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revision 645, Tue Mar 15 00:51:42 2005 UTC revision 1682, Fri Dec 1 18:42:40 2006 UTC
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1  2005-03-14  Douglas Bates  <bates@bates1-home>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
4    
5    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
8            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
9            is exactly singular.
10    
11    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * DESCRIPTION (Date): updated -> release 0.9975-6
14    
15    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
18            now returns symmetric.
19    
20            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
21    
22            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
23            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
24    
25            * R/Auxiliaries.R (.type.kind): added
26    
27    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
30            running src/CSparse_install.sh
31    
32            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
33    
34    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
37            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
38    
39            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
40    
41            * tests/Class+Meth.R (tstMatrixClass): now assure
42            the (important in method programming) property :
43    
44                    ###>>  Every "Matrix" is either
45                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
46    
47                    (where "*" stands for "Matrix")
48    
49            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
50    
51            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
52            * tests/validObj.R: checks for "comparison"
53    
54            * R/sparseMatrix.R ([): improved indexing for sparse;
55                    trying to keep <symmetric>[ n, n] symmmetric
56    
57            * tests/indexing.R: indexing for logical sparse now ok
58    
59    
60    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/Tsparse.c: use xTsparse_validate() , and hence remove
63    
64            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
65    
66    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
69    
70            * tests/simple.R: validObject() checking the above.
71    
72            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
73            replacing both dgCMatrix_validate and lgCM*.
74    
75            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
76            fix dimnames setting in other places.
77            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
78    
79    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
82    
83            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
84            symmetry test, via
85            * R/Auxiliaries.R (.as.dgC.0.factors):
86    
87    2006-11-01  Douglas Bates  <bates@r-project.org>
88    
89            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
90            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
91            <CsparseMatrix>) added
92    
93    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * tests/matprod.R: add a variation of Harri's example
96    
97            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
98            recursive infinitely.
99    
100            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
101    
102            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
103    
104    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
107            matrix if possible; test m+m == 2*m; now test dgRMatrix.
108            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
109            satisfy the above test.
110    
111    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
114    
115            * R/dgCMatrix.R: solve(a, b="missing") based on
116            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
117            RHS = NULL.
118    
119            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
120            add more (needed) [t]crossprod() methods.
121    
122            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
123    
124            * R/Auxiliaries.R (as_CspClass): cleanup
125            (drop0): internal utility for "Csparse_drop(*, 0)"
126            (.bail.out.2): encourage active feedback
127    
128    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dMatrix.R(Compare): new(), then slots [no validity check]
131    
132            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
133            non-valid or 'sorted' case).
134    
135            * R/dsparseMatrix.R: add "chol" method.
136            * R/ddenseMatrix.R: ditto
137    
138            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
139            * NAMESPACE (Ops)
140            * R/diagMatrix.R (diag2T): simple utility used "higher level"
141            coercion; deprecating direct lower level coercions.
142    
143            * R/*.R (seq): use seq_len() and seq_along() where possible.
144    
145    
146    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * DESCRIPTION (Version): 0.9975-5 ready for release
149    
150    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
153    
154    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/AllClass.R (corMatrix): add 'validity' check;
157                    comment out unused "LDL" class definition
158            * NAMESPACE: mention, but do not export "LDL" class
159            * R/corMatrix.R: new (simple), needed for R-devel with
160            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
161              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
162    
163    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
166            use Rprintf and R's error handling.
167    
168    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
171            * tests/matprod.R: add tests for the bug fixed.
172    
173    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
176            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
177    
178    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
179    
180            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
181    
182    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version): 0.9975-3
185    
186            * R/diagMatrix.R (bdiag): new function constructing block diagonal
187            (sparse) matrices.
188            * man/bdiag.Rd: docu + examples
189    
190            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
191    
192            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
193            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
194    
195            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
196            that result is sparse or diagonal (and not dense).
197    
198            * man/Subassign-methods.Rd: fix examples
199    
200            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
201            should always return a sparse (and not sometimes a diagonal) matrix.
202    
203    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
206    
207    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * DESCRIPTION (Version): 0.9975-2
210    
211            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
212    
213    2006-10-02  Douglas Bates  <bates@R-project.org>
214    
215            * tests/dg_Matrix.R: Simplify test taking into account new code.
216    
217    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
220    
221            * R/lsTMatrix.R: new files w/ missing methods
222            * R/nsTMatrix.R:  "  'for completeness'
223    
224            * tests/Class+Meth.R: a bit less 'not.ok.classes'
225    
226            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
227    
228    
229    2006-09-28  Douglas Bates  <bates@R-project.org>
230    
231            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
232            included.
233    
234            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
235            Export C-callable functions used in Zt_create in lme4.
236    
237    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * DESCRIPTION (Version): 0.9975-1
240    
241            * tests/simple.R: less checks fail; using NA, found that our
242                    kronecker() is not base-compatible with NA's.
243    
244            * R/dMatrix.R: "Compare" method now implemented for all cases
245    
246            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
247    
248            * man/dtpMatrix-class.Rd: mention length of 'x' slot
249    
250            * src/dtpMatrix.c (dtpMatrix_validate): fix check
251            * src/dspMatrix.c (dspMatrix_validate): ditto
252    
253            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
254              including coercion to [nl]tTMatrix.
255    
256            * R/diagMatrix.R (show): print a header line as for other classes.
257    
258    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * src/Makefile.win (SUBDIRS): fix typo
261    
262    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
265    
266    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
267    
268            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
269            symmetric and y missing in R code using %*% (cholmod_aat doesn't
270            accept a symmetric matrix).
271            * tests/group-methods.R: Uncomment test of crossprod applied to
272            lsCMatrix objects.
273    
274    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/AllClass.R (symmetricMatrix): add validity method (available
277            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
278    
279            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
280    
281            * tests/indexing.Rout.save:
282            * tests/indexing.R: additions, mainly for 'lsparse'
283    
284            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
285            case.
286    
287            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
288    
289    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
292                    as 'N' (1-letter - Ok?)
293    
294            * tests/group-methods.R: add test for logical + NAs
295    
296            * R/dMatrix.R ("Compare"): fix to work with NA's
297    
298            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
299    
300            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
301                    which is implemented.
302    
303    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * src/chm_common.c: coerce logical <-> double instead of
306            typecasting;  needed for "l" matrix handling in cholmod.
307    
308            * tests/other-pkgs.R (graph): small extension in "graph" checks.
309    
310            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
311            (Tsp2grNEL): other fixes needed
312    
313    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
316                    Matrices, since "lMatrix", also "lsparseM" can have NA
317            * R/ndenseMatrix.R, etc: new source files
318            * man/nsparseMatrix-classes.Rd, etc: new help files
319            * tests/: adaptions
320            * src/chm_common.c (chm_dense_to_SEXP): and others:
321                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
322            * src/Csparse.c, etc: ditto
323    
324    2006-09-11  Douglas Bates  <bates@R-project.org>
325    
326            * src/Mutils.[ch],init.c inst/include/*.h: Move the
327            alloc_d**Matrix functions to the lme4 package.
328    
329    2006-09-09  Douglas Bates  <bates@R-project.org>
330    
331            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
332            fixed
333    
334    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/lMatrix.R: new
337    
338            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
339    
340            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
341            * man/tcrossprod.Rd: ditto
342    
343    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
344    
345            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
346            for exported functions
347            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
348            Remove partitioning algorithms for sparse matrix reordering.  The
349            copyright on the Metis code was problematic and the methods were
350            rarely used.
351            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
352            operations are now done entirely in CHOLMOD code.
353    
354    2006-09-06  Douglas Bates  <bates@R-project.org>
355    
356            * src/Mutils.h: Remove functions that are no longer used.
357    
358    2006-09-04  Douglas Bates  <bates@R-project.org>
359    
360            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
361            * src/DEPS.mkf: update
362    
363    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * created branches/Matrix-for-R-2.3.x;  on trunk: do
366            * DESCRIPTION (Version): 0.9975-0
367            (Depends): R (>= 2.4.0)
368    
369    2006-09-01  Douglas Bates  <bates@R-project.org>
370    
371            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
372    
373    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
376            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
377    
378            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
379    
380    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
383            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
384            * R/dsparseMatrix.R: ditto
385            * R/Csparse.R: ditto
386    
387    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dMatrix.R (Compare): improve availability of "<", etc
390            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
391    
392    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
395            of a 0-index which was used as 1-index (..hmm)
396    
397            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
398    
399            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
400            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
401            (.is.diagonal): ditto
402    
403            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
404    
405            * R/Matrix.R (Matrix): also work for NA data
406    
407    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
410            in all cases.
411    
412    2006-08-27  Douglas Bates  <bates@R-project.org>
413    
414            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
415            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
416    
417    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
420            subclasses of "ddenseMatrix"
421            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
422            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
423            instead of half dozen specialized ones.
424    
425    2006-08-25  Douglas Bates  <bates@R-project.org>
426    
427            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
428            <tillard@cirad.fr> - ordering standard errors to match effects.
429    
430    2006-08-24  Douglas Bates  <bates@R-project.org>
431    
432            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
433            on R_ldl.
434            * R/lCholCMatrix.R,
435            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
436            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
437            * many files in ./R and ./src: Use more general version of
438            dup_mMatrix_as_dgeMatrix to simplify method definitions.
439            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
440            dtpMatrix, dspMatrix and dppMatrix conversions.
441    
442    
443    2006-08-23  Douglas Bates  <bates@R-project.org>
444    
445            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
446            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
447            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
448            dgeMatrix_crossprod (may need to do this in other places).
449            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
450            generic and method for dsCMatrix.  Use CHOLMOD for chol().
451    
452    2006-08-22  Douglas Bates  <bates@R-project.org>
453    
454            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
455            types of classed Matrices, matrices or numeric or logical vectors.
456            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
457            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
458            to Mutils.h (as an inline) and change name to Matrix_check_class;
459            fixes in as_cholmod_factor and chm_factor_to_SEXP.
460            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
461            dsCMatrix_matrix_solve.  Comment out vestigial functions.
462            * src/Csparse.c: use diag_P and uplo_P macros.
463    
464    2006-08-21  Douglas Bates  <bates@R-project.org>
465    
466            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
467            valgrind.
468            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
469            inverses.
470            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
471            -Wall warnings.
472            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
473            Use dup_mMatrix_as_dgeMatrix.
474    
475    2006-08-20  Douglas Bates  <bates@R-project.org>
476    
477            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
478            * tests/sparseQR.R: Added
479            * man/sparseQR-class.Rd: Document methods for qr.* generics
480            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
481    
482    2006-08-19  Douglas Bates  <bates@R-project.org>
483    
484            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
485            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
486            and qr.fitted.
487            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
488            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
489    
490    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
493            the base version has no "..." argument.
494    
495            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
496    
497            * R/Matrix.R: define and
498            * NAMESPACE: export as.numeric() and as.logical() methods.
499                    Let's hope these do not badly slow down something...
500            Finally export the zapsmall() method.
501    
502    2006-08-17  Douglas Bates  <bates@R-project.org>
503    
504            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
505            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
506            * src/dtCMatrix.c :Remove code that is no longer used
507            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
508    
509    2006-08-14  Douglas Bates  <bates@R-project.org>
510    
511            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
512            Csparse_to_logical and Csparse_symmetric_to_general.
513            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
514            coercion methods between CsparseMatrix and TsparseMatrix.
515    
516    2006-08-14  Douglas Bates  <bates@R-project.org>
517    
518            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
519            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
520            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
521            possible.
522    
523    2006-08-12  Douglas Bates  <bates@R-project.org>
524    
525            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
526              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
527              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
528              generalize conversions between TsparseMatrix, CsparseMatrix,
529              denseMatrix and matrix.  Preserve triangularity property and
530              propagate Dimnames in the easy cases.
531    
532    2006-08-10  Douglas Bates  <bates@R-project.org>
533    
534            * src/lmer.c: adjust checks in glmer_init for S4SXP
535            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
536            before S4SXP but for the wrong reasons.
537    
538    2006-08-08  Douglas Bates  <bates@R-project.org>
539    
540            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
541            Later modified to return the upper triangle only.
542            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
543    
544    2006-08-07  Douglas Bates  <bates@R-project.org>
545    
546            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
547            R-level conversion to a sparse symmetric class.
548            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
549            Remove conversion to sparse symmetric classes (now done in C code).
550    
551    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
554            * man/band.Rd:  adapt the \dontshow{} unit test.
555    
556    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * DESCRIPTION (Version): 0.995-14  for CRAN
559    
560            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
561    
562            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
563            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
564    
565            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
566            * R/Tsparse.R (tril, triu, band): methods
567            * R/dgRMatrix.R (tril, ...):    ditto
568            * man/band.Rd:                  ditto
569    
570    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * R/Matrix.R (head, tail): directly use utils:::head.matrix
573                    to be up-to-date automatically.
574    
575    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
578    
579            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
580            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
581            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
582            such that the S4 objects are always created by the current version
583            of R and 'Matrix' class definitions.
584    
585    2006-08-01  Douglas Bates  <bates@R-project.org>
586    
587            * R/lmer.R (LMEoptimize method), tests/lmer.R,
588            inst/external/test3comp.rda: Added warnings for convergence on
589            boundary and test cases.
590    
591            * src/lmer.c (mer_postVar): Modified to return the variances that
592            are marginal to the fixed effects, not conditional on them (which
593            is what the bVar slot contents represent).
594    
595    2006-07-31  Douglas Bates  <bates@R-project.org>
596    
597            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
598            function which calls the C function mer_hat_trace2.
599    
600            * man/ranef.Rd: Include description of "postVar" argument and
601            producing a caterpillar plot.
602    
603    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * NAMESPACE:    change  "correlation" to "corMatrix"
606            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
607            * R/dpoMatrix.R: ditto
608            * R/lmer.R:      ditto
609    
610    2006-07-28  Douglas Bates  <bates@R-project.org>
611    
612            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
613            RZXinv slot's contents into a separate internal function that can
614            be used in mer_hat_trace.
615    
616    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
619            via new smart
620            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
621            utility functions.
622    
623    
624    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Csparse.R (tril, triu, band): do return *triangular* classed
627            matrices when appropriate; band() even symmetric ones.
628            (replCmat): extend to potentially all "CsparseMatrix"
629            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
630            allow subassignment for special sparse matrices.
631    
632            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
633    
634            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
635            argument; in glmer_*(): print only if(verbose).
636    
637            speed-optimize a few places by moving REAL(.) out of loops.
638    
639            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
640    
641    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
644                    since that wrongly triggers also for M[ logi , ]
645    
646            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
647            a symmetric matrix that results in a non-symmetric one.
648            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
649    
650            * R/dMatrix.R: make round(M) work as round(M, 0)
651    
652            * R/dgTMatrix.R (image): coordinate system and axis now use
653            1-based indices, not 0-based ones.
654    
655            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
656            * tests/indexing.R: test it.
657    
658            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
659            * man/isSymmetric-methods.Rd: and document it.
660    
661            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
662            * man/SparseM-conv.Rd: docu them
663    
664            * tests/other-pkgs.R: renamed from tests/graph.R and add example
665                    for 'SparseM' conversions
666    
667    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
668    
669            * R/Matrix.R (head): added head() and tail() methods.
670    
671    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * DESCRIPTION (Version): 0.995-12 released to CRAN
674    
675    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * tests/simple.R: add check for correct dsT -> dgT coercion;
678                    add check for correct printing of symmetric sparse matrices.
679    
680            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
681            for sparse symmetric matrices.
682    
683            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
684            diagonal twice.
685    
686    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
687    
688            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
689            being applied to the x slot (detected by Brian Ripley).
690    
691    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
694    
695            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
696    
697    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * src/lgCMatrix.c (lgCMatrix_diag): new function
700            * R/lgCMatrix.R (diag): for new method
701    
702            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
703                 ==> construction of illegal "*gTMatrix" via new() should
704                 now be much less easy:
705            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
706    
707            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
708                    directly.
709            * man/Matrix.Rd: documents it.
710    
711    2006-07-06  Douglas Bates  <bates@R-project.org>
712    
713            * src/pedigree.c (pedigree_inbreeding): Correction in
714            initialization.  This function is not currently being used and is
715            not fully tested.
716    
717            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
718            Introduced the glmer class.  Added code for mcmcmsamp on glmer
719            objects.  Modified validity check on pedigree objects to account
720            for nonparallel patterns of missingness of parents.
721    
722            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
723            class.
724    
725    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/pMatrix.R: coercion pMatrix -> Tsparse
728    
729    2006-06-12  Douglas Bates  <bates@R-project.org>
730    
731            * DESCRIPTION (Version): 0.995-11 released to CRAN
732    
733            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
734            the output from mcmcsamp.
735    
736    2006-06-10  Douglas Bates  <bates@R-project.org>
737    
738            * R/lmer.R (simulestimate): added C code for calculating the trace
739            of the hat matrix.
740    
741    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
744            classes.
745            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
746    
747    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/dgTMatrix.R (colSums): etc. All four of
750            colSums(), rowSums(), colMeans(), rowMeans() now should work for
751            all "Matrices".
752    
753    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
754    
755            * R/lmer.R (panel.ci): Add a reference line at zero and a
756            background grid to the qqmath plot of ranef.lmer.
757    
758    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
759    
760            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
761            grouping factors to be specified in the formula as (1|foo/bar).
762    
763    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
764    
765            * R/lmer.R (findbars and others): Change check of is.numeric to
766            !is.language to resolve the bug reported by Jacob Wegelin.
767    
768            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
769            code to evaluate inbreeding coefficients without calculating T,
770            based on code in Sargolzaei and Iwaisaki's paper.
771    
772    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
773    
774            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
775            generic and mer methods for isNested and denomDF. This denomDF was
776            an attempt to emulate that in lme but I don't think that makes
777            sense.  Use the trace of the hat matrix instead.
778    
779    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
782            the C code depending on a slot structure that's no longer valid.
783            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
784    
785    
786    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
787    
788            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
789            of lowerTriMatrix generic and methods to tril (also upper to triu)
790            and added a general band extractor.
791    
792    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
793    
794            * R/pedigree.R (pedigree): Replace sire and dam values outside the
795            allowable range with NAs. Added a corresponding check in the
796            validity check for the pedigree class.
797    
798            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
799            crossprod methods now inherits from symmetricMatrix.
800    
801    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
802    
803            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
804            generics lowerTriMatrix and upperTriMatrix along with methods for
805            the Csparse virtual class.  Also added a C function Csparse_band
806            that implements these methods by calling cholmod_band.
807    
808    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
811            erased when it was NULL.  This led to invalid subselections!
812    
813    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
814    
815            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
816            in method for "t" so as not to lose the unit diagonal property.
817    
818    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
819    
820            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
821            and methods.  This is now an option to the ranef method for the
822            mer class.
823    
824            * src/cs_utils.c: Ensure that the nz component is -1 for a
825            compressed column-oriented matrix.  Minor formatting cleanup.
826    
827            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
828            objects.
829    
830    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
833            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
834    
835    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
836    
837            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
838            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
839    
840            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
841            for the dtCMatrix class.
842    
843    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
844    
845            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
846            and methods for it.
847    
848    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
851            arguments, such that M %*% 1:6 now works
852            * Tests/matprod.R: test the above
853    
854    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
855    
856            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
857            the ranef.lmer class.
858    
859            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
860            methods to extract the posterior variances from the bVar slot.
861    
862    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
865            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
866    
867            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
868            * tests/simple: (extended)
869    
870            * R/sparseMatrix.R (isTriangular): now using much improved
871            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
872    
873    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
874    
875            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
876            (problem report from Franklin Parlamis).  This should be done
877            generally.
878    
879    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
880    
881            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
882            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
883            update the plot methods.
884    
885    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
886    
887            * R/lmer.R (resid and ranef methods):  Added methods for the
888            "residuals" and "resid" generic but only for linear mixed model
889            fits.  Changed the ranef method to return a list of data frames so
890            that the plot methods now work.
891    
892    2006-03-16  Douglas Bates  <bates@bates2>
893    
894            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
895            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
896    
897            * DESCRIPTION (Date): New release
898    
899    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
902    
903            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
904            * man/KNex.Rd: and other help files
905            * tests/*.R: several ones needed adaption
906            * inst/doc/Comparisons.Rnw: ditto
907    
908    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
911    
912            * tests/indexing.R: tests for new [<- methods for sparse matrices.
913    
914    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
917    
918            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
919    
920    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * R/dMatrix.R: enable things like  M [ M < 10 ]
923            * R/dgeMatrix.R: implement it
924    
925    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/AllClass.R: define "summary.mer" and "*.lmer"
928            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
929            * R/lmer.R (show): now works with summary()
930    
931    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
934            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
935                    support the above
936    
937    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
938    
939            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
940            Use glmFit$prior.weights for weights in a glmm.
941            Allow an option usePQL = FALSE to skip the PQL steps for the
942            Laplace method (and, in time, the AGQ method).
943    
944            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
945            into a separate function internal_mer_Xfactor to be able to call
946            it from internal_bhat.
947    
948    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * tests/Class+Meth.R (tstMatrixClass): function for much better
951            testing; now again of all actual classes.
952    
953            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
954                    use macros and define make_d_matrix_* and make_i_matrix_*
955                    where _i_ is for the ldense routines:
956    
957            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
958            * src/ldense.c (lsyMatrix_as_lgeMatrix):
959    
960            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
961    
962    
963    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
966                    many different kinds of matrices.
967            * R/*.R: quite a few new methods were needed for R CMD check with
968                    new Matrix().  Very good for users playing around.
969    
970    
971    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * src/dgeMatrix.c (dMatrix_validate): new
974            * src/Mutils.c (dense_nonpacked_validate): new
975    
976            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
977    
978    
979    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
980    
981            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
982    
983    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
984    
985            * DESCRIPTION (Version): 0.99-6 released to CRAN
986    
987            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
988            segfault in cases with multiple non-nested grouping factors.
989    
990    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
993                    (Depends): also on 'utils'
994    
995            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
996            * R/diagMatrix.R (Diagonal): constructor and methods for
997            diagonal matrices
998    
999            * R/ltTMatrix.R: new "minimal methods"
1000    
1001    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1002    
1003            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1004            all methods (and help files).
1005    
1006    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1009                    for case (dimn.  op  no_dimn.)
1010    
1011    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1012    
1013            * DESCRIPTION (Version): 0.99-2  released to CRAN
1014    
1015    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1016    
1017            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1018            by Julian Faraway.
1019    
1020    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * R/Auxiliaries.R (try_as): new utility
1023            * R/sparseMatrix.R: use try_as() in coercion to original class
1024    
1025    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1028    
1029    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1030    
1031            * R/Auxiliaries.R (dimNamesCheck): added
1032    
1033            * R/Matrix.R (as.array), (as.vector): new
1034    
1035    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1038                    default.
1039            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1040                    "pMatrix" now contains "sparseMatrix"
1041    
1042    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * tests/Class+Meth.R: new tests; t(t(m)) == m
1045    
1046            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1047    
1048            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1049            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1050    
1051            * R/dspMatrix.R: typo in "t" method
1052    
1053    2005-09-18  Douglas Bates  <bates@wisc.edu>
1054    
1055            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1056            * R/Tsparse.R: instead of R/gTMatrix.R
1057            * R/Csparse.R: new
1058            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1059            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1060            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1061                            via cholmod
1062    
1063    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * R/Auxiliaries.R (non0ind): new function using new C code
1066            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1067    
1068    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1069    
1070            * src/chm_common.h: header file required by all C sources that
1071            call CHOLMOD functions.  It defines a cholmod_common structure
1072            called 'c' whose address is passed as the last argument to
1073            (virtually) every CHOLMOD function.
1074    
1075            * src/Pattern.c: Simple example of the use of CHOLMOD.
1076    
1077            * src/init.c: initialize and finalize the cholmod_common structure.
1078    
1079            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1080            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1081    
1082    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1083    
1084            * inst/test-tools.R: new file collecting the utility functions used
1085                    in ./tests/*.R
1086    
1087            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1088            * R/Matrix.R (cbind2): methods for NULL and missing
1089    
1090    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1091    
1092            * R/AllClass.R: new "index" class for "[" and "[<-":
1093                    First cut at "symmetricMatrix" and "triangularMatrix"
1094            * R/gTMatrix.R (.ind.prep): new function;
1095                    Logical and character indexing now work too.
1096            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1097            * tests/indexing.R: new, including *.Rout.save
1098            * tests/dgTMatrix.R: new
1099    
1100    2005-08-29  Douglas Bates  <bates@wisc.edu>
1101    
1102            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1103            indicator pos not being updated.  Also enforced upper triangular
1104            for symmetric case.  Need to coerce edges component of elements of
1105            edge list - grr! (Why don't they define their classes cleanly?)
1106    
1107    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1108    
1109            * R/Matrix.R:  added first "[<-" methods; not yet functional
1110            * R/denseMatrix.R: ditto
1111            * man/Subassign-methods.Rd: new help file for these
1112    
1113    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1114    
1115            * DESCRIPTION (Version): 0.98-6
1116    
1117            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1118            matrices.
1119    
1120    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1123                    as( <logical>, "matrix")
1124    
1125            * R/pMatrix.R: coercion to "lgTMatrix"
1126    
1127            * R/gTMatrix.R: new virtual class to define "[" methods for.
1128            * man/gTMatrix-class.Rd:
1129            * General slight re-organization of where "[" methods are defined.
1130              more to come.
1131    
1132    2005-08-18  Douglas Bates  <bates@wisc.edu>
1133    
1134            * DESCRIPTION (Version): 0.98-5  released to CRAN
1135    
1136            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1137            * .....
1138    
1139    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1140    
1141            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1142            or glmer objects.
1143    
1144    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1145    
1146            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1147    
1148    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1149    
1150            * R/HBMM.R: finish re-writing R-only code.
1151    
1152    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1153    
1154            * man/externalFormats.Rd: move documentation for writeHB and
1155            writeMM here.
1156    
1157            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1158            (suggested by Paul Roecker).
1159    
1160            * tests/validObj.R (assertError): Comment out test that is failing
1161            after recent changes in r-devel.
1162    
1163    
1164    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1165    
1166            * R/AllClass.R: intermediate virtual class "denseMatrix"
1167            * man/denseMatrix-class.Rd
1168            * NAMESPACE: export it, and also export
1169            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1170    
1171    2005-08-10  Douglas Bates  <bates@wisc.edu>
1172    
1173            * DESCRIPTION (Version): 0.98-3 to CRAN
1174    
1175            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1176            matrix_solve code (which was really, really wrong).
1177    
1178    2005-08-07  Douglas Bates  <bates@wisc.edu>
1179    
1180            * DESCRIPTION (Version): 0.98-2
1181    
1182            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1183    
1184            * R/lmer.R (abbrvNms): new
1185            * R/lmer.R (mcmcsamp): allow transformed parameters
1186            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1187            for the Harwell-Boeing and the MatrixMarket formats.
1188    
1189    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1190    
1191            * man/dtrMatrix-class.Rd: add examples
1192            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1193    
1194            * TODO: note the dtpMatrix (docu) bug
1195    
1196            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1197            in order to ensure that new as.matrix() is used by old functions,
1198            e.g., svd(), qr(), eigen(), dist(),..;
1199                  apply(), also matplot() or pairs().
1200    
1201    
1202    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1203    
1204            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1205              add comments about 'control' / lmerControl() arguments
1206    
1207    2005-07-27  Douglas Bates  <bates@wisc.edu>
1208    
1209            * man/sleepstudy.Rd: Added the sleep data set.
1210            * DESCRIPTION (Version): 0.98-1  released to CRAN
1211    
1212    2005-07-12  Douglas Bates  <bates@wisc.edu>
1213            * man/sleepstudy.Rd: Added the sleep data set.
1214    
1215            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1216            .Call calls that were producing spurious output.
1217    
1218    2005-07-05  Douglas Bates  <bates@wisc.edu>
1219    
1220            * R/lmer.R (lmer): stored updated variance component estimates in
1221            mer object for the generalized model.  (Bug reported by Renaud
1222            Lancelot).
1223    
1224    2005-07-03  Douglas Bates  <bates@wisc.edu>
1225    
1226            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1227            unidimensional case.
1228    
1229    2005-06-08  Douglas Bates  <bates@wisc.edu>
1230    
1231            * DESCRIPTION (Version): 0.96-1
1232    
1233            * moved  lmer-class' R and C code moved from lme4 to here
1234    
1235    2005-06-04  Douglas Bates  <bates@wisc.edu>
1236    
1237            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1238            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1239    
1240    2005-06-02  Douglas Bates  <bates@wisc.edu>
1241    
1242            * src/Makefile.win: Forgot to update this when Makefile changed.
1243    
1244    2005-05-11  Douglas Bates  <bates@wisc.edu>
1245    
1246            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1247            bug reported by Kurt Hornik and Michael Hahsler.
1248    
1249    2005-05-10  Douglas Bates  <bates@wisc.edu>
1250    
1251            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1252            logical sparse matrices.  These will also be used in the symbolic
1253            analysis for lmer objects.
1254    
1255            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1256            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1257    
1258    2005-05-06  Douglas Bates  <bates@wisc.edu>
1259    
1260            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1261            colMeans, colSums, rowMeans and rowSums.
1262    
1263    2005-04-18  Douglas Bates  <bates@wisc.edu>
1264    
1265            * src/lgCMatrix.[ch]: code for _validate method and stub for
1266            multiplication operation.
1267    
1268            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1269            to dgetrs.
1270    
1271            * src/init.c: Fix cut-and-paste error in definition of
1272            dgeMatrix_matrix_solve
1273    
1274            * src/{many files}: Tighten code by using ALLOC_SLOT.
1275    
1276    2005-04-15  Douglas Bates  <bates@wisc.edu>
1277    
1278            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1279    
1280            * DESCRIPTION: Eliminate import of stats.
1281    
1282    
1283    2005-04-06  Douglas Bates  <bates@wisc.edu>
1284    
1285            * R/AllClass.R : add logical sparse matrix classes
1286    
1287    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1288    
1289            * R/dgTMatrix.R: add "[" method for triplet matrices
1290            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1291    
1292    2005-03-31  Douglas Bates  <bates@wisc.edu>
1293    
1294            * DESCRIPTION (Version): release 0.95-5 to CRAN
1295    
1296            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1297            * R/sparseMatrix.R: %*%, crossprod()
1298            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1299            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1300            * src/lmer.c (lmer_fitted): fix thinko
1301    
1302    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * R/AllClass.R: add two virtual sparse classes ``on top''
1305    
1306    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1307    
1308            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1309                    correspondingly fix examples and tests/ since new()
1310                    doesn't work for virtual classes.
1311    
1312    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1313    
1314            * R/Matrix.R (as.matrix): method and one for unname()
1315            * tests/dpoMatrix.R: tests should now be less platform dependent;
1316              also run for R 2.1.0; using as.matrix()
1317    
1318    2005-03-15  Douglas Bates  <bates@wisc.edu>
1319    
1320            * R/pMatrix.R: "pMatrix" class added
1321            * ....
1322    
1323    2005-03-14  Douglas Bates  <bates@wisc.edu>
1324    
1325          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1326    
1327          * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization          * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1328          of general symmetric matrices and associated S4 methods.          of general symmetric matrices and associated S4 methods.
1329    
1330  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1331            +
1332    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1333    
1334            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1335              crossprod() and "%*%" methods added; tests, too.
1336            * tests/matprod.R: new, for testing these
1337    
1338    2005-03-03  Douglas Bates  <bates@wisc.edu>
1339    
1340          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1341    
1342  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1343    
1344          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1345    
1346  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1347    
1348          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1349          the package.          the package.
# Line 61  Line 1391 
1391    
1392          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1393    
1394  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1395    
1396          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1397          for the geMatrix class.          for the geMatrix class.
1398    
1399  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1400    
1401          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1402    
1403          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1404    
1405  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1406    
1407          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1408          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1409    
1410  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1411    
1412          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1413    
1414  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1415    
1416          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1417          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1418    
1419  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1420    
1421          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1422    
1423          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1424          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1425    
1426  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1427    
1428          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1429          no longer used.          no longer used.
# Line 105  Line 1435 
1435          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1436          Fixes part but not all of #15.          Fixes part but not all of #15.
1437    
1438  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1439    
1440          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1441          scalar grouping factors corrected.          scalar grouping factors corrected.
1442    
1443  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1444    
1445          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1446    
1447  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1448    
1449          * 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
1450          .h file can be included.          .h file can be included.
1451    
1452  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1453    
1454          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1455          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1456    
1457          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1458    
1459  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1460    
1461          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1462    
1463  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1464    
1465          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1466    
1467  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1468    
1469          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1470    
1471  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1472    
1473          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1474    
1475  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1476    
1477          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1478          routines.          routines.
1479    
1480  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1481    
1482          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1483    
1484  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1485    
1486          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1487    

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