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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1659, Wed Nov 1 17:50:15 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for symmetry test, via
4            * R/Auxiliaries.R (.as.dgC.0.factors):
5    
6    2006-11-01  Douglas Bates  <bates@r-project.org>
7    
8            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
9            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
10            <CsparseMatrix>) added
11    
12    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * tests/matprod.R: add a variation of Harri's example
15    
16            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
17            recursive infinitely.
18    
19            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
20    
21            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
22    
23    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
26            matrix if possible; test m+m == 2*m; now test dgRMatrix.
27            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
28            satisfy the above test.
29    
30    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
33    
34            * R/dgCMatrix.R: solve(a, b="missing") based on
35            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
36            RHS = NULL.
37    
38            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
39            add more (needed) [t]crossprod() methods.
40    
41            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
42    
43            * R/Auxiliaries.R (as_CspClass): cleanup
44            (drop0): internal utility for "Csparse_drop(*, 0)"
45            (.bail.out.2): encourage active feedback
46    
47    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/dMatrix.R(Compare): new(), then slots [no validity check]
50    
51            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
52            non-valid or 'sorted' case).
53    
54            * R/dsparseMatrix.R: add "chol" method.
55            * R/ddenseMatrix.R: ditto
56    
57            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
58            * NAMESPACE (Ops)
59            * R/diagMatrix.R (diag2T): simple utility used "higher level"
60            coercion; deprecating direct lower level coercions.
61    
62            * R/*.R (seq): use seq_len() and seq_along() where possible.
63    
64    
65    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * DESCRIPTION (Version): 0.9975-5 ready for release
68    
69    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
70    
71            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
72    
73    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/AllClass.R (corMatrix): add 'validity' check;
76                    comment out unused "LDL" class definition
77            * NAMESPACE: mention, but do not export "LDL" class
78            * R/corMatrix.R: new (simple), needed for R-devel with
79            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
80              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
81    
82    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
83    
84            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
85            use Rprintf and R's error handling.
86    
87    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
90            * tests/matprod.R: add tests for the bug fixed.
91    
92    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
95            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
96    
97    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
100    
101    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * DESCRIPTION (Version): 0.9975-3
104    
105            * R/diagMatrix.R (bdiag): new function constructing block diagonal
106            (sparse) matrices.
107            * man/bdiag.Rd: docu + examples
108    
109            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
110    
111            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
112            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
113    
114            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
115            that result is sparse or diagonal (and not dense).
116    
117            * man/Subassign-methods.Rd: fix examples
118    
119            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
120            should always return a sparse (and not sometimes a diagonal) matrix.
121    
122    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
125    
126    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
127    
128            * DESCRIPTION (Version): 0.9975-2
129    
130            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
131    
132    2006-10-02  Douglas Bates  <bates@R-project.org>
133    
134            * tests/dg_Matrix.R: Simplify test taking into account new code.
135    
136    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
139    
140            * R/lsTMatrix.R: new files w/ missing methods
141            * R/nsTMatrix.R:  "  'for completeness'
142    
143            * tests/Class+Meth.R: a bit less 'not.ok.classes'
144    
145            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
146    
147    
148    2006-09-28  Douglas Bates  <bates@R-project.org>
149    
150            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
151            included.
152    
153            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
154            Export C-callable functions used in Zt_create in lme4.
155    
156    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * DESCRIPTION (Version): 0.9975-1
159    
160            * tests/simple.R: less checks fail; using NA, found that our
161                    kronecker() is not base-compatible with NA's.
162    
163            * R/dMatrix.R: "Compare" method now implemented for all cases
164    
165            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
166    
167            * man/dtpMatrix-class.Rd: mention length of 'x' slot
168    
169            * src/dtpMatrix.c (dtpMatrix_validate): fix check
170            * src/dspMatrix.c (dspMatrix_validate): ditto
171    
172            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
173              including coercion to [nl]tTMatrix.
174    
175            * R/diagMatrix.R (show): print a header line as for other classes.
176    
177    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * src/Makefile.win (SUBDIRS): fix typo
180    
181    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
184    
185    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
186    
187            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
188            symmetric and y missing in R code using %*% (cholmod_aat doesn't
189            accept a symmetric matrix).
190            * tests/group-methods.R: Uncomment test of crossprod applied to
191            lsCMatrix objects.
192    
193    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/AllClass.R (symmetricMatrix): add validity method (available
196            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
197    
198            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
199    
200            * tests/indexing.Rout.save:
201            * tests/indexing.R: additions, mainly for 'lsparse'
202    
203            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
204            case.
205    
206            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
207    
208    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
211                    as 'N' (1-letter - Ok?)
212    
213            * tests/group-methods.R: add test for logical + NAs
214    
215            * R/dMatrix.R ("Compare"): fix to work with NA's
216    
217            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
218    
219            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
220                    which is implemented.
221    
222    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * src/chm_common.c: coerce logical <-> double instead of
225            typecasting;  needed for "l" matrix handling in cholmod.
226    
227            * tests/other-pkgs.R (graph): small extension in "graph" checks.
228    
229            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
230            (Tsp2grNEL): other fixes needed
231    
232    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
235                    Matrices, since "lMatrix", also "lsparseM" can have NA
236            * R/ndenseMatrix.R, etc: new source files
237            * man/nsparseMatrix-classes.Rd, etc: new help files
238            * tests/: adaptions
239            * src/chm_common.c (chm_dense_to_SEXP): and others:
240                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
241            * src/Csparse.c, etc: ditto
242    
243    2006-09-11  Douglas Bates  <bates@R-project.org>
244    
245            * src/Mutils.[ch],init.c inst/include/*.h: Move the
246            alloc_d**Matrix functions to the lme4 package.
247    
248    2006-09-09  Douglas Bates  <bates@R-project.org>
249    
250            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
251            fixed
252    
253    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/lMatrix.R: new
256    
257            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
258    
259            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
260            * man/tcrossprod.Rd: ditto
261    
262    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
265            for exported functions
266            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
267            Remove partitioning algorithms for sparse matrix reordering.  The
268            copyright on the Metis code was problematic and the methods were
269            rarely used.
270            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
271            operations are now done entirely in CHOLMOD code.
272    
273    2006-09-06  Douglas Bates  <bates@R-project.org>
274    
275            * src/Mutils.h: Remove functions that are no longer used.
276    
277    2006-09-04  Douglas Bates  <bates@R-project.org>
278    
279            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
280            * src/DEPS.mkf: update
281    
282    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * created branches/Matrix-for-R-2.3.x;  on trunk: do
285            * DESCRIPTION (Version): 0.9975-0
286            (Depends): R (>= 2.4.0)
287    
288    2006-09-01  Douglas Bates  <bates@R-project.org>
289    
290            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
291    
292    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
295            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
296    
297            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
298    
299    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
302            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
303            * R/dsparseMatrix.R: ditto
304            * R/Csparse.R: ditto
305    
306    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/dMatrix.R (Compare): improve availability of "<", etc
309            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
310    
311    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
314            of a 0-index which was used as 1-index (..hmm)
315    
316            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
317    
318            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
319            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
320            (.is.diagonal): ditto
321    
322            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
323    
324            * R/Matrix.R (Matrix): also work for NA data
325    
326    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
329            in all cases.
330    
331    2006-08-27  Douglas Bates  <bates@R-project.org>
332    
333            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
334            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
335    
336    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
339            subclasses of "ddenseMatrix"
340            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
341            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
342            instead of half dozen specialized ones.
343    
344    2006-08-25  Douglas Bates  <bates@R-project.org>
345    
346            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
347            <tillard@cirad.fr> - ordering standard errors to match effects.
348    
349    2006-08-24  Douglas Bates  <bates@R-project.org>
350    
351            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
352            on R_ldl.
353            * R/lCholCMatrix.R,
354            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
355            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
356            * many files in ./R and ./src: Use more general version of
357            dup_mMatrix_as_dgeMatrix to simplify method definitions.
358            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
359            dtpMatrix, dspMatrix and dppMatrix conversions.
360    
361    
362    2006-08-23  Douglas Bates  <bates@R-project.org>
363    
364            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
365            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
366            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
367            dgeMatrix_crossprod (may need to do this in other places).
368            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
369            generic and method for dsCMatrix.  Use CHOLMOD for chol().
370    
371    2006-08-22  Douglas Bates  <bates@R-project.org>
372    
373            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
374            types of classed Matrices, matrices or numeric or logical vectors.
375            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
376            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
377            to Mutils.h (as an inline) and change name to Matrix_check_class;
378            fixes in as_cholmod_factor and chm_factor_to_SEXP.
379            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
380            dsCMatrix_matrix_solve.  Comment out vestigial functions.
381            * src/Csparse.c: use diag_P and uplo_P macros.
382    
383    2006-08-21  Douglas Bates  <bates@R-project.org>
384    
385            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
386            valgrind.
387            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
388            inverses.
389            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
390            -Wall warnings.
391            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
392            Use dup_mMatrix_as_dgeMatrix.
393    
394    2006-08-20  Douglas Bates  <bates@R-project.org>
395    
396            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
397            * tests/sparseQR.R: Added
398            * man/sparseQR-class.Rd: Document methods for qr.* generics
399            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
400    
401    2006-08-19  Douglas Bates  <bates@R-project.org>
402    
403            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
404            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
405            and qr.fitted.
406            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
407            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
408    
409    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
412            the base version has no "..." argument.
413    
414            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
415    
416            * R/Matrix.R: define and
417            * NAMESPACE: export as.numeric() and as.logical() methods.
418                    Let's hope these do not badly slow down something...
419            Finally export the zapsmall() method.
420    
421    2006-08-17  Douglas Bates  <bates@R-project.org>
422    
423            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
424            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
425            * src/dtCMatrix.c :Remove code that is no longer used
426            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
427    
428    2006-08-14  Douglas Bates  <bates@R-project.org>
429    
430            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
431            Csparse_to_logical and Csparse_symmetric_to_general.
432            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
433            coercion methods between CsparseMatrix and TsparseMatrix.
434    
435    2006-08-14  Douglas Bates  <bates@R-project.org>
436    
437            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
438            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
439            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
440            possible.
441    
442    2006-08-12  Douglas Bates  <bates@R-project.org>
443    
444            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
445              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
446              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
447              generalize conversions between TsparseMatrix, CsparseMatrix,
448              denseMatrix and matrix.  Preserve triangularity property and
449              propagate Dimnames in the easy cases.
450    
451    2006-08-10  Douglas Bates  <bates@R-project.org>
452    
453            * src/lmer.c: adjust checks in glmer_init for S4SXP
454            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
455            before S4SXP but for the wrong reasons.
456    
457    2006-08-08  Douglas Bates  <bates@R-project.org>
458    
459            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
460            Later modified to return the upper triangle only.
461            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
462    
463    2006-08-07  Douglas Bates  <bates@R-project.org>
464    
465            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
466            R-level conversion to a sparse symmetric class.
467            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
468            Remove conversion to sparse symmetric classes (now done in C code).
469    
470    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
473            * man/band.Rd:  adapt the \dontshow{} unit test.
474    
475    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * DESCRIPTION (Version): 0.995-14  for CRAN
478    
479            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
480    
481            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
482            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
483    
484            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
485            * R/Tsparse.R (tril, triu, band): methods
486            * R/dgRMatrix.R (tril, ...):    ditto
487            * man/band.Rd:                  ditto
488    
489    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/Matrix.R (head, tail): directly use utils:::head.matrix
492                    to be up-to-date automatically.
493    
494    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
497    
498            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
499            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
500            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
501            such that the S4 objects are always created by the current version
502            of R and 'Matrix' class definitions.
503    
504    2006-08-01  Douglas Bates  <bates@R-project.org>
505    
506            * R/lmer.R (LMEoptimize method), tests/lmer.R,
507            inst/external/test3comp.rda: Added warnings for convergence on
508            boundary and test cases.
509    
510            * src/lmer.c (mer_postVar): Modified to return the variances that
511            are marginal to the fixed effects, not conditional on them (which
512            is what the bVar slot contents represent).
513    
514    2006-07-31  Douglas Bates  <bates@R-project.org>
515    
516            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
517            function which calls the C function mer_hat_trace2.
518    
519            * man/ranef.Rd: Include description of "postVar" argument and
520            producing a caterpillar plot.
521    
522    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * NAMESPACE:    change  "correlation" to "corMatrix"
525            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
526            * R/dpoMatrix.R: ditto
527            * R/lmer.R:      ditto
528    
529    2006-07-28  Douglas Bates  <bates@R-project.org>
530    
531            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
532            RZXinv slot's contents into a separate internal function that can
533            be used in mer_hat_trace.
534    
535    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
538            via new smart
539            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
540            utility functions.
541    
542    
543    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Csparse.R (tril, triu, band): do return *triangular* classed
546            matrices when appropriate; band() even symmetric ones.
547            (replCmat): extend to potentially all "CsparseMatrix"
548            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
549            allow subassignment for special sparse matrices.
550    
551            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
552    
553            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
554            argument; in glmer_*(): print only if(verbose).
555    
556            speed-optimize a few places by moving REAL(.) out of loops.
557    
558            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
559    
560    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
563                    since that wrongly triggers also for M[ logi , ]
564    
565            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
566            a symmetric matrix that results in a non-symmetric one.
567            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
568    
569            * R/dMatrix.R: make round(M) work as round(M, 0)
570    
571            * R/dgTMatrix.R (image): coordinate system and axis now use
572            1-based indices, not 0-based ones.
573    
574            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
575            * tests/indexing.R: test it.
576    
577            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
578            * man/isSymmetric-methods.Rd: and document it.
579    
580            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
581            * man/SparseM-conv.Rd: docu them
582    
583            * tests/other-pkgs.R: renamed from tests/graph.R and add example
584                    for 'SparseM' conversions
585    
586    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
587    
588            * R/Matrix.R (head): added head() and tail() methods.
589    
590    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * DESCRIPTION (Version): 0.995-12 released to CRAN
593    
594    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * tests/simple.R: add check for correct dsT -> dgT coercion;
597                    add check for correct printing of symmetric sparse matrices.
598    
599            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
600            for sparse symmetric matrices.
601    
602            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
603            diagonal twice.
604    
605    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
606    
607            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
608            being applied to the x slot (detected by Brian Ripley).
609    
610    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
613    
614            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
615    
616    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * src/lgCMatrix.c (lgCMatrix_diag): new function
619            * R/lgCMatrix.R (diag): for new method
620    
621            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
622                 ==> construction of illegal "*gTMatrix" via new() should
623                 now be much less easy:
624            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
625    
626            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
627                    directly.
628            * man/Matrix.Rd: documents it.
629    
630    2006-07-06  Douglas Bates  <bates@R-project.org>
631    
632            * src/pedigree.c (pedigree_inbreeding): Correction in
633            initialization.  This function is not currently being used and is
634            not fully tested.
635    
636            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
637            Introduced the glmer class.  Added code for mcmcmsamp on glmer
638            objects.  Modified validity check on pedigree objects to account
639            for nonparallel patterns of missingness of parents.
640    
641            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
642            class.
643    
644    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/pMatrix.R: coercion pMatrix -> Tsparse
647    
648    2006-06-12  Douglas Bates  <bates@R-project.org>
649    
650            * DESCRIPTION (Version): 0.995-11 released to CRAN
651    
652            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
653            the output from mcmcsamp.
654    
655    2006-06-10  Douglas Bates  <bates@R-project.org>
656    
657            * R/lmer.R (simulestimate): added C code for calculating the trace
658            of the hat matrix.
659    
660    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
663            classes.
664            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
665    
666    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/dgTMatrix.R (colSums): etc. All four of
669            colSums(), rowSums(), colMeans(), rowMeans() now should work for
670            all "Matrices".
671    
672    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
673    
674            * R/lmer.R (panel.ci): Add a reference line at zero and a
675            background grid to the qqmath plot of ranef.lmer.
676    
677    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
678    
679            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
680            grouping factors to be specified in the formula as (1|foo/bar).
681    
682    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
683    
684            * R/lmer.R (findbars and others): Change check of is.numeric to
685            !is.language to resolve the bug reported by Jacob Wegelin.
686    
687            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
688            code to evaluate inbreeding coefficients without calculating T,
689            based on code in Sargolzaei and Iwaisaki's paper.
690    
691    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
692    
693            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
694            generic and mer methods for isNested and denomDF. This denomDF was
695            an attempt to emulate that in lme but I don't think that makes
696            sense.  Use the trace of the hat matrix instead.
697    
698    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
701            the C code depending on a slot structure that's no longer valid.
702            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
703    
704    
705    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
706    
707            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
708            of lowerTriMatrix generic and methods to tril (also upper to triu)
709            and added a general band extractor.
710    
711    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
712    
713            * R/pedigree.R (pedigree): Replace sire and dam values outside the
714            allowable range with NAs. Added a corresponding check in the
715            validity check for the pedigree class.
716    
717            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
718            crossprod methods now inherits from symmetricMatrix.
719    
720    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
721    
722            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
723            generics lowerTriMatrix and upperTriMatrix along with methods for
724            the Csparse virtual class.  Also added a C function Csparse_band
725            that implements these methods by calling cholmod_band.
726    
727    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
730            erased when it was NULL.  This led to invalid subselections!
731    
732    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
733    
734            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
735            in method for "t" so as not to lose the unit diagonal property.
736    
737    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
738    
739            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
740            and methods.  This is now an option to the ranef method for the
741            mer class.
742    
743            * src/cs_utils.c: Ensure that the nz component is -1 for a
744            compressed column-oriented matrix.  Minor formatting cleanup.
745    
746            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
747            objects.
748    
749    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
752            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
753    
754    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
757            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
758    
759            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
760            for the dtCMatrix class.
761    
762    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
763    
764            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
765            and methods for it.
766    
767    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
770            arguments, such that M %*% 1:6 now works
771            * Tests/matprod.R: test the above
772    
773    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
774    
775            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
776            the ranef.lmer class.
777    
778            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
779            methods to extract the posterior variances from the bVar slot.
780    
781    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
784            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
785    
786            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
787            * tests/simple: (extended)
788    
789            * R/sparseMatrix.R (isTriangular): now using much improved
790            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
791    
792    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
793    
794            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
795            (problem report from Franklin Parlamis).  This should be done
796            generally.
797    
798    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
799    
800            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
801            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
802            update the plot methods.
803    
804    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
805    
806            * R/lmer.R (resid and ranef methods):  Added methods for the
807            "residuals" and "resid" generic but only for linear mixed model
808            fits.  Changed the ranef method to return a list of data frames so
809            that the plot methods now work.
810    
811    2006-03-16  Douglas Bates  <bates@bates2>
812    
813            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
814            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
815    
816            * DESCRIPTION (Date): New release
817    
818    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
821    
822            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
823            * man/KNex.Rd: and other help files
824            * tests/*.R: several ones needed adaption
825            * inst/doc/Comparisons.Rnw: ditto
826    
827    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
830    
831            * tests/indexing.R: tests for new [<- methods for sparse matrices.
832    
833    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
836    
837            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
838    
839    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * R/dMatrix.R: enable things like  M [ M < 10 ]
842            * R/dgeMatrix.R: implement it
843    
844    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * R/AllClass.R: define "summary.mer" and "*.lmer"
847            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
848            * R/lmer.R (show): now works with summary()
849    
850    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
853            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
854                    support the above
855    
856    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
857    
858            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
859            Use glmFit$prior.weights for weights in a glmm.
860            Allow an option usePQL = FALSE to skip the PQL steps for the
861            Laplace method (and, in time, the AGQ method).
862    
863            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
864            into a separate function internal_mer_Xfactor to be able to call
865            it from internal_bhat.
866    
867    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * tests/Class+Meth.R (tstMatrixClass): function for much better
870            testing; now again of all actual classes.
871    
872            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
873                    use macros and define make_d_matrix_* and make_i_matrix_*
874                    where _i_ is for the ldense routines:
875    
876            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
877            * src/ldense.c (lsyMatrix_as_lgeMatrix):
878    
879            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
880    
881    
882    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
885                    many different kinds of matrices.
886            * R/*.R: quite a few new methods were needed for R CMD check with
887                    new Matrix().  Very good for users playing around.
888    
889    
890    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * src/dgeMatrix.c (dMatrix_validate): new
893            * src/Mutils.c (dense_nonpacked_validate): new
894    
895            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
896    
897    
898    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
899    
900            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
901    
902    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
903    
904            * DESCRIPTION (Version): 0.99-6 released to CRAN
905    
906            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
907            segfault in cases with multiple non-nested grouping factors.
908    
909    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
912                    (Depends): also on 'utils'
913    
914            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
915            * R/diagMatrix.R (Diagonal): constructor and methods for
916            diagonal matrices
917    
918            * R/ltTMatrix.R: new "minimal methods"
919    
920    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
923            all methods (and help files).
924    
925    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
928                    for case (dimn.  op  no_dimn.)
929    
930    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
931    
932            * DESCRIPTION (Version): 0.99-2  released to CRAN
933    
934    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
935    
936            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
937            by Julian Faraway.
938    
939    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * R/Auxiliaries.R (try_as): new utility
942            * R/sparseMatrix.R: use try_as() in coercion to original class
943    
944    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
947    
948    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * R/Auxiliaries.R (dimNamesCheck): added
951    
952            * R/Matrix.R (as.array), (as.vector): new
953    
954    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
957                    default.
958            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
959                    "pMatrix" now contains "sparseMatrix"
960    
961    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * tests/Class+Meth.R: new tests; t(t(m)) == m
964    
965            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
966    
967            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
968            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
969    
970            * R/dspMatrix.R: typo in "t" method
971    
972    2005-09-18  Douglas Bates  <bates@wisc.edu>
973    
974            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
975            * R/Tsparse.R: instead of R/gTMatrix.R
976            * R/Csparse.R: new
977            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
978            * src/Tsparse.c: new; many trivial methods calling cholmod_()
979            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
980                            via cholmod
981    
982    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * R/Auxiliaries.R (non0ind): new function using new C code
985            * src/dgCMatrix.c (compressed_non_0_ij): new utility
986    
987    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
988    
989            * src/chm_common.h: header file required by all C sources that
990            call CHOLMOD functions.  It defines a cholmod_common structure
991            called 'c' whose address is passed as the last argument to
992            (virtually) every CHOLMOD function.
993    
994            * src/Pattern.c: Simple example of the use of CHOLMOD.
995    
996            * src/init.c: initialize and finalize the cholmod_common structure.
997    
998            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
999            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1000    
1001    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1002    
1003            * inst/test-tools.R: new file collecting the utility functions used
1004                    in ./tests/*.R
1005    
1006            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1007            * R/Matrix.R (cbind2): methods for NULL and missing
1008    
1009    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * R/AllClass.R: new "index" class for "[" and "[<-":
1012                    First cut at "symmetricMatrix" and "triangularMatrix"
1013            * R/gTMatrix.R (.ind.prep): new function;
1014                    Logical and character indexing now work too.
1015            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1016            * tests/indexing.R: new, including *.Rout.save
1017            * tests/dgTMatrix.R: new
1018    
1019    2005-08-29  Douglas Bates  <bates@wisc.edu>
1020    
1021            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1022            indicator pos not being updated.  Also enforced upper triangular
1023            for symmetric case.  Need to coerce edges component of elements of
1024            edge list - grr! (Why don't they define their classes cleanly?)
1025    
1026    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028            * R/Matrix.R:  added first "[<-" methods; not yet functional
1029            * R/denseMatrix.R: ditto
1030            * man/Subassign-methods.Rd: new help file for these
1031    
1032    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * DESCRIPTION (Version): 0.98-6
1035    
1036            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1037            matrices.
1038    
1039    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1040    
1041            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1042                    as( <logical>, "matrix")
1043    
1044            * R/pMatrix.R: coercion to "lgTMatrix"
1045    
1046            * R/gTMatrix.R: new virtual class to define "[" methods for.
1047            * man/gTMatrix-class.Rd:
1048            * General slight re-organization of where "[" methods are defined.
1049              more to come.
1050    
1051    2005-08-18  Douglas Bates  <bates@wisc.edu>
1052    
1053            * DESCRIPTION (Version): 0.98-5  released to CRAN
1054    
1055            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1056            * .....
1057    
1058    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1059    
1060            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1061            or glmer objects.
1062    
1063    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1066    
1067    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1068    
1069            * R/HBMM.R: finish re-writing R-only code.
1070    
1071    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1072    
1073            * man/externalFormats.Rd: move documentation for writeHB and
1074            writeMM here.
1075    
1076            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1077            (suggested by Paul Roecker).
1078    
1079            * tests/validObj.R (assertError): Comment out test that is failing
1080            after recent changes in r-devel.
1081    
1082    
1083    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * R/AllClass.R: intermediate virtual class "denseMatrix"
1086            * man/denseMatrix-class.Rd
1087            * NAMESPACE: export it, and also export
1088            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1089    
1090    2005-08-10  Douglas Bates  <bates@wisc.edu>
1091    
1092            * DESCRIPTION (Version): 0.98-3 to CRAN
1093    
1094            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1095            matrix_solve code (which was really, really wrong).
1096    
1097    2005-08-07  Douglas Bates  <bates@wisc.edu>
1098    
1099            * DESCRIPTION (Version): 0.98-2
1100    
1101            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1102    
1103            * R/lmer.R (abbrvNms): new
1104            * R/lmer.R (mcmcsamp): allow transformed parameters
1105            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1106            for the Harwell-Boeing and the MatrixMarket formats.
1107    
1108    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1109    
1110            * man/dtrMatrix-class.Rd: add examples
1111            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1112    
1113            * TODO: note the dtpMatrix (docu) bug
1114    
1115            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1116            in order to ensure that new as.matrix() is used by old functions,
1117            e.g., svd(), qr(), eigen(), dist(),..;
1118                  apply(), also matplot() or pairs().
1119    
1120    
1121    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1124              add comments about 'control' / lmerControl() arguments
1125    
1126    2005-07-27  Douglas Bates  <bates@wisc.edu>
1127    
1128            * man/sleepstudy.Rd: Added the sleep data set.
1129            * DESCRIPTION (Version): 0.98-1  released to CRAN
1130    
1131    2005-07-12  Douglas Bates  <bates@wisc.edu>
1132            * man/sleepstudy.Rd: Added the sleep data set.
1133    
1134            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1135            .Call calls that were producing spurious output.
1136    
1137    2005-07-05  Douglas Bates  <bates@wisc.edu>
1138    
1139            * R/lmer.R (lmer): stored updated variance component estimates in
1140            mer object for the generalized model.  (Bug reported by Renaud
1141            Lancelot).
1142    
1143    2005-07-03  Douglas Bates  <bates@wisc.edu>
1144    
1145            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1146            unidimensional case.
1147    
1148    2005-06-08  Douglas Bates  <bates@wisc.edu>
1149    
1150            * DESCRIPTION (Version): 0.96-1
1151    
1152            * moved  lmer-class' R and C code moved from lme4 to here
1153    
1154    2005-06-04  Douglas Bates  <bates@wisc.edu>
1155    
1156            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1157            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1158    
1159    2005-06-02  Douglas Bates  <bates@wisc.edu>
1160    
1161            * src/Makefile.win: Forgot to update this when Makefile changed.
1162    
1163    2005-05-11  Douglas Bates  <bates@wisc.edu>
1164    
1165            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1166            bug reported by Kurt Hornik and Michael Hahsler.
1167    
1168    2005-05-10  Douglas Bates  <bates@wisc.edu>
1169    
1170            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1171            logical sparse matrices.  These will also be used in the symbolic
1172            analysis for lmer objects.
1173    
1174            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1175            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1176    
1177    2005-05-06  Douglas Bates  <bates@wisc.edu>
1178    
1179            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1180            colMeans, colSums, rowMeans and rowSums.
1181    
1182    2005-04-18  Douglas Bates  <bates@wisc.edu>
1183    
1184            * src/lgCMatrix.[ch]: code for _validate method and stub for
1185            multiplication operation.
1186    
1187            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1188            to dgetrs.
1189    
1190            * src/init.c: Fix cut-and-paste error in definition of
1191            dgeMatrix_matrix_solve
1192    
1193            * src/{many files}: Tighten code by using ALLOC_SLOT.
1194    
1195    2005-04-15  Douglas Bates  <bates@wisc.edu>
1196    
1197            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1198    
1199            * DESCRIPTION: Eliminate import of stats.
1200    
1201    
1202    2005-04-06  Douglas Bates  <bates@wisc.edu>
1203    
1204            * R/AllClass.R : add logical sparse matrix classes
1205    
1206    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1207    
1208            * R/dgTMatrix.R: add "[" method for triplet matrices
1209            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1210    
1211    2005-03-31  Douglas Bates  <bates@wisc.edu>
1212    
1213            * DESCRIPTION (Version): release 0.95-5 to CRAN
1214    
1215            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1216            * R/sparseMatrix.R: %*%, crossprod()
1217            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1218            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1219            * src/lmer.c (lmer_fitted): fix thinko
1220    
1221    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1222    
1223            * R/AllClass.R: add two virtual sparse classes ``on top''
1224    
1225    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1226    
1227            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1228                    correspondingly fix examples and tests/ since new()
1229                    doesn't work for virtual classes.
1230    
1231    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1232    
1233            * R/Matrix.R (as.matrix): method and one for unname()
1234            * tests/dpoMatrix.R: tests should now be less platform dependent;
1235              also run for R 2.1.0; using as.matrix()
1236    
1237    2005-03-15  Douglas Bates  <bates@wisc.edu>
1238    
1239            * R/pMatrix.R: "pMatrix" class added
1240            * ....
1241    
1242    2005-03-14  Douglas Bates  <bates@wisc.edu>
1243    
1244            * R/dtpMatrix.R: Add unpack method and an example.
1245    
1246            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1247            of general symmetric matrices and associated S4 methods.
1248    
1249    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1250            +
1251    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1254              crossprod() and "%*%" methods added; tests, too.
1255            * tests/matprod.R: new, for testing these
1256    
1257    2005-03-03  Douglas Bates  <bates@wisc.edu>
1258    
1259            * src/lmer.c (lmer_fitted): Added.
1260    
1261    2005-03-02  Douglas Bates  <bates@wisc.edu>
1262    
1263            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1264    
1265    2005-02-28  Douglas Bates  <bates@wisc.edu>
1266    
1267            * src/*.c,po/,inst/po: Internationalization and localization of
1268            the package.
1269    
1270            * src/ldl.[ch]: Removed these as their contents are referenced in the
1271            R_ldl.c file.
1272    
1273            * src/flame.[ch]: Removed these source files.
1274    
1275            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1276    
1277            * src/LU.[ch],src/init.c: absorb in factorizations
1278    
1279            * src/Mutils.h: prepare for internationalization
1280    
1281            * src/cblas.h: move the enum definitions to Mutils.h and remove
1282            this file
1283    
1284    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1285    
1286            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1287    
1288            * R/dtrMatrix.R: fix t() method
1289    
1290            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1291            * NAMESPACE: export them (and import generics from "methods")
1292            * tests/group-methods.R : and test them.
1293    
1294            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1295            border case
1296    
1297    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1298    
1299            * DESCRIPTION (Version): 0.95-2  released to CRAN
1300    
1301            * src/dgBCMatrix.c:
1302            * src/lmer.c: many changes
1303            * ...
1304    
1305    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * R/Matrix.R: add more sophisticated show() method.
1308    
1309    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1310    
1311            * */* : almost complete reorganization of classes.
1312    
1313    2005-01-26  Douglas Bates  <bates@wisc.edu>
1314    
1315            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1316            for the geMatrix class.
1317    
1318    2005-01-24  Douglas Bates  <bates@wisc.edu>
1319    
1320            * src/Makefile (clean): Remove *.a and *.so
1321    
1322            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1323    
1324    2005-01-23  Douglas Bates  <bates@wisc.edu>
1325    
1326            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1327            had an effect in cases with more than 2 grouping factors.
1328    
1329    2005-01-03  Douglas Bates  <bates@wisc.edu>
1330    
1331            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1332    
1333    2004-12-23  Douglas Bates  <bates@wisc.edu>
1334    
1335            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1336            and R_useDynamicSymbols (suggested by B.D.Ripley).
1337    
1338    2004-12-14  Douglas Bates  <bates@wisc.edu>
1339    
1340            * R/sscMatrix.R: Add determinant methods
1341    
1342            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1343            for tripletMatrix to matrix.
1344    
1345    2004-12-13  Douglas Bates  <bates@wisc.edu>
1346    
1347            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1348            no longer used.
1349    
1350            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1351            with dynamic allocation of scratch arrays.
1352    
1353            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1354            for multivariate random effects with multiple grouping factors.
1355            Fixes part but not all of #15.
1356    
1357    2004-12-03  Douglas Bates  <bates@wisc.edu>
1358    
1359            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1360            scalar grouping factors corrected.
1361    
1362    2004-11-29  Douglas Bates  <bates@wisc.edu>
1363    
1364            * src/bCrosstab.c: remove diag_update which is no longer used
1365    
1366    2004-11-16  Douglas Bates  <bates@wisc.edu>
1367    
1368          * 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
1369          .h file can be included.          .h file can be included.
1370    
1371  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1372    
1373          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1374          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1375    
1376          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1377    
1378  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1379    
1380          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1381    
1382  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1383    
1384          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1385    
1386  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1387    
1388          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1389    
1390  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1391    
1392          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1393    
1394  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1395    
1396          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1397          routines.          routines.
1398    
1399  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1400    
1401          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1402    
1403  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1404    
1405          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1406    

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