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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1681, Wed Nov 29 15:55:03 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
4            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
5            is exactly singular.
6    
7    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * DESCRIPTION (Date): updated -> release 0.9975-6
10    
11    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
14            now returns symmetric.
15    
16            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
17    
18            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
19            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
20    
21            * R/Auxiliaries.R (.type.kind): added
22    
23    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
26            running src/CSparse_install.sh
27    
28            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
29    
30    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
33            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
34    
35            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
36    
37            * tests/Class+Meth.R (tstMatrixClass): now assure
38            the (important in method programming) property :
39    
40                    ###>>  Every "Matrix" is either
41                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
42    
43                    (where "*" stands for "Matrix")
44    
45            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
46    
47            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
48            * tests/validObj.R: checks for "comparison"
49    
50            * R/sparseMatrix.R ([): improved indexing for sparse;
51                    trying to keep <symmetric>[ n, n] symmmetric
52    
53            * tests/indexing.R: indexing for logical sparse now ok
54    
55    
56    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/Tsparse.c: use xTsparse_validate() , and hence remove
59    
60            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
61    
62    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
65    
66            * tests/simple.R: validObject() checking the above.
67    
68            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
69            replacing both dgCMatrix_validate and lgCM*.
70    
71            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
72            fix dimnames setting in other places.
73            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
74    
75    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
78    
79            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
80            symmetry test, via
81            * R/Auxiliaries.R (.as.dgC.0.factors):
82    
83    2006-11-01  Douglas Bates  <bates@r-project.org>
84    
85            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
86            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
87            <CsparseMatrix>) added
88    
89    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * tests/matprod.R: add a variation of Harri's example
92    
93            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
94            recursive infinitely.
95    
96            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
97    
98            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
99    
100    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
103            matrix if possible; test m+m == 2*m; now test dgRMatrix.
104            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
105            satisfy the above test.
106    
107    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
110    
111            * R/dgCMatrix.R: solve(a, b="missing") based on
112            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
113            RHS = NULL.
114    
115            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
116            add more (needed) [t]crossprod() methods.
117    
118            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
119    
120            * R/Auxiliaries.R (as_CspClass): cleanup
121            (drop0): internal utility for "Csparse_drop(*, 0)"
122            (.bail.out.2): encourage active feedback
123    
124    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dMatrix.R(Compare): new(), then slots [no validity check]
127    
128            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
129            non-valid or 'sorted' case).
130    
131            * R/dsparseMatrix.R: add "chol" method.
132            * R/ddenseMatrix.R: ditto
133    
134            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
135            * NAMESPACE (Ops)
136            * R/diagMatrix.R (diag2T): simple utility used "higher level"
137            coercion; deprecating direct lower level coercions.
138    
139            * R/*.R (seq): use seq_len() and seq_along() where possible.
140    
141    
142    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * DESCRIPTION (Version): 0.9975-5 ready for release
145    
146    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
147    
148            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
149    
150    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/AllClass.R (corMatrix): add 'validity' check;
153                    comment out unused "LDL" class definition
154            * NAMESPACE: mention, but do not export "LDL" class
155            * R/corMatrix.R: new (simple), needed for R-devel with
156            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
157              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
158    
159    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
162            use Rprintf and R's error handling.
163    
164    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
167            * tests/matprod.R: add tests for the bug fixed.
168    
169    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
170    
171            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
172            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
173    
174    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
175    
176            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
177    
178    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Version): 0.9975-3
181    
182            * R/diagMatrix.R (bdiag): new function constructing block diagonal
183            (sparse) matrices.
184            * man/bdiag.Rd: docu + examples
185    
186            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
187    
188            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
189            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
190    
191            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
192            that result is sparse or diagonal (and not dense).
193    
194            * man/Subassign-methods.Rd: fix examples
195    
196            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
197            should always return a sparse (and not sometimes a diagonal) matrix.
198    
199    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
202    
203    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * DESCRIPTION (Version): 0.9975-2
206    
207            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
208    
209    2006-10-02  Douglas Bates  <bates@R-project.org>
210    
211            * tests/dg_Matrix.R: Simplify test taking into account new code.
212    
213    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
216    
217            * R/lsTMatrix.R: new files w/ missing methods
218            * R/nsTMatrix.R:  "  'for completeness'
219    
220            * tests/Class+Meth.R: a bit less 'not.ok.classes'
221    
222            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
223    
224    
225    2006-09-28  Douglas Bates  <bates@R-project.org>
226    
227            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
228            included.
229    
230            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
231            Export C-callable functions used in Zt_create in lme4.
232    
233    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * DESCRIPTION (Version): 0.9975-1
236    
237            * tests/simple.R: less checks fail; using NA, found that our
238                    kronecker() is not base-compatible with NA's.
239    
240            * R/dMatrix.R: "Compare" method now implemented for all cases
241    
242            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
243    
244            * man/dtpMatrix-class.Rd: mention length of 'x' slot
245    
246            * src/dtpMatrix.c (dtpMatrix_validate): fix check
247            * src/dspMatrix.c (dspMatrix_validate): ditto
248    
249            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
250              including coercion to [nl]tTMatrix.
251    
252            * R/diagMatrix.R (show): print a header line as for other classes.
253    
254    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * src/Makefile.win (SUBDIRS): fix typo
257    
258    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
261    
262    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
265            symmetric and y missing in R code using %*% (cholmod_aat doesn't
266            accept a symmetric matrix).
267            * tests/group-methods.R: Uncomment test of crossprod applied to
268            lsCMatrix objects.
269    
270    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/AllClass.R (symmetricMatrix): add validity method (available
273            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
274    
275            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
276    
277            * tests/indexing.Rout.save:
278            * tests/indexing.R: additions, mainly for 'lsparse'
279    
280            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
281            case.
282    
283            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
284    
285    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
288                    as 'N' (1-letter - Ok?)
289    
290            * tests/group-methods.R: add test for logical + NAs
291    
292            * R/dMatrix.R ("Compare"): fix to work with NA's
293    
294            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
295    
296            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
297                    which is implemented.
298    
299    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/chm_common.c: coerce logical <-> double instead of
302            typecasting;  needed for "l" matrix handling in cholmod.
303    
304            * tests/other-pkgs.R (graph): small extension in "graph" checks.
305    
306            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
307            (Tsp2grNEL): other fixes needed
308    
309    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
312                    Matrices, since "lMatrix", also "lsparseM" can have NA
313            * R/ndenseMatrix.R, etc: new source files
314            * man/nsparseMatrix-classes.Rd, etc: new help files
315            * tests/: adaptions
316            * src/chm_common.c (chm_dense_to_SEXP): and others:
317                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
318            * src/Csparse.c, etc: ditto
319    
320    2006-09-11  Douglas Bates  <bates@R-project.org>
321    
322            * src/Mutils.[ch],init.c inst/include/*.h: Move the
323            alloc_d**Matrix functions to the lme4 package.
324    
325    2006-09-09  Douglas Bates  <bates@R-project.org>
326    
327            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
328            fixed
329    
330    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/lMatrix.R: new
333    
334            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
335    
336            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
337            * man/tcrossprod.Rd: ditto
338    
339    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
342            for exported functions
343            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
344            Remove partitioning algorithms for sparse matrix reordering.  The
345            copyright on the Metis code was problematic and the methods were
346            rarely used.
347            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
348            operations are now done entirely in CHOLMOD code.
349    
350    2006-09-06  Douglas Bates  <bates@R-project.org>
351    
352            * src/Mutils.h: Remove functions that are no longer used.
353    
354    2006-09-04  Douglas Bates  <bates@R-project.org>
355    
356            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
357            * src/DEPS.mkf: update
358    
359    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * created branches/Matrix-for-R-2.3.x;  on trunk: do
362            * DESCRIPTION (Version): 0.9975-0
363            (Depends): R (>= 2.4.0)
364    
365    2006-09-01  Douglas Bates  <bates@R-project.org>
366    
367            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
368    
369    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
372            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
373    
374            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
375    
376    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
379            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
380            * R/dsparseMatrix.R: ditto
381            * R/Csparse.R: ditto
382    
383    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/dMatrix.R (Compare): improve availability of "<", etc
386            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
387    
388    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
391            of a 0-index which was used as 1-index (..hmm)
392    
393            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
394    
395            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
396            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
397            (.is.diagonal): ditto
398    
399            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
400    
401            * R/Matrix.R (Matrix): also work for NA data
402    
403    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
406            in all cases.
407    
408    2006-08-27  Douglas Bates  <bates@R-project.org>
409    
410            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
411            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
412    
413    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
416            subclasses of "ddenseMatrix"
417            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
418            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
419            instead of half dozen specialized ones.
420    
421    2006-08-25  Douglas Bates  <bates@R-project.org>
422    
423            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
424            <tillard@cirad.fr> - ordering standard errors to match effects.
425    
426    2006-08-24  Douglas Bates  <bates@R-project.org>
427    
428            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
429            on R_ldl.
430            * R/lCholCMatrix.R,
431            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
432            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
433            * many files in ./R and ./src: Use more general version of
434            dup_mMatrix_as_dgeMatrix to simplify method definitions.
435            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
436            dtpMatrix, dspMatrix and dppMatrix conversions.
437    
438    
439    2006-08-23  Douglas Bates  <bates@R-project.org>
440    
441            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
442            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
443            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
444            dgeMatrix_crossprod (may need to do this in other places).
445            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
446            generic and method for dsCMatrix.  Use CHOLMOD for chol().
447    
448    2006-08-22  Douglas Bates  <bates@R-project.org>
449    
450            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
451            types of classed Matrices, matrices or numeric or logical vectors.
452            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
453            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
454            to Mutils.h (as an inline) and change name to Matrix_check_class;
455            fixes in as_cholmod_factor and chm_factor_to_SEXP.
456            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
457            dsCMatrix_matrix_solve.  Comment out vestigial functions.
458            * src/Csparse.c: use diag_P and uplo_P macros.
459    
460    2006-08-21  Douglas Bates  <bates@R-project.org>
461    
462            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
463            valgrind.
464            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
465            inverses.
466            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
467            -Wall warnings.
468            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
469            Use dup_mMatrix_as_dgeMatrix.
470    
471    2006-08-20  Douglas Bates  <bates@R-project.org>
472    
473            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
474            * tests/sparseQR.R: Added
475            * man/sparseQR-class.Rd: Document methods for qr.* generics
476            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
477    
478    2006-08-19  Douglas Bates  <bates@R-project.org>
479    
480            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
481            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
482            and qr.fitted.
483            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
484            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
485    
486    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
489            the base version has no "..." argument.
490    
491            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
492    
493            * R/Matrix.R: define and
494            * NAMESPACE: export as.numeric() and as.logical() methods.
495                    Let's hope these do not badly slow down something...
496            Finally export the zapsmall() method.
497    
498    2006-08-17  Douglas Bates  <bates@R-project.org>
499    
500            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
501            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
502            * src/dtCMatrix.c :Remove code that is no longer used
503            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
504    
505    2006-08-14  Douglas Bates  <bates@R-project.org>
506    
507            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
508            Csparse_to_logical and Csparse_symmetric_to_general.
509            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
510            coercion methods between CsparseMatrix and TsparseMatrix.
511    
512    2006-08-14  Douglas Bates  <bates@R-project.org>
513    
514            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
515            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
516            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
517            possible.
518    
519    2006-08-12  Douglas Bates  <bates@R-project.org>
520    
521            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
522              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
523              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
524              generalize conversions between TsparseMatrix, CsparseMatrix,
525              denseMatrix and matrix.  Preserve triangularity property and
526              propagate Dimnames in the easy cases.
527    
528    2006-08-10  Douglas Bates  <bates@R-project.org>
529    
530            * src/lmer.c: adjust checks in glmer_init for S4SXP
531            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
532            before S4SXP but for the wrong reasons.
533    
534    2006-08-08  Douglas Bates  <bates@R-project.org>
535    
536            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
537            Later modified to return the upper triangle only.
538            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
539    
540    2006-08-07  Douglas Bates  <bates@R-project.org>
541    
542            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
543            R-level conversion to a sparse symmetric class.
544            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
545            Remove conversion to sparse symmetric classes (now done in C code).
546    
547    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
550            * man/band.Rd:  adapt the \dontshow{} unit test.
551    
552    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * DESCRIPTION (Version): 0.995-14  for CRAN
555    
556            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
557    
558            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
559            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
560    
561            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
562            * R/Tsparse.R (tril, triu, band): methods
563            * R/dgRMatrix.R (tril, ...):    ditto
564            * man/band.Rd:                  ditto
565    
566    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/Matrix.R (head, tail): directly use utils:::head.matrix
569                    to be up-to-date automatically.
570    
571    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
574    
575            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
576            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
577            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
578            such that the S4 objects are always created by the current version
579            of R and 'Matrix' class definitions.
580    
581    2006-08-01  Douglas Bates  <bates@R-project.org>
582    
583            * R/lmer.R (LMEoptimize method), tests/lmer.R,
584            inst/external/test3comp.rda: Added warnings for convergence on
585            boundary and test cases.
586    
587            * src/lmer.c (mer_postVar): Modified to return the variances that
588            are marginal to the fixed effects, not conditional on them (which
589            is what the bVar slot contents represent).
590    
591    2006-07-31  Douglas Bates  <bates@R-project.org>
592    
593            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
594            function which calls the C function mer_hat_trace2.
595    
596            * man/ranef.Rd: Include description of "postVar" argument and
597            producing a caterpillar plot.
598    
599    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * NAMESPACE:    change  "correlation" to "corMatrix"
602            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
603            * R/dpoMatrix.R: ditto
604            * R/lmer.R:      ditto
605    
606    2006-07-28  Douglas Bates  <bates@R-project.org>
607    
608            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
609            RZXinv slot's contents into a separate internal function that can
610            be used in mer_hat_trace.
611    
612    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
615            via new smart
616            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
617            utility functions.
618    
619    
620    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/Csparse.R (tril, triu, band): do return *triangular* classed
623            matrices when appropriate; band() even symmetric ones.
624            (replCmat): extend to potentially all "CsparseMatrix"
625            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
626            allow subassignment for special sparse matrices.
627    
628            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
629    
630            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
631            argument; in glmer_*(): print only if(verbose).
632    
633            speed-optimize a few places by moving REAL(.) out of loops.
634    
635            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
636    
637    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
640                    since that wrongly triggers also for M[ logi , ]
641    
642            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
643            a symmetric matrix that results in a non-symmetric one.
644            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
645    
646            * R/dMatrix.R: make round(M) work as round(M, 0)
647    
648            * R/dgTMatrix.R (image): coordinate system and axis now use
649            1-based indices, not 0-based ones.
650    
651            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
652            * tests/indexing.R: test it.
653    
654            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
655            * man/isSymmetric-methods.Rd: and document it.
656    
657            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
658            * man/SparseM-conv.Rd: docu them
659    
660            * tests/other-pkgs.R: renamed from tests/graph.R and add example
661                    for 'SparseM' conversions
662    
663    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
664    
665            * R/Matrix.R (head): added head() and tail() methods.
666    
667    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * DESCRIPTION (Version): 0.995-12 released to CRAN
670    
671    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * tests/simple.R: add check for correct dsT -> dgT coercion;
674                    add check for correct printing of symmetric sparse matrices.
675    
676            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
677            for sparse symmetric matrices.
678    
679            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
680            diagonal twice.
681    
682    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
683    
684            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
685            being applied to the x slot (detected by Brian Ripley).
686    
687    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
690    
691            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
692    
693    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * src/lgCMatrix.c (lgCMatrix_diag): new function
696            * R/lgCMatrix.R (diag): for new method
697    
698            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
699                 ==> construction of illegal "*gTMatrix" via new() should
700                 now be much less easy:
701            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
702    
703            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
704                    directly.
705            * man/Matrix.Rd: documents it.
706    
707    2006-07-06  Douglas Bates  <bates@R-project.org>
708    
709            * src/pedigree.c (pedigree_inbreeding): Correction in
710            initialization.  This function is not currently being used and is
711            not fully tested.
712    
713            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
714            Introduced the glmer class.  Added code for mcmcmsamp on glmer
715            objects.  Modified validity check on pedigree objects to account
716            for nonparallel patterns of missingness of parents.
717    
718            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
719            class.
720    
721    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * R/pMatrix.R: coercion pMatrix -> Tsparse
724    
725    2006-06-12  Douglas Bates  <bates@R-project.org>
726    
727            * DESCRIPTION (Version): 0.995-11 released to CRAN
728    
729            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
730            the output from mcmcsamp.
731    
732    2006-06-10  Douglas Bates  <bates@R-project.org>
733    
734            * R/lmer.R (simulestimate): added C code for calculating the trace
735            of the hat matrix.
736    
737    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
740            classes.
741            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
742    
743    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * R/dgTMatrix.R (colSums): etc. All four of
746            colSums(), rowSums(), colMeans(), rowMeans() now should work for
747            all "Matrices".
748    
749    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
750    
751            * R/lmer.R (panel.ci): Add a reference line at zero and a
752            background grid to the qqmath plot of ranef.lmer.
753    
754    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
757            grouping factors to be specified in the formula as (1|foo/bar).
758    
759    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
760    
761            * R/lmer.R (findbars and others): Change check of is.numeric to
762            !is.language to resolve the bug reported by Jacob Wegelin.
763    
764            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
765            code to evaluate inbreeding coefficients without calculating T,
766            based on code in Sargolzaei and Iwaisaki's paper.
767    
768    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
771            generic and mer methods for isNested and denomDF. This denomDF was
772            an attempt to emulate that in lme but I don't think that makes
773            sense.  Use the trace of the hat matrix instead.
774    
775    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
778            the C code depending on a slot structure that's no longer valid.
779            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
780    
781    
782    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
783    
784            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
785            of lowerTriMatrix generic and methods to tril (also upper to triu)
786            and added a general band extractor.
787    
788    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
789    
790            * R/pedigree.R (pedigree): Replace sire and dam values outside the
791            allowable range with NAs. Added a corresponding check in the
792            validity check for the pedigree class.
793    
794            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
795            crossprod methods now inherits from symmetricMatrix.
796    
797    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
798    
799            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
800            generics lowerTriMatrix and upperTriMatrix along with methods for
801            the Csparse virtual class.  Also added a C function Csparse_band
802            that implements these methods by calling cholmod_band.
803    
804    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
807            erased when it was NULL.  This led to invalid subselections!
808    
809    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
810    
811            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
812            in method for "t" so as not to lose the unit diagonal property.
813    
814    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
815    
816            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
817            and methods.  This is now an option to the ranef method for the
818            mer class.
819    
820            * src/cs_utils.c: Ensure that the nz component is -1 for a
821            compressed column-oriented matrix.  Minor formatting cleanup.
822    
823            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
824            objects.
825    
826    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
829            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
830    
831    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
832    
833            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
834            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
835    
836            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
837            for the dtCMatrix class.
838    
839    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
840    
841            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
842            and methods for it.
843    
844    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
847            arguments, such that M %*% 1:6 now works
848            * Tests/matprod.R: test the above
849    
850    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
851    
852            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
853            the ranef.lmer class.
854    
855            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
856            methods to extract the posterior variances from the bVar slot.
857    
858    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
861            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
862    
863            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
864            * tests/simple: (extended)
865    
866            * R/sparseMatrix.R (isTriangular): now using much improved
867            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
868    
869    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
870    
871            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
872            (problem report from Franklin Parlamis).  This should be done
873            generally.
874    
875    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
876    
877            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
878            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
879            update the plot methods.
880    
881    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
882    
883            * R/lmer.R (resid and ranef methods):  Added methods for the
884            "residuals" and "resid" generic but only for linear mixed model
885            fits.  Changed the ranef method to return a list of data frames so
886            that the plot methods now work.
887    
888    2006-03-16  Douglas Bates  <bates@bates2>
889    
890            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
891            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
892    
893            * DESCRIPTION (Date): New release
894    
895    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
898    
899            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
900            * man/KNex.Rd: and other help files
901            * tests/*.R: several ones needed adaption
902            * inst/doc/Comparisons.Rnw: ditto
903    
904    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
907    
908            * tests/indexing.R: tests for new [<- methods for sparse matrices.
909    
910    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
913    
914            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
915    
916    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
917    
918            * R/dMatrix.R: enable things like  M [ M < 10 ]
919            * R/dgeMatrix.R: implement it
920    
921    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
922    
923            * R/AllClass.R: define "summary.mer" and "*.lmer"
924            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
925            * R/lmer.R (show): now works with summary()
926    
927    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
928    
929            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
930            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
931                    support the above
932    
933    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
934    
935            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
936            Use glmFit$prior.weights for weights in a glmm.
937            Allow an option usePQL = FALSE to skip the PQL steps for the
938            Laplace method (and, in time, the AGQ method).
939    
940            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
941            into a separate function internal_mer_Xfactor to be able to call
942            it from internal_bhat.
943    
944    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * tests/Class+Meth.R (tstMatrixClass): function for much better
947            testing; now again of all actual classes.
948    
949            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
950                    use macros and define make_d_matrix_* and make_i_matrix_*
951                    where _i_ is for the ldense routines:
952    
953            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
954            * src/ldense.c (lsyMatrix_as_lgeMatrix):
955    
956            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
957    
958    
959    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
960    
961            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
962                    many different kinds of matrices.
963            * R/*.R: quite a few new methods were needed for R CMD check with
964                    new Matrix().  Very good for users playing around.
965    
966    
967    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
968    
969            * src/dgeMatrix.c (dMatrix_validate): new
970            * src/Mutils.c (dense_nonpacked_validate): new
971    
972            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
973    
974    
975    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
976    
977            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
978    
979    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
980    
981            * DESCRIPTION (Version): 0.99-6 released to CRAN
982    
983            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
984            segfault in cases with multiple non-nested grouping factors.
985    
986    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
989                    (Depends): also on 'utils'
990    
991            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
992            * R/diagMatrix.R (Diagonal): constructor and methods for
993            diagonal matrices
994    
995            * R/ltTMatrix.R: new "minimal methods"
996    
997    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1000            all methods (and help files).
1001    
1002    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1005                    for case (dimn.  op  no_dimn.)
1006    
1007    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1008    
1009            * DESCRIPTION (Version): 0.99-2  released to CRAN
1010    
1011    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1012    
1013            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1014            by Julian Faraway.
1015    
1016    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/Auxiliaries.R (try_as): new utility
1019            * R/sparseMatrix.R: use try_as() in coercion to original class
1020    
1021    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1024    
1025    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Auxiliaries.R (dimNamesCheck): added
1028    
1029            * R/Matrix.R (as.array), (as.vector): new
1030    
1031    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1034                    default.
1035            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1036                    "pMatrix" now contains "sparseMatrix"
1037    
1038    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1039    
1040            * tests/Class+Meth.R: new tests; t(t(m)) == m
1041    
1042            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1043    
1044            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1045            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1046    
1047            * R/dspMatrix.R: typo in "t" method
1048    
1049    2005-09-18  Douglas Bates  <bates@wisc.edu>
1050    
1051            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1052            * R/Tsparse.R: instead of R/gTMatrix.R
1053            * R/Csparse.R: new
1054            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1055            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1056            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1057                            via cholmod
1058    
1059    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1060    
1061            * R/Auxiliaries.R (non0ind): new function using new C code
1062            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1063    
1064    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1065    
1066            * src/chm_common.h: header file required by all C sources that
1067            call CHOLMOD functions.  It defines a cholmod_common structure
1068            called 'c' whose address is passed as the last argument to
1069            (virtually) every CHOLMOD function.
1070    
1071            * src/Pattern.c: Simple example of the use of CHOLMOD.
1072    
1073            * src/init.c: initialize and finalize the cholmod_common structure.
1074    
1075            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1076            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1077    
1078    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * inst/test-tools.R: new file collecting the utility functions used
1081                    in ./tests/*.R
1082    
1083            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1084            * R/Matrix.R (cbind2): methods for NULL and missing
1085    
1086    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1087    
1088            * R/AllClass.R: new "index" class for "[" and "[<-":
1089                    First cut at "symmetricMatrix" and "triangularMatrix"
1090            * R/gTMatrix.R (.ind.prep): new function;
1091                    Logical and character indexing now work too.
1092            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1093            * tests/indexing.R: new, including *.Rout.save
1094            * tests/dgTMatrix.R: new
1095    
1096    2005-08-29  Douglas Bates  <bates@wisc.edu>
1097    
1098            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1099            indicator pos not being updated.  Also enforced upper triangular
1100            for symmetric case.  Need to coerce edges component of elements of
1101            edge list - grr! (Why don't they define their classes cleanly?)
1102    
1103    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1104    
1105            * R/Matrix.R:  added first "[<-" methods; not yet functional
1106            * R/denseMatrix.R: ditto
1107            * man/Subassign-methods.Rd: new help file for these
1108    
1109    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * DESCRIPTION (Version): 0.98-6
1112    
1113            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1114            matrices.
1115    
1116    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1119                    as( <logical>, "matrix")
1120    
1121            * R/pMatrix.R: coercion to "lgTMatrix"
1122    
1123            * R/gTMatrix.R: new virtual class to define "[" methods for.
1124            * man/gTMatrix-class.Rd:
1125            * General slight re-organization of where "[" methods are defined.
1126              more to come.
1127    
1128    2005-08-18  Douglas Bates  <bates@wisc.edu>
1129    
1130            * DESCRIPTION (Version): 0.98-5  released to CRAN
1131    
1132            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1133            * .....
1134    
1135    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1136    
1137            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1138            or glmer objects.
1139    
1140    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1143    
1144    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1145    
1146            * R/HBMM.R: finish re-writing R-only code.
1147    
1148    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1149    
1150            * man/externalFormats.Rd: move documentation for writeHB and
1151            writeMM here.
1152    
1153            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1154            (suggested by Paul Roecker).
1155    
1156            * tests/validObj.R (assertError): Comment out test that is failing
1157            after recent changes in r-devel.
1158    
1159    
1160    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1161    
1162            * R/AllClass.R: intermediate virtual class "denseMatrix"
1163            * man/denseMatrix-class.Rd
1164            * NAMESPACE: export it, and also export
1165            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1166    
1167    2005-08-10  Douglas Bates  <bates@wisc.edu>
1168    
1169            * DESCRIPTION (Version): 0.98-3 to CRAN
1170    
1171            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1172            matrix_solve code (which was really, really wrong).
1173    
1174    2005-08-07  Douglas Bates  <bates@wisc.edu>
1175    
1176            * DESCRIPTION (Version): 0.98-2
1177    
1178            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1179    
1180            * R/lmer.R (abbrvNms): new
1181            * R/lmer.R (mcmcsamp): allow transformed parameters
1182            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1183            for the Harwell-Boeing and the MatrixMarket formats.
1184    
1185    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * man/dtrMatrix-class.Rd: add examples
1188            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1189    
1190            * TODO: note the dtpMatrix (docu) bug
1191    
1192            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1193            in order to ensure that new as.matrix() is used by old functions,
1194            e.g., svd(), qr(), eigen(), dist(),..;
1195                  apply(), also matplot() or pairs().
1196    
1197    
1198    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1199    
1200            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1201              add comments about 'control' / lmerControl() arguments
1202    
1203    2005-07-27  Douglas Bates  <bates@wisc.edu>
1204    
1205            * man/sleepstudy.Rd: Added the sleep data set.
1206            * DESCRIPTION (Version): 0.98-1  released to CRAN
1207    
1208    2005-07-12  Douglas Bates  <bates@wisc.edu>
1209            * man/sleepstudy.Rd: Added the sleep data set.
1210    
1211            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1212            .Call calls that were producing spurious output.
1213    
1214    2005-07-05  Douglas Bates  <bates@wisc.edu>
1215    
1216            * R/lmer.R (lmer): stored updated variance component estimates in
1217            mer object for the generalized model.  (Bug reported by Renaud
1218            Lancelot).
1219    
1220    2005-07-03  Douglas Bates  <bates@wisc.edu>
1221    
1222            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1223            unidimensional case.
1224    
1225    2005-06-08  Douglas Bates  <bates@wisc.edu>
1226    
1227            * DESCRIPTION (Version): 0.96-1
1228    
1229            * moved  lmer-class' R and C code moved from lme4 to here
1230    
1231    2005-06-04  Douglas Bates  <bates@wisc.edu>
1232    
1233            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1234            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1235    
1236    2005-06-02  Douglas Bates  <bates@wisc.edu>
1237    
1238            * src/Makefile.win: Forgot to update this when Makefile changed.
1239    
1240    2005-05-11  Douglas Bates  <bates@wisc.edu>
1241    
1242            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1243            bug reported by Kurt Hornik and Michael Hahsler.
1244    
1245    2005-05-10  Douglas Bates  <bates@wisc.edu>
1246    
1247            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1248            logical sparse matrices.  These will also be used in the symbolic
1249            analysis for lmer objects.
1250    
1251            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1252            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1253    
1254    2005-05-06  Douglas Bates  <bates@wisc.edu>
1255    
1256            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1257            colMeans, colSums, rowMeans and rowSums.
1258    
1259    2005-04-18  Douglas Bates  <bates@wisc.edu>
1260    
1261            * src/lgCMatrix.[ch]: code for _validate method and stub for
1262            multiplication operation.
1263    
1264            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1265            to dgetrs.
1266    
1267            * src/init.c: Fix cut-and-paste error in definition of
1268            dgeMatrix_matrix_solve
1269    
1270            * src/{many files}: Tighten code by using ALLOC_SLOT.
1271    
1272    2005-04-15  Douglas Bates  <bates@wisc.edu>
1273    
1274            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1275    
1276            * DESCRIPTION: Eliminate import of stats.
1277    
1278    
1279    2005-04-06  Douglas Bates  <bates@wisc.edu>
1280    
1281            * R/AllClass.R : add logical sparse matrix classes
1282    
1283    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1284    
1285            * R/dgTMatrix.R: add "[" method for triplet matrices
1286            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1287    
1288    2005-03-31  Douglas Bates  <bates@wisc.edu>
1289    
1290            * DESCRIPTION (Version): release 0.95-5 to CRAN
1291    
1292            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1293            * R/sparseMatrix.R: %*%, crossprod()
1294            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1295            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1296            * src/lmer.c (lmer_fitted): fix thinko
1297    
1298    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1299    
1300            * R/AllClass.R: add two virtual sparse classes ``on top''
1301    
1302    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1305                    correspondingly fix examples and tests/ since new()
1306                    doesn't work for virtual classes.
1307    
1308    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1309    
1310            * R/Matrix.R (as.matrix): method and one for unname()
1311            * tests/dpoMatrix.R: tests should now be less platform dependent;
1312              also run for R 2.1.0; using as.matrix()
1313    
1314    2005-03-15  Douglas Bates  <bates@wisc.edu>
1315    
1316            * R/pMatrix.R: "pMatrix" class added
1317            * ....
1318    
1319    2005-03-14  Douglas Bates  <bates@wisc.edu>
1320    
1321            * R/dtpMatrix.R: Add unpack method and an example.
1322    
1323            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1324            of general symmetric matrices and associated S4 methods.
1325    
1326    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1327            +
1328    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1331              crossprod() and "%*%" methods added; tests, too.
1332            * tests/matprod.R: new, for testing these
1333    
1334    2005-03-03  Douglas Bates  <bates@wisc.edu>
1335    
1336            * src/lmer.c (lmer_fitted): Added.
1337    
1338    2005-03-02  Douglas Bates  <bates@wisc.edu>
1339    
1340            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1341    
1342    2005-02-28  Douglas Bates  <bates@wisc.edu>
1343    
1344            * src/*.c,po/,inst/po: Internationalization and localization of
1345            the package.
1346    
1347            * src/ldl.[ch]: Removed these as their contents are referenced in the
1348            R_ldl.c file.
1349    
1350            * src/flame.[ch]: Removed these source files.
1351    
1352            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1353    
1354            * src/LU.[ch],src/init.c: absorb in factorizations
1355    
1356            * src/Mutils.h: prepare for internationalization
1357    
1358            * src/cblas.h: move the enum definitions to Mutils.h and remove
1359            this file
1360    
1361    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1362    
1363            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1364    
1365            * R/dtrMatrix.R: fix t() method
1366    
1367            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1368            * NAMESPACE: export them (and import generics from "methods")
1369            * tests/group-methods.R : and test them.
1370    
1371            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1372            border case
1373    
1374    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1375    
1376            * DESCRIPTION (Version): 0.95-2  released to CRAN
1377    
1378            * src/dgBCMatrix.c:
1379            * src/lmer.c: many changes
1380            * ...
1381    
1382    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1383    
1384            * R/Matrix.R: add more sophisticated show() method.
1385    
1386    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1387    
1388            * */* : almost complete reorganization of classes.
1389    
1390    2005-01-26  Douglas Bates  <bates@wisc.edu>
1391    
1392            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1393            for the geMatrix class.
1394    
1395    2005-01-24  Douglas Bates  <bates@wisc.edu>
1396    
1397            * src/Makefile (clean): Remove *.a and *.so
1398    
1399            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1400    
1401    2005-01-23  Douglas Bates  <bates@wisc.edu>
1402    
1403            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1404            had an effect in cases with more than 2 grouping factors.
1405    
1406    2005-01-03  Douglas Bates  <bates@wisc.edu>
1407    
1408            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1409    
1410    2004-12-23  Douglas Bates  <bates@wisc.edu>
1411    
1412            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1413            and R_useDynamicSymbols (suggested by B.D.Ripley).
1414    
1415    2004-12-14  Douglas Bates  <bates@wisc.edu>
1416    
1417            * R/sscMatrix.R: Add determinant methods
1418    
1419            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1420            for tripletMatrix to matrix.
1421    
1422    2004-12-13  Douglas Bates  <bates@wisc.edu>
1423    
1424            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1425            no longer used.
1426    
1427          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1428          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1431 
1431          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1432          Fixes part but not all of #15.          Fixes part but not all of #15.
1433    
1434  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1435    
1436          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1437          scalar grouping factors corrected.          scalar grouping factors corrected.
1438    
1439  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1440    
1441          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1442    
1443  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1444    
1445          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1446          .h file can be included.          .h file can be included.
1447    
1448  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1449    
1450          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1451          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1452    
1453          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1454    
1455  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1456    
1457          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1458    
1459  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1460    
1461          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1462    
1463  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1464    
1465          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1466    
1467  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1468    
1469          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1470    
1471  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1472    
1473          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1474          routines.          routines.
1475    
1476  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1477    
1478          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1479    
1480  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1481    
1482          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1483    

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