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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1647, Mon Oct 23 12:36:27 2006 UTC
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1    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-5 ready for release
4    
5    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
8    
9    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R (corMatrix): add 'validity' check;
12                    comment out unused "LDL" class definition
13            * NAMESPACE: mention, but do not export "LDL" class
14            * R/corMatrix.R: new (simple), needed for R-devel with
15            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
16              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
17    
18    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
21            use Rprintf and R's error handling.
22    
23    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
26            * tests/matprod.R: add tests for the bug fixed.
27    
28    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
31            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
32    
33    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
36    
37    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * DESCRIPTION (Version): 0.9975-3
40    
41            * R/diagMatrix.R (bdiag): new function constructing block diagonal
42            (sparse) matrices.
43            * man/bdiag.Rd: docu + examples
44    
45            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
46    
47            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
48            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
49    
50            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
51            that result is sparse or diagonal (and not dense).
52    
53            * man/Subassign-methods.Rd: fix examples
54    
55            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
56            should always return a sparse (and not sometimes a diagonal) matrix.
57    
58    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
61    
62    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
63    
64            * DESCRIPTION (Version): 0.9975-2
65    
66            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
67    
68    2006-10-02  Douglas Bates  <bates@R-project.org>
69    
70            * tests/dg_Matrix.R: Simplify test taking into account new code.
71    
72    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
75    
76            * R/lsTMatrix.R: new files w/ missing methods
77            * R/nsTMatrix.R:  "  'for completeness'
78    
79            * tests/Class+Meth.R: a bit less 'not.ok.classes'
80    
81            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
82    
83    
84    2006-09-28  Douglas Bates  <bates@R-project.org>
85    
86            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
87            included.
88    
89            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
90            Export C-callable functions used in Zt_create in lme4.
91    
92    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION (Version): 0.9975-1
95    
96            * tests/simple.R: less checks fail; using NA, found that our
97                    kronecker() is not base-compatible with NA's.
98    
99            * R/dMatrix.R: "Compare" method now implemented for all cases
100    
101            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
102    
103            * man/dtpMatrix-class.Rd: mention length of 'x' slot
104    
105            * src/dtpMatrix.c (dtpMatrix_validate): fix check
106            * src/dspMatrix.c (dspMatrix_validate): ditto
107    
108            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
109              including coercion to [nl]tTMatrix.
110    
111            * R/diagMatrix.R (show): print a header line as for other classes.
112    
113    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * src/Makefile.win (SUBDIRS): fix typo
116    
117    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
120    
121    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
124            symmetric and y missing in R code using %*% (cholmod_aat doesn't
125            accept a symmetric matrix).
126            * tests/group-methods.R: Uncomment test of crossprod applied to
127            lsCMatrix objects.
128    
129    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/AllClass.R (symmetricMatrix): add validity method (available
132            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
133    
134            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
135    
136            * tests/indexing.Rout.save:
137            * tests/indexing.R: additions, mainly for 'lsparse'
138    
139            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
140            case.
141    
142            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
143    
144    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
147                    as 'N' (1-letter - Ok?)
148    
149            * tests/group-methods.R: add test for logical + NAs
150    
151            * R/dMatrix.R ("Compare"): fix to work with NA's
152    
153            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
154    
155            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
156                    which is implemented.
157    
158    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * src/chm_common.c: coerce logical <-> double instead of
161            typecasting;  needed for "l" matrix handling in cholmod.
162    
163            * tests/other-pkgs.R (graph): small extension in "graph" checks.
164    
165            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
166            (Tsp2grNEL): other fixes needed
167    
168    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
171                    Matrices, since "lMatrix", also "lsparseM" can have NA
172            * R/ndenseMatrix.R, etc: new source files
173            * man/nsparseMatrix-classes.Rd, etc: new help files
174            * tests/: adaptions
175            * src/chm_common.c (chm_dense_to_SEXP): and others:
176                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
177            * src/Csparse.c, etc: ditto
178    
179    2006-09-11  Douglas Bates  <bates@R-project.org>
180    
181            * src/Mutils.[ch],init.c inst/include/*.h: Move the
182            alloc_d**Matrix functions to the lme4 package.
183    
184    2006-09-09  Douglas Bates  <bates@R-project.org>
185    
186            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
187            fixed
188    
189    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/lMatrix.R: new
192    
193            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
194    
195            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
196            * man/tcrossprod.Rd: ditto
197    
198    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
201            for exported functions
202            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
203            Remove partitioning algorithms for sparse matrix reordering.  The
204            copyright on the Metis code was problematic and the methods were
205            rarely used.
206            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
207            operations are now done entirely in CHOLMOD code.
208    
209    2006-09-06  Douglas Bates  <bates@R-project.org>
210    
211            * src/Mutils.h: Remove functions that are no longer used.
212    
213    2006-09-04  Douglas Bates  <bates@R-project.org>
214    
215            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
216            * src/DEPS.mkf: update
217    
218    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * created branches/Matrix-for-R-2.3.x;  on trunk: do
221            * DESCRIPTION (Version): 0.9975-0
222            (Depends): R (>= 2.4.0)
223    
224    2006-09-01  Douglas Bates  <bates@R-project.org>
225    
226            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
227    
228    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
231            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
232    
233            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
234    
235    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
238            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
239            * R/dsparseMatrix.R: ditto
240            * R/Csparse.R: ditto
241    
242    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/dMatrix.R (Compare): improve availability of "<", etc
245            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
246    
247    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
250            of a 0-index which was used as 1-index (..hmm)
251    
252            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
253    
254            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
255            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
256            (.is.diagonal): ditto
257    
258            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
259    
260            * R/Matrix.R (Matrix): also work for NA data
261    
262    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
265            in all cases.
266    
267    2006-08-27  Douglas Bates  <bates@R-project.org>
268    
269            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
270            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
271    
272    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
275            subclasses of "ddenseMatrix"
276            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
277            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
278            instead of half dozen specialized ones.
279    
280    2006-08-25  Douglas Bates  <bates@R-project.org>
281    
282            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
283            <tillard@cirad.fr> - ordering standard errors to match effects.
284    
285    2006-08-24  Douglas Bates  <bates@R-project.org>
286    
287            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
288            on R_ldl.
289            * R/lCholCMatrix.R,
290            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
291            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
292            * many files in ./R and ./src: Use more general version of
293            dup_mMatrix_as_dgeMatrix to simplify method definitions.
294            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
295            dtpMatrix, dspMatrix and dppMatrix conversions.
296    
297    
298    2006-08-23  Douglas Bates  <bates@R-project.org>
299    
300            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
301            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
302            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
303            dgeMatrix_crossprod (may need to do this in other places).
304            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
305            generic and method for dsCMatrix.  Use CHOLMOD for chol().
306    
307    2006-08-22  Douglas Bates  <bates@R-project.org>
308    
309            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
310            types of classed Matrices, matrices or numeric or logical vectors.
311            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
312            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
313            to Mutils.h (as an inline) and change name to Matrix_check_class;
314            fixes in as_cholmod_factor and chm_factor_to_SEXP.
315            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
316            dsCMatrix_matrix_solve.  Comment out vestigial functions.
317            * src/Csparse.c: use diag_P and uplo_P macros.
318    
319    2006-08-21  Douglas Bates  <bates@R-project.org>
320    
321            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
322            valgrind.
323            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
324            inverses.
325            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
326            -Wall warnings.
327            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
328            Use dup_mMatrix_as_dgeMatrix.
329    
330    2006-08-20  Douglas Bates  <bates@R-project.org>
331    
332            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
333            * tests/sparseQR.R: Added
334            * man/sparseQR-class.Rd: Document methods for qr.* generics
335            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
336    
337    2006-08-19  Douglas Bates  <bates@R-project.org>
338    
339            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
340            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
341            and qr.fitted.
342            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
343            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
344    
345    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
348            the base version has no "..." argument.
349    
350            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
351    
352            * R/Matrix.R: define and
353            * NAMESPACE: export as.numeric() and as.logical() methods.
354                    Let's hope these do not badly slow down something...
355            Finally export the zapsmall() method.
356    
357    2006-08-17  Douglas Bates  <bates@R-project.org>
358    
359            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
360            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
361            * src/dtCMatrix.c :Remove code that is no longer used
362            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
363    
364    2006-08-14  Douglas Bates  <bates@R-project.org>
365    
366            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
367            Csparse_to_logical and Csparse_symmetric_to_general.
368            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
369            coercion methods between CsparseMatrix and TsparseMatrix.
370    
371    2006-08-14  Douglas Bates  <bates@R-project.org>
372    
373            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
374            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
375            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
376            possible.
377    
378    2006-08-12  Douglas Bates  <bates@R-project.org>
379    
380            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
381              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
382              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
383              generalize conversions between TsparseMatrix, CsparseMatrix,
384              denseMatrix and matrix.  Preserve triangularity property and
385              propagate Dimnames in the easy cases.
386    
387    2006-08-10  Douglas Bates  <bates@R-project.org>
388    
389            * src/lmer.c: adjust checks in glmer_init for S4SXP
390            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
391            before S4SXP but for the wrong reasons.
392    
393    2006-08-08  Douglas Bates  <bates@R-project.org>
394    
395            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
396            Later modified to return the upper triangle only.
397            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
398    
399    2006-08-07  Douglas Bates  <bates@R-project.org>
400    
401            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
402            R-level conversion to a sparse symmetric class.
403            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
404            Remove conversion to sparse symmetric classes (now done in C code).
405    
406    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
409            * man/band.Rd:  adapt the \dontshow{} unit test.
410    
411    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * DESCRIPTION (Version): 0.995-14  for CRAN
414    
415            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
416    
417            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
418            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
419    
420            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
421            * R/Tsparse.R (tril, triu, band): methods
422            * R/dgRMatrix.R (tril, ...):    ditto
423            * man/band.Rd:                  ditto
424    
425    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Matrix.R (head, tail): directly use utils:::head.matrix
428                    to be up-to-date automatically.
429    
430    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
433    
434            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
435            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
436            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
437            such that the S4 objects are always created by the current version
438            of R and 'Matrix' class definitions.
439    
440    2006-08-01  Douglas Bates  <bates@R-project.org>
441    
442            * R/lmer.R (LMEoptimize method), tests/lmer.R,
443            inst/external/test3comp.rda: Added warnings for convergence on
444            boundary and test cases.
445    
446            * src/lmer.c (mer_postVar): Modified to return the variances that
447            are marginal to the fixed effects, not conditional on them (which
448            is what the bVar slot contents represent).
449    
450    2006-07-31  Douglas Bates  <bates@R-project.org>
451    
452            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
453            function which calls the C function mer_hat_trace2.
454    
455            * man/ranef.Rd: Include description of "postVar" argument and
456            producing a caterpillar plot.
457    
458    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * NAMESPACE:    change  "correlation" to "corMatrix"
461            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
462            * R/dpoMatrix.R: ditto
463            * R/lmer.R:      ditto
464    
465    2006-07-28  Douglas Bates  <bates@R-project.org>
466    
467            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
468            RZXinv slot's contents into a separate internal function that can
469            be used in mer_hat_trace.
470    
471    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
474            via new smart
475            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
476            utility functions.
477    
478    
479    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/Csparse.R (tril, triu, band): do return *triangular* classed
482            matrices when appropriate; band() even symmetric ones.
483            (replCmat): extend to potentially all "CsparseMatrix"
484            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
485            allow subassignment for special sparse matrices.
486    
487            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
488    
489            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
490            argument; in glmer_*(): print only if(verbose).
491    
492            speed-optimize a few places by moving REAL(.) out of loops.
493    
494            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
495    
496    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
499                    since that wrongly triggers also for M[ logi , ]
500    
501            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
502            a symmetric matrix that results in a non-symmetric one.
503            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
504    
505            * R/dMatrix.R: make round(M) work as round(M, 0)
506    
507            * R/dgTMatrix.R (image): coordinate system and axis now use
508            1-based indices, not 0-based ones.
509    
510            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
511            * tests/indexing.R: test it.
512    
513            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
514            * man/isSymmetric-methods.Rd: and document it.
515    
516            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
517            * man/SparseM-conv.Rd: docu them
518    
519            * tests/other-pkgs.R: renamed from tests/graph.R and add example
520                    for 'SparseM' conversions
521    
522    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
523    
524            * R/Matrix.R (head): added head() and tail() methods.
525    
526    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * DESCRIPTION (Version): 0.995-12 released to CRAN
529    
530    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * tests/simple.R: add check for correct dsT -> dgT coercion;
533                    add check for correct printing of symmetric sparse matrices.
534    
535            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
536            for sparse symmetric matrices.
537    
538            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
539            diagonal twice.
540    
541    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
542    
543            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
544            being applied to the x slot (detected by Brian Ripley).
545    
546    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
549    
550            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
551    
552    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * src/lgCMatrix.c (lgCMatrix_diag): new function
555            * R/lgCMatrix.R (diag): for new method
556    
557            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
558                 ==> construction of illegal "*gTMatrix" via new() should
559                 now be much less easy:
560            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
561    
562            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
563                    directly.
564            * man/Matrix.Rd: documents it.
565    
566    2006-07-06  Douglas Bates  <bates@R-project.org>
567    
568            * src/pedigree.c (pedigree_inbreeding): Correction in
569            initialization.  This function is not currently being used and is
570            not fully tested.
571    
572            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
573            Introduced the glmer class.  Added code for mcmcmsamp on glmer
574            objects.  Modified validity check on pedigree objects to account
575            for nonparallel patterns of missingness of parents.
576    
577            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
578            class.
579    
580    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/pMatrix.R: coercion pMatrix -> Tsparse
583    
584    2006-06-12  Douglas Bates  <bates@R-project.org>
585    
586            * DESCRIPTION (Version): 0.995-11 released to CRAN
587    
588            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
589            the output from mcmcsamp.
590    
591  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
592    
593          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
594            of the hat matrix.
595    
596  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
599          classes.          classes.
600            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
601    
602  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
# Line 43  Line 635 
635    
636          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
637          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.
638          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
639    
640    
641  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 758 
758          * 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)
759          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
760          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
761          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
762    
763  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
# Line 370  Line 962 
962  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
965          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
966          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
967    
968  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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