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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1659, Wed Nov 1 17:50:15 2006 UTC
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1    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>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
673    
674          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 699 
699    
700          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
701          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
702          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
703    
704    
705  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 822 
822          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
823          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
824          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
825          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
826    
827  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
# Line 355  Line 1026 
1026  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1029          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1030          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1031    
1032  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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