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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1660, Thu Nov 2 11:05:35 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
4    
5            * tests/simple.R: validObject() checking the above.
6    
7            * src/dgCMatrix.c (gCMatrix_validate): new, small and simple,
8            replacing both dgCMatrix_validate and lgCM*.
9    
10            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
11            fix dimnames setting in other places.
12            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
13    
14    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
17    
18            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
19            symmetry test, via
20            * R/Auxiliaries.R (.as.dgC.0.factors):
21    
22    2006-11-01  Douglas Bates  <bates@r-project.org>
23    
24            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
25            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
26            <CsparseMatrix>) added
27    
28    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * tests/matprod.R: add a variation of Harri's example
31    
32            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
33            recursive infinitely.
34    
35            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
36    
37            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
38    
39    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
42            matrix if possible; test m+m == 2*m; now test dgRMatrix.
43            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
44            satisfy the above test.
45    
46    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
49    
50            * R/dgCMatrix.R: solve(a, b="missing") based on
51            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
52            RHS = NULL.
53    
54            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
55            add more (needed) [t]crossprod() methods.
56    
57            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
58    
59            * R/Auxiliaries.R (as_CspClass): cleanup
60            (drop0): internal utility for "Csparse_drop(*, 0)"
61            (.bail.out.2): encourage active feedback
62    
63    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/dMatrix.R(Compare): new(), then slots [no validity check]
66    
67            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
68            non-valid or 'sorted' case).
69    
70            * R/dsparseMatrix.R: add "chol" method.
71            * R/ddenseMatrix.R: ditto
72    
73            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
74            * NAMESPACE (Ops)
75            * R/diagMatrix.R (diag2T): simple utility used "higher level"
76            coercion; deprecating direct lower level coercions.
77    
78            * R/*.R (seq): use seq_len() and seq_along() where possible.
79    
80    
81    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * DESCRIPTION (Version): 0.9975-5 ready for release
84    
85    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
88    
89    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/AllClass.R (corMatrix): add 'validity' check;
92                    comment out unused "LDL" class definition
93            * NAMESPACE: mention, but do not export "LDL" class
94            * R/corMatrix.R: new (simple), needed for R-devel with
95            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
96              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
97    
98    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
101            use Rprintf and R's error handling.
102    
103    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
106            * tests/matprod.R: add tests for the bug fixed.
107    
108    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
111            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
112    
113    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
116    
117    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Version): 0.9975-3
120    
121            * R/diagMatrix.R (bdiag): new function constructing block diagonal
122            (sparse) matrices.
123            * man/bdiag.Rd: docu + examples
124    
125            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
126    
127            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
128            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
129    
130            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
131            that result is sparse or diagonal (and not dense).
132    
133            * man/Subassign-methods.Rd: fix examples
134    
135            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
136            should always return a sparse (and not sometimes a diagonal) matrix.
137    
138    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
141    
142    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
143    
144            * DESCRIPTION (Version): 0.9975-2
145    
146            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
147    
148    2006-10-02  Douglas Bates  <bates@R-project.org>
149    
150            * tests/dg_Matrix.R: Simplify test taking into account new code.
151    
152    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
155    
156            * R/lsTMatrix.R: new files w/ missing methods
157            * R/nsTMatrix.R:  "  'for completeness'
158    
159            * tests/Class+Meth.R: a bit less 'not.ok.classes'
160    
161            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
162    
163    
164    2006-09-28  Douglas Bates  <bates@R-project.org>
165    
166            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
167            included.
168    
169            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
170            Export C-callable functions used in Zt_create in lme4.
171    
172    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.9975-1
175    
176            * tests/simple.R: less checks fail; using NA, found that our
177                    kronecker() is not base-compatible with NA's.
178    
179            * R/dMatrix.R: "Compare" method now implemented for all cases
180    
181            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
182    
183            * man/dtpMatrix-class.Rd: mention length of 'x' slot
184    
185            * src/dtpMatrix.c (dtpMatrix_validate): fix check
186            * src/dspMatrix.c (dspMatrix_validate): ditto
187    
188            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
189              including coercion to [nl]tTMatrix.
190    
191            * R/diagMatrix.R (show): print a header line as for other classes.
192    
193    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/Makefile.win (SUBDIRS): fix typo
196    
197    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
200    
201    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
202    
203            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
204            symmetric and y missing in R code using %*% (cholmod_aat doesn't
205            accept a symmetric matrix).
206            * tests/group-methods.R: Uncomment test of crossprod applied to
207            lsCMatrix objects.
208    
209    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/AllClass.R (symmetricMatrix): add validity method (available
212            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
213    
214            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
215    
216            * tests/indexing.Rout.save:
217            * tests/indexing.R: additions, mainly for 'lsparse'
218    
219            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
220            case.
221    
222            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
223    
224    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
227                    as 'N' (1-letter - Ok?)
228    
229            * tests/group-methods.R: add test for logical + NAs
230    
231            * R/dMatrix.R ("Compare"): fix to work with NA's
232    
233            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
234    
235            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
236                    which is implemented.
237    
238    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * src/chm_common.c: coerce logical <-> double instead of
241            typecasting;  needed for "l" matrix handling in cholmod.
242    
243            * tests/other-pkgs.R (graph): small extension in "graph" checks.
244    
245            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
246            (Tsp2grNEL): other fixes needed
247    
248    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
251                    Matrices, since "lMatrix", also "lsparseM" can have NA
252            * R/ndenseMatrix.R, etc: new source files
253            * man/nsparseMatrix-classes.Rd, etc: new help files
254            * tests/: adaptions
255            * src/chm_common.c (chm_dense_to_SEXP): and others:
256                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
257            * src/Csparse.c, etc: ditto
258    
259    2006-09-11  Douglas Bates  <bates@R-project.org>
260    
261            * src/Mutils.[ch],init.c inst/include/*.h: Move the
262            alloc_d**Matrix functions to the lme4 package.
263    
264    2006-09-09  Douglas Bates  <bates@R-project.org>
265    
266            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
267            fixed
268    
269    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/lMatrix.R: new
272    
273            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
274    
275            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
276            * man/tcrossprod.Rd: ditto
277    
278    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
281            for exported functions
282            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
283            Remove partitioning algorithms for sparse matrix reordering.  The
284            copyright on the Metis code was problematic and the methods were
285            rarely used.
286            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
287            operations are now done entirely in CHOLMOD code.
288    
289    2006-09-06  Douglas Bates  <bates@R-project.org>
290    
291            * src/Mutils.h: Remove functions that are no longer used.
292    
293    2006-09-04  Douglas Bates  <bates@R-project.org>
294    
295            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
296            * src/DEPS.mkf: update
297    
298    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * created branches/Matrix-for-R-2.3.x;  on trunk: do
301            * DESCRIPTION (Version): 0.9975-0
302            (Depends): R (>= 2.4.0)
303    
304    2006-09-01  Douglas Bates  <bates@R-project.org>
305    
306            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
307    
308    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
311            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
312    
313            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
314    
315    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
318            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
319            * R/dsparseMatrix.R: ditto
320            * R/Csparse.R: ditto
321    
322    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/dMatrix.R (Compare): improve availability of "<", etc
325            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
326    
327    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
330            of a 0-index which was used as 1-index (..hmm)
331    
332            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
333    
334            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
335            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
336            (.is.diagonal): ditto
337    
338            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
339    
340            * R/Matrix.R (Matrix): also work for NA data
341    
342    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
345            in all cases.
346    
347    2006-08-27  Douglas Bates  <bates@R-project.org>
348    
349            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
350            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
351    
352    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
355            subclasses of "ddenseMatrix"
356            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
357            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
358            instead of half dozen specialized ones.
359    
360    2006-08-25  Douglas Bates  <bates@R-project.org>
361    
362            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
363            <tillard@cirad.fr> - ordering standard errors to match effects.
364    
365    2006-08-24  Douglas Bates  <bates@R-project.org>
366    
367            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
368            on R_ldl.
369            * R/lCholCMatrix.R,
370            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
371            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
372            * many files in ./R and ./src: Use more general version of
373            dup_mMatrix_as_dgeMatrix to simplify method definitions.
374            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
375            dtpMatrix, dspMatrix and dppMatrix conversions.
376    
377    
378    2006-08-23  Douglas Bates  <bates@R-project.org>
379    
380            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
381            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
382            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
383            dgeMatrix_crossprod (may need to do this in other places).
384            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
385            generic and method for dsCMatrix.  Use CHOLMOD for chol().
386    
387    2006-08-22  Douglas Bates  <bates@R-project.org>
388    
389            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
390            types of classed Matrices, matrices or numeric or logical vectors.
391            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
392            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
393            to Mutils.h (as an inline) and change name to Matrix_check_class;
394            fixes in as_cholmod_factor and chm_factor_to_SEXP.
395            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
396            dsCMatrix_matrix_solve.  Comment out vestigial functions.
397            * src/Csparse.c: use diag_P and uplo_P macros.
398    
399    2006-08-21  Douglas Bates  <bates@R-project.org>
400    
401            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
402            valgrind.
403            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
404            inverses.
405            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
406            -Wall warnings.
407            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
408            Use dup_mMatrix_as_dgeMatrix.
409    
410    2006-08-20  Douglas Bates  <bates@R-project.org>
411    
412            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
413            * tests/sparseQR.R: Added
414            * man/sparseQR-class.Rd: Document methods for qr.* generics
415            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
416    
417    2006-08-19  Douglas Bates  <bates@R-project.org>
418    
419            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
420            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
421            and qr.fitted.
422            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
423            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
424    
425    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
428            the base version has no "..." argument.
429    
430            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
431    
432            * R/Matrix.R: define and
433            * NAMESPACE: export as.numeric() and as.logical() methods.
434                    Let's hope these do not badly slow down something...
435            Finally export the zapsmall() method.
436    
437    2006-08-17  Douglas Bates  <bates@R-project.org>
438    
439            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
440            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
441            * src/dtCMatrix.c :Remove code that is no longer used
442            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
443    
444    2006-08-14  Douglas Bates  <bates@R-project.org>
445    
446            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
447            Csparse_to_logical and Csparse_symmetric_to_general.
448            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
449            coercion methods between CsparseMatrix and TsparseMatrix.
450    
451    2006-08-14  Douglas Bates  <bates@R-project.org>
452    
453            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
454            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
455            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
456            possible.
457    
458    2006-08-12  Douglas Bates  <bates@R-project.org>
459    
460            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
461              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
462              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
463              generalize conversions between TsparseMatrix, CsparseMatrix,
464              denseMatrix and matrix.  Preserve triangularity property and
465              propagate Dimnames in the easy cases.
466    
467    2006-08-10  Douglas Bates  <bates@R-project.org>
468    
469            * src/lmer.c: adjust checks in glmer_init for S4SXP
470            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
471            before S4SXP but for the wrong reasons.
472    
473    2006-08-08  Douglas Bates  <bates@R-project.org>
474    
475            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
476            Later modified to return the upper triangle only.
477            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
478    
479    2006-08-07  Douglas Bates  <bates@R-project.org>
480    
481            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
482            R-level conversion to a sparse symmetric class.
483            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
484            Remove conversion to sparse symmetric classes (now done in C code).
485    
486    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
489            * man/band.Rd:  adapt the \dontshow{} unit test.
490    
491    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * DESCRIPTION (Version): 0.995-14  for CRAN
494    
495            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
496    
497            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
498            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
499    
500            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
501            * R/Tsparse.R (tril, triu, band): methods
502            * R/dgRMatrix.R (tril, ...):    ditto
503            * man/band.Rd:                  ditto
504    
505    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/Matrix.R (head, tail): directly use utils:::head.matrix
508                    to be up-to-date automatically.
509    
510    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
513    
514            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
515            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
516            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
517            such that the S4 objects are always created by the current version
518            of R and 'Matrix' class definitions.
519    
520    2006-08-01  Douglas Bates  <bates@R-project.org>
521    
522            * R/lmer.R (LMEoptimize method), tests/lmer.R,
523            inst/external/test3comp.rda: Added warnings for convergence on
524            boundary and test cases.
525    
526            * src/lmer.c (mer_postVar): Modified to return the variances that
527            are marginal to the fixed effects, not conditional on them (which
528            is what the bVar slot contents represent).
529    
530    2006-07-31  Douglas Bates  <bates@R-project.org>
531    
532            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
533            function which calls the C function mer_hat_trace2.
534    
535            * man/ranef.Rd: Include description of "postVar" argument and
536            producing a caterpillar plot.
537    
538    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * NAMESPACE:    change  "correlation" to "corMatrix"
541            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
542            * R/dpoMatrix.R: ditto
543            * R/lmer.R:      ditto
544    
545    2006-07-28  Douglas Bates  <bates@R-project.org>
546    
547            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
548            RZXinv slot's contents into a separate internal function that can
549            be used in mer_hat_trace.
550    
551    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
554            via new smart
555            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
556            utility functions.
557    
558    
559    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/Csparse.R (tril, triu, band): do return *triangular* classed
562            matrices when appropriate; band() even symmetric ones.
563            (replCmat): extend to potentially all "CsparseMatrix"
564            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
565            allow subassignment for special sparse matrices.
566    
567            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
568    
569            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
570            argument; in glmer_*(): print only if(verbose).
571    
572            speed-optimize a few places by moving REAL(.) out of loops.
573    
574            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
575    
576    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
579                    since that wrongly triggers also for M[ logi , ]
580    
581            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
582            a symmetric matrix that results in a non-symmetric one.
583            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
584    
585            * R/dMatrix.R: make round(M) work as round(M, 0)
586    
587            * R/dgTMatrix.R (image): coordinate system and axis now use
588            1-based indices, not 0-based ones.
589    
590            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
591            * tests/indexing.R: test it.
592    
593            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
594            * man/isSymmetric-methods.Rd: and document it.
595    
596            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
597            * man/SparseM-conv.Rd: docu them
598    
599            * tests/other-pkgs.R: renamed from tests/graph.R and add example
600                    for 'SparseM' conversions
601    
602    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
603    
604            * R/Matrix.R (head): added head() and tail() methods.
605    
606    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * DESCRIPTION (Version): 0.995-12 released to CRAN
609    
610    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * tests/simple.R: add check for correct dsT -> dgT coercion;
613                    add check for correct printing of symmetric sparse matrices.
614    
615            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
616            for sparse symmetric matrices.
617    
618            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
619            diagonal twice.
620    
621    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
622    
623            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
624            being applied to the x slot (detected by Brian Ripley).
625    
626    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
629    
630            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
631    
632    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * src/lgCMatrix.c (lgCMatrix_diag): new function
635            * R/lgCMatrix.R (diag): for new method
636    
637            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
638                 ==> construction of illegal "*gTMatrix" via new() should
639                 now be much less easy:
640            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
641    
642            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
643                    directly.
644            * man/Matrix.Rd: documents it.
645    
646    2006-07-06  Douglas Bates  <bates@R-project.org>
647    
648            * src/pedigree.c (pedigree_inbreeding): Correction in
649            initialization.  This function is not currently being used and is
650            not fully tested.
651    
652            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
653            Introduced the glmer class.  Added code for mcmcmsamp on glmer
654            objects.  Modified validity check on pedigree objects to account
655            for nonparallel patterns of missingness of parents.
656    
657            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
658            class.
659    
660    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/pMatrix.R: coercion pMatrix -> Tsparse
663    
664    2006-06-12  Douglas Bates  <bates@R-project.org>
665    
666            * DESCRIPTION (Version): 0.995-11 released to CRAN
667    
668            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
669            the output from mcmcsamp.
670    
671    2006-06-10  Douglas Bates  <bates@R-project.org>
672    
673            * R/lmer.R (simulestimate): added C code for calculating the trace
674            of the hat matrix.
675    
676    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
679            classes.
680            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
681    
682    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/dgTMatrix.R (colSums): etc. All four of
685            colSums(), rowSums(), colMeans(), rowMeans() now should work for
686            all "Matrices".
687    
688    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
689    
690            * R/lmer.R (panel.ci): Add a reference line at zero and a
691            background grid to the qqmath plot of ranef.lmer.
692    
693    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
694    
695            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
696            grouping factors to be specified in the formula as (1|foo/bar).
697    
698    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
699    
700            * R/lmer.R (findbars and others): Change check of is.numeric to
701            !is.language to resolve the bug reported by Jacob Wegelin.
702    
703            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
704            code to evaluate inbreeding coefficients without calculating T,
705            based on code in Sargolzaei and Iwaisaki's paper.
706    
707    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
708    
709            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
710            generic and mer methods for isNested and denomDF. This denomDF was
711            an attempt to emulate that in lme but I don't think that makes
712            sense.  Use the trace of the hat matrix instead.
713    
714    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
717            the C code depending on a slot structure that's no longer valid.
718            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
719    
720    
721    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
722    
723            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
724            of lowerTriMatrix generic and methods to tril (also upper to triu)
725            and added a general band extractor.
726    
727    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * R/pedigree.R (pedigree): Replace sire and dam values outside the
730            allowable range with NAs. Added a corresponding check in the
731            validity check for the pedigree class.
732    
733            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
734            crossprod methods now inherits from symmetricMatrix.
735    
736    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
737    
738            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
739            generics lowerTriMatrix and upperTriMatrix along with methods for
740            the Csparse virtual class.  Also added a C function Csparse_band
741            that implements these methods by calling cholmod_band.
742    
743    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
746            erased when it was NULL.  This led to invalid subselections!
747    
748    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
749    
750            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
751            in method for "t" so as not to lose the unit diagonal property.
752    
753    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
754    
755            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
756            and methods.  This is now an option to the ranef method for the
757            mer class.
758    
759            * src/cs_utils.c: Ensure that the nz component is -1 for a
760            compressed column-oriented matrix.  Minor formatting cleanup.
761    
762            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
763            objects.
764    
765    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
768            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
769    
770    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
771    
772            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
773            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
774    
775            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
776            for the dtCMatrix class.
777    
778    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
779    
780            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
781            and methods for it.
782    
783    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
786            arguments, such that M %*% 1:6 now works
787            * Tests/matprod.R: test the above
788    
789    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
790    
791            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
792            the ranef.lmer class.
793    
794            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
795            methods to extract the posterior variances from the bVar slot.
796    
797    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
800            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
801    
802            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
803            * tests/simple: (extended)
804    
805            * R/sparseMatrix.R (isTriangular): now using much improved
806            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
807    
808    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
809    
810            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
811            (problem report from Franklin Parlamis).  This should be done
812            generally.
813    
814    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
815    
816            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
817            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
818            update the plot methods.
819    
820    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
821    
822            * R/lmer.R (resid and ranef methods):  Added methods for the
823            "residuals" and "resid" generic but only for linear mixed model
824            fits.  Changed the ranef method to return a list of data frames so
825            that the plot methods now work.
826    
827    2006-03-16  Douglas Bates  <bates@bates2>
828    
829            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
830            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
831    
832            * DESCRIPTION (Date): New release
833    
834    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
837    
838            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
839            * man/KNex.Rd: and other help files
840            * tests/*.R: several ones needed adaption
841            * inst/doc/Comparisons.Rnw: ditto
842    
843    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
846    
847            * tests/indexing.R: tests for new [<- methods for sparse matrices.
848    
849    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
852    
853            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
854    
855    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/dMatrix.R: enable things like  M [ M < 10 ]
858            * R/dgeMatrix.R: implement it
859    
860    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * R/AllClass.R: define "summary.mer" and "*.lmer"
863            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
864            * R/lmer.R (show): now works with summary()
865    
866    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
869            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
870                    support the above
871    
872    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
873    
874            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
875            Use glmFit$prior.weights for weights in a glmm.
876            Allow an option usePQL = FALSE to skip the PQL steps for the
877            Laplace method (and, in time, the AGQ method).
878    
879            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
880            into a separate function internal_mer_Xfactor to be able to call
881            it from internal_bhat.
882    
883    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * tests/Class+Meth.R (tstMatrixClass): function for much better
886            testing; now again of all actual classes.
887    
888            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
889                    use macros and define make_d_matrix_* and make_i_matrix_*
890                    where _i_ is for the ldense routines:
891    
892            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
893            * src/ldense.c (lsyMatrix_as_lgeMatrix):
894    
895            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
896    
897    
898    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
900            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
901                    many different kinds of matrices.
902            * R/*.R: quite a few new methods were needed for R CMD check with
903                    new Matrix().  Very good for users playing around.
904    
905    
906    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908            * src/dgeMatrix.c (dMatrix_validate): new
909            * src/Mutils.c (dense_nonpacked_validate): new
910    
911            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
912    
913    
914    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
915    
916            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
917    
918    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
919    
920            * DESCRIPTION (Version): 0.99-6 released to CRAN
921    
922            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
923            segfault in cases with multiple non-nested grouping factors.
924    
925    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
928                    (Depends): also on 'utils'
929    
930            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
931            * R/diagMatrix.R (Diagonal): constructor and methods for
932            diagonal matrices
933    
934            * R/ltTMatrix.R: new "minimal methods"
935    
936    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
939            all methods (and help files).
940    
941    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
944                    for case (dimn.  op  no_dimn.)
945    
946    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
947    
948            * DESCRIPTION (Version): 0.99-2  released to CRAN
949    
950    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
951    
952            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
953            by Julian Faraway.
954    
955    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * R/Auxiliaries.R (try_as): new utility
958            * R/sparseMatrix.R: use try_as() in coercion to original class
959    
960    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
963    
964    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * R/Auxiliaries.R (dimNamesCheck): added
967    
968            * R/Matrix.R (as.array), (as.vector): new
969    
970    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
971    
972            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
973                    default.
974            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
975                    "pMatrix" now contains "sparseMatrix"
976    
977    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * tests/Class+Meth.R: new tests; t(t(m)) == m
980    
981            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
982    
983            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
984            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
985    
986            * R/dspMatrix.R: typo in "t" method
987    
988    2005-09-18  Douglas Bates  <bates@wisc.edu>
989    
990            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
991            * R/Tsparse.R: instead of R/gTMatrix.R
992            * R/Csparse.R: new
993            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
994            * src/Tsparse.c: new; many trivial methods calling cholmod_()
995            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
996                            via cholmod
997    
998    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/Auxiliaries.R (non0ind): new function using new C code
1001            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1002    
1003    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1004    
1005            * src/chm_common.h: header file required by all C sources that
1006            call CHOLMOD functions.  It defines a cholmod_common structure
1007            called 'c' whose address is passed as the last argument to
1008            (virtually) every CHOLMOD function.
1009    
1010            * src/Pattern.c: Simple example of the use of CHOLMOD.
1011    
1012            * src/init.c: initialize and finalize the cholmod_common structure.
1013    
1014            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1015            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1016    
1017    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * inst/test-tools.R: new file collecting the utility functions used
1020                    in ./tests/*.R
1021    
1022            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1023            * R/Matrix.R (cbind2): methods for NULL and missing
1024    
1025    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/AllClass.R: new "index" class for "[" and "[<-":
1028                    First cut at "symmetricMatrix" and "triangularMatrix"
1029            * R/gTMatrix.R (.ind.prep): new function;
1030                    Logical and character indexing now work too.
1031            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1032            * tests/indexing.R: new, including *.Rout.save
1033            * tests/dgTMatrix.R: new
1034    
1035    2005-08-29  Douglas Bates  <bates@wisc.edu>
1036    
1037            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1038            indicator pos not being updated.  Also enforced upper triangular
1039            for symmetric case.  Need to coerce edges component of elements of
1040            edge list - grr! (Why don't they define their classes cleanly?)
1041    
1042    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/Matrix.R:  added first "[<-" methods; not yet functional
1045            * R/denseMatrix.R: ditto
1046            * man/Subassign-methods.Rd: new help file for these
1047    
1048    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1049    
1050            * DESCRIPTION (Version): 0.98-6
1051    
1052            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1053            matrices.
1054    
1055    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1058                    as( <logical>, "matrix")
1059    
1060            * R/pMatrix.R: coercion to "lgTMatrix"
1061    
1062            * R/gTMatrix.R: new virtual class to define "[" methods for.
1063            * man/gTMatrix-class.Rd:
1064            * General slight re-organization of where "[" methods are defined.
1065              more to come.
1066    
1067    2005-08-18  Douglas Bates  <bates@wisc.edu>
1068    
1069            * DESCRIPTION (Version): 0.98-5  released to CRAN
1070    
1071            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1072            * .....
1073    
1074    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1075    
1076            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1077            or glmer objects.
1078    
1079    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1082    
1083    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1084    
1085            * R/HBMM.R: finish re-writing R-only code.
1086    
1087    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1088    
1089            * man/externalFormats.Rd: move documentation for writeHB and
1090            writeMM here.
1091    
1092            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1093            (suggested by Paul Roecker).
1094    
1095            * tests/validObj.R (assertError): Comment out test that is failing
1096            after recent changes in r-devel.
1097    
1098    
1099    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * R/AllClass.R: intermediate virtual class "denseMatrix"
1102            * man/denseMatrix-class.Rd
1103            * NAMESPACE: export it, and also export
1104            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1105    
1106    2005-08-10  Douglas Bates  <bates@wisc.edu>
1107    
1108            * DESCRIPTION (Version): 0.98-3 to CRAN
1109    
1110            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1111            matrix_solve code (which was really, really wrong).
1112    
1113    2005-08-07  Douglas Bates  <bates@wisc.edu>
1114    
1115            * DESCRIPTION (Version): 0.98-2
1116    
1117            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1118    
1119            * R/lmer.R (abbrvNms): new
1120            * R/lmer.R (mcmcsamp): allow transformed parameters
1121            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1122            for the Harwell-Boeing and the MatrixMarket formats.
1123    
1124    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1125    
1126            * man/dtrMatrix-class.Rd: add examples
1127            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1128    
1129            * TODO: note the dtpMatrix (docu) bug
1130    
1131            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1132            in order to ensure that new as.matrix() is used by old functions,
1133            e.g., svd(), qr(), eigen(), dist(),..;
1134                  apply(), also matplot() or pairs().
1135    
1136    
1137    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1138    
1139            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1140              add comments about 'control' / lmerControl() arguments
1141    
1142    2005-07-27  Douglas Bates  <bates@wisc.edu>
1143    
1144            * man/sleepstudy.Rd: Added the sleep data set.
1145            * DESCRIPTION (Version): 0.98-1  released to CRAN
1146    
1147    2005-07-12  Douglas Bates  <bates@wisc.edu>
1148            * man/sleepstudy.Rd: Added the sleep data set.
1149    
1150            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1151            .Call calls that were producing spurious output.
1152    
1153    2005-07-05  Douglas Bates  <bates@wisc.edu>
1154    
1155            * R/lmer.R (lmer): stored updated variance component estimates in
1156            mer object for the generalized model.  (Bug reported by Renaud
1157            Lancelot).
1158    
1159    2005-07-03  Douglas Bates  <bates@wisc.edu>
1160    
1161            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1162            unidimensional case.
1163    
1164    2005-06-08  Douglas Bates  <bates@wisc.edu>
1165    
1166            * DESCRIPTION (Version): 0.96-1
1167    
1168            * moved  lmer-class' R and C code moved from lme4 to here
1169    
1170    2005-06-04  Douglas Bates  <bates@wisc.edu>
1171    
1172            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1173            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1174    
1175    2005-06-02  Douglas Bates  <bates@wisc.edu>
1176    
1177            * src/Makefile.win: Forgot to update this when Makefile changed.
1178    
1179    2005-05-11  Douglas Bates  <bates@wisc.edu>
1180    
1181            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1182            bug reported by Kurt Hornik and Michael Hahsler.
1183    
1184    2005-05-10  Douglas Bates  <bates@wisc.edu>
1185    
1186            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1187            logical sparse matrices.  These will also be used in the symbolic
1188            analysis for lmer objects.
1189    
1190            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1191            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1192    
1193    2005-05-06  Douglas Bates  <bates@wisc.edu>
1194    
1195            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1196            colMeans, colSums, rowMeans and rowSums.
1197    
1198    2005-04-18  Douglas Bates  <bates@wisc.edu>
1199    
1200            * src/lgCMatrix.[ch]: code for _validate method and stub for
1201            multiplication operation.
1202    
1203            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1204            to dgetrs.
1205    
1206            * src/init.c: Fix cut-and-paste error in definition of
1207            dgeMatrix_matrix_solve
1208    
1209            * src/{many files}: Tighten code by using ALLOC_SLOT.
1210    
1211    2005-04-15  Douglas Bates  <bates@wisc.edu>
1212    
1213            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1214    
1215            * DESCRIPTION: Eliminate import of stats.
1216    
1217    
1218    2005-04-06  Douglas Bates  <bates@wisc.edu>
1219    
1220            * R/AllClass.R : add logical sparse matrix classes
1221    
1222    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1223    
1224            * R/dgTMatrix.R: add "[" method for triplet matrices
1225            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1226    
1227    2005-03-31  Douglas Bates  <bates@wisc.edu>
1228    
1229            * DESCRIPTION (Version): release 0.95-5 to CRAN
1230    
1231            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1232            * R/sparseMatrix.R: %*%, crossprod()
1233            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1234            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1235            * src/lmer.c (lmer_fitted): fix thinko
1236    
1237    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * R/AllClass.R: add two virtual sparse classes ``on top''
1240    
1241    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1242    
1243            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1244                    correspondingly fix examples and tests/ since new()
1245                    doesn't work for virtual classes.
1246    
1247    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1248    
1249            * R/Matrix.R (as.matrix): method and one for unname()
1250            * tests/dpoMatrix.R: tests should now be less platform dependent;
1251              also run for R 2.1.0; using as.matrix()
1252    
1253    2005-03-15  Douglas Bates  <bates@wisc.edu>
1254    
1255            * R/pMatrix.R: "pMatrix" class added
1256            * ....
1257    
1258    2005-03-14  Douglas Bates  <bates@wisc.edu>
1259    
1260            * R/dtpMatrix.R: Add unpack method and an example.
1261    
1262            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1263            of general symmetric matrices and associated S4 methods.
1264    
1265    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1266            +
1267    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1268    
1269            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1270              crossprod() and "%*%" methods added; tests, too.
1271            * tests/matprod.R: new, for testing these
1272    
1273    2005-03-03  Douglas Bates  <bates@wisc.edu>
1274    
1275            * src/lmer.c (lmer_fitted): Added.
1276    
1277    2005-03-02  Douglas Bates  <bates@wisc.edu>
1278    
1279            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1280    
1281    2005-02-28  Douglas Bates  <bates@wisc.edu>
1282    
1283            * src/*.c,po/,inst/po: Internationalization and localization of
1284            the package.
1285    
1286            * src/ldl.[ch]: Removed these as their contents are referenced in the
1287            R_ldl.c file.
1288    
1289            * src/flame.[ch]: Removed these source files.
1290    
1291            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1292    
1293            * src/LU.[ch],src/init.c: absorb in factorizations
1294    
1295            * src/Mutils.h: prepare for internationalization
1296    
1297            * src/cblas.h: move the enum definitions to Mutils.h and remove
1298            this file
1299    
1300    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1303    
1304            * R/dtrMatrix.R: fix t() method
1305    
1306            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1307            * NAMESPACE: export them (and import generics from "methods")
1308            * tests/group-methods.R : and test them.
1309    
1310            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1311            border case
1312    
1313    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1314    
1315            * DESCRIPTION (Version): 0.95-2  released to CRAN
1316    
1317            * src/dgBCMatrix.c:
1318            * src/lmer.c: many changes
1319            * ...
1320    
1321    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1322    
1323            * R/Matrix.R: add more sophisticated show() method.
1324    
1325    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1326    
1327            * */* : almost complete reorganization of classes.
1328    
1329    2005-01-26  Douglas Bates  <bates@wisc.edu>
1330    
1331            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1332            for the geMatrix class.
1333    
1334    2005-01-24  Douglas Bates  <bates@wisc.edu>
1335    
1336            * src/Makefile (clean): Remove *.a and *.so
1337    
1338            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1339    
1340    2005-01-23  Douglas Bates  <bates@wisc.edu>
1341    
1342            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1343            had an effect in cases with more than 2 grouping factors.
1344    
1345    2005-01-03  Douglas Bates  <bates@wisc.edu>
1346    
1347            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1348    
1349    2004-12-23  Douglas Bates  <bates@wisc.edu>
1350    
1351            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1352            and R_useDynamicSymbols (suggested by B.D.Ripley).
1353    
1354    2004-12-14  Douglas Bates  <bates@wisc.edu>
1355    
1356          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1357    
1358          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1359          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1360    
1361  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1362    
1363          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1364          no longer used.          no longer used.
# Line 17  Line 1370 
1370          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1371          Fixes part but not all of #15.          Fixes part but not all of #15.
1372    
1373  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1374    
1375          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1376          scalar grouping factors corrected.          scalar grouping factors corrected.
1377    
1378  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1379    
1380          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1381    
1382  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1383    
1384          * 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
1385          .h file can be included.          .h file can be included.
1386    
1387  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1388    
1389          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1390          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1391    
1392          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1393    
1394  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1395    
1396          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1397    
1398  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1399    
1400          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1401    
1402  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1403    
1404          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1405    
1406  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1407    
1408          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1409    
1410  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1411    
1412          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1413          routines.          routines.
1414    
1415  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1416    
1417          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1418    
1419  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1420    
1421          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1422    

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