
618    
619            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
620    
621            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
622            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
623    
624            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
625            * R/Tsparse.R (tril, triu, band): methods
626            * R/dgRMatrix.R (tril, ...):    ditto
627            * man/band.Rd:                  ditto
628    
629    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Matrix.R (head, tail): directly use utils:::head.matrix
632                    to be up-to-date automatically.
633    
634    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
637    
638            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
639            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
640            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
641            such that the S4 objects are always created by the current version
642            of R and 'Matrix' class definitions.
643    
644    2006-08-01  Douglas Bates  <bates@R-project.org>
645    
646            * R/lmer.R (LMEoptimize method), tests/lmer.R,
647            inst/external/test3comp.rda: Added warnings for convergence on
648            boundary and test cases.
649    
650            * src/lmer.c (mer_postVar): Modified to return the variances that
651            are marginal to the fixed effects, not conditional on them (which
652            is what the bVar slot contents represent).
653    
654    2006-07-31  Douglas Bates  <bates@R-project.org>
655    
656            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
657            function which calls the C function mer_hat_trace2.
658    
659            * man/ranef.Rd: Include description of "postVar" argument and
660            producing a caterpillar plot.
661    
662    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * NAMESPACE:    change  "correlation" to "corMatrix"
665            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
666            * R/dpoMatrix.R: ditto
667            * R/lmer.R:      ditto
668    
669    2006-07-28  Douglas Bates  <bates@R-project.org>
670    
671            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
672            RZXinv slot's contents into a separate internal function that can
673            be used in mer_hat_trace.
674    
675    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
678            via new smart
679            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
680            utility functions.
681    
682    
683    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/Csparse.R (tril, triu, band): do return *triangular* classed
686            matrices when appropriate; band() even symmetric ones.
687            (replCmat): extend to potentially all "CsparseMatrix"
688            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
689            allow subassignment for special sparse matrices.
690    
691            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
692    
693            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
694            argument; in glmer_*(): print only if(verbose).
695    
696            speed-optimize a few places by moving REAL(.) out of loops.
697    
698            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
699    
700    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
703                    since that wrongly triggers also for M[ logi , ]
704    
705            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
706            a symmetric matrix that results in a non-symmetric one.
707            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
708    
709            * R/dMatrix.R: make round(M) work as round(M, 0)
710    
711            * R/dgTMatrix.R (image): coordinate system and axis now use
712            1-based indices, not 0-based ones.
713    
714            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
715            * tests/indexing.R: test it.
716    
717            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
718            * man/isSymmetric-methods.Rd: and document it.
719    
720            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
721            * man/SparseM-conv.Rd: docu them
722    
723            * tests/other-pkgs.R: renamed from tests/graph.R and add example
724                    for 'SparseM' conversions
725    
726    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
727    
728            * R/Matrix.R (head): added head() and tail() methods.
729    
730    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * DESCRIPTION (Version): 0.995-12 released to CRAN
733    
734    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * tests/simple.R: add check for correct dsT -> dgT coercion;
737                    add check for correct printing of symmetric sparse matrices.
738    
739            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
740            for sparse symmetric matrices.
741    
742            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
743            diagonal twice.
744    
745    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
746    
747            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
748            being applied to the x slot (detected by Brian Ripley).
749    
750    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
753    
754            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
755    
756    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * src/lgCMatrix.c (lgCMatrix_diag): new function
759            * R/lgCMatrix.R (diag): for new method
760    
761            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
762                 ==> construction of illegal "*gTMatrix" via new() should
763                 now be much less easy:
764            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
765    
766            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
767                    directly.
768            * man/Matrix.Rd: documents it.
769    
770    2006-07-06  Douglas Bates  <bates@R-project.org>
771    
772            * src/pedigree.c (pedigree_inbreeding): Correction in
773            initialization.  This function is not currently being used and is
774            not fully tested.
775    
776            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
777            Introduced the glmer class.  Added code for mcmcmsamp on glmer
778            objects.  Modified validity check on pedigree objects to account
779            for nonparallel patterns of missingness of parents.
780    
781            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
782            class.
783    
784    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/pMatrix.R: coercion pMatrix -> Tsparse
787    
788    2006-06-12  Douglas Bates  <bates@R-project.org>
789    
790            * DESCRIPTION (Version): 0.995-11 released to CRAN
791    
792            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
793            the output from mcmcsamp.
794    
795    2006-06-10  Douglas Bates  <bates@R-project.org>
796    
797            * R/lmer.R (simulestimate): added C code for calculating the trace
798            of the hat matrix.
799    
800    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
803            classes.
804            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
805    
806    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * R/dgTMatrix.R (colSums): etc. All four of
809            colSums(), rowSums(), colMeans(), rowMeans() now should work for
810            all "Matrices".
811    
812    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
813    
814            * R/lmer.R (panel.ci): Add a reference line at zero and a
815            background grid to the qqmath plot of ranef.lmer.
816    
817    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
818    
819            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
820            grouping factors to be specified in the formula as (1|foo/bar).
821    
822    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
823    
824            * R/lmer.R (findbars and others): Change check of is.numeric to
825            !is.language to resolve the bug reported by Jacob Wegelin.
826    
827            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
828            code to evaluate inbreeding coefficients without calculating T,
829            based on code in Sargolzaei and Iwaisaki's paper.
830    
831    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
832    
833            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
834            generic and mer methods for isNested and denomDF. This denomDF was
835            an attempt to emulate that in lme but I don't think that makes
836            sense.  Use the trace of the hat matrix instead.
837    
838  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
841          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
842          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
843    
844    
845  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 962 
962          * 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)
963          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
964          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
965          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
966    
967  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
968    
# Line 329  Line 1166 
1166  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1169          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1170          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1171    
1172  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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