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revision 1165, Sat Jan 14 23:41:55 2006 UTC revision 1642, Fri Oct 20 21:08:28 2006 UTC
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1    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (corMatrix): add 'validity' check;
4                    comment out unused "LDL" class definition
5            * NAMESPACE: mention, but do not export "LDL" class
6            * R/corMatrix.R: new (simple), needed for R-devel with
7            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
8              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
9    
10    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
13            use Rprintf and R's error handling.
14    
15    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
18            * tests/matprod.R: add tests for the bug fixed.
19    
20    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
23            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
24    
25    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
26    
27            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
28    
29    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * DESCRIPTION (Version): 0.9975-3
32    
33            * R/diagMatrix.R (bdiag): new function constructing block diagonal
34            (sparse) matrices.
35            * man/bdiag.Rd: docu + examples
36    
37            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
38    
39            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
40            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
41    
42            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
43            that result is sparse or diagonal (and not dense).
44    
45            * man/Subassign-methods.Rd: fix examples
46    
47            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
48            should always return a sparse (and not sometimes a diagonal) matrix.
49    
50    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
53    
54    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * DESCRIPTION (Version): 0.9975-2
57    
58            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
59    
60    2006-10-02  Douglas Bates  <bates@R-project.org>
61    
62            * tests/dg_Matrix.R: Simplify test taking into account new code.
63    
64    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
67    
68            * R/lsTMatrix.R: new files w/ missing methods
69            * R/nsTMatrix.R:  "  'for completeness'
70    
71            * tests/Class+Meth.R: a bit less 'not.ok.classes'
72    
73            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
74    
75    
76    2006-09-28  Douglas Bates  <bates@R-project.org>
77    
78            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
79            included.
80    
81            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
82            Export C-callable functions used in Zt_create in lme4.
83    
84    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * DESCRIPTION (Version): 0.9975-1
87    
88            * tests/simple.R: less checks fail; using NA, found that our
89                    kronecker() is not base-compatible with NA's.
90    
91            * R/dMatrix.R: "Compare" method now implemented for all cases
92    
93            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
94    
95            * man/dtpMatrix-class.Rd: mention length of 'x' slot
96    
97            * src/dtpMatrix.c (dtpMatrix_validate): fix check
98            * src/dspMatrix.c (dspMatrix_validate): ditto
99    
100            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
101              including coercion to [nl]tTMatrix.
102    
103            * R/diagMatrix.R (show): print a header line as for other classes.
104    
105    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Makefile.win (SUBDIRS): fix typo
108    
109    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
112    
113    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
116            symmetric and y missing in R code using %*% (cholmod_aat doesn't
117            accept a symmetric matrix).
118            * tests/group-methods.R: Uncomment test of crossprod applied to
119            lsCMatrix objects.
120    
121    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/AllClass.R (symmetricMatrix): add validity method (available
124            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
125    
126            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
127    
128            * tests/indexing.Rout.save:
129            * tests/indexing.R: additions, mainly for 'lsparse'
130    
131            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
132            case.
133    
134            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
135    
136    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
139                    as 'N' (1-letter - Ok?)
140    
141            * tests/group-methods.R: add test for logical + NAs
142    
143            * R/dMatrix.R ("Compare"): fix to work with NA's
144    
145            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
146    
147            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
148                    which is implemented.
149    
150    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * src/chm_common.c: coerce logical <-> double instead of
153            typecasting;  needed for "l" matrix handling in cholmod.
154    
155            * tests/other-pkgs.R (graph): small extension in "graph" checks.
156    
157            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
158            (Tsp2grNEL): other fixes needed
159    
160    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
163                    Matrices, since "lMatrix", also "lsparseM" can have NA
164            * R/ndenseMatrix.R, etc: new source files
165            * man/nsparseMatrix-classes.Rd, etc: new help files
166            * tests/: adaptions
167            * src/chm_common.c (chm_dense_to_SEXP): and others:
168                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
169            * src/Csparse.c, etc: ditto
170    
171    2006-09-11  Douglas Bates  <bates@R-project.org>
172    
173            * src/Mutils.[ch],init.c inst/include/*.h: Move the
174            alloc_d**Matrix functions to the lme4 package.
175    
176    2006-09-09  Douglas Bates  <bates@R-project.org>
177    
178            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
179            fixed
180    
181    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/lMatrix.R: new
184    
185            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
186    
187            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
188            * man/tcrossprod.Rd: ditto
189    
190    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
191    
192            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
193            for exported functions
194            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
195            Remove partitioning algorithms for sparse matrix reordering.  The
196            copyright on the Metis code was problematic and the methods were
197            rarely used.
198            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
199            operations are now done entirely in CHOLMOD code.
200    
201    2006-09-06  Douglas Bates  <bates@R-project.org>
202    
203            * src/Mutils.h: Remove functions that are no longer used.
204    
205    2006-09-04  Douglas Bates  <bates@R-project.org>
206    
207            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
208            * src/DEPS.mkf: update
209    
210    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * created branches/Matrix-for-R-2.3.x;  on trunk: do
213            * DESCRIPTION (Version): 0.9975-0
214            (Depends): R (>= 2.4.0)
215    
216    2006-09-01  Douglas Bates  <bates@R-project.org>
217    
218            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
219    
220    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
223            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
224    
225            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
226    
227    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
230            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
231            * R/dsparseMatrix.R: ditto
232            * R/Csparse.R: ditto
233    
234    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/dMatrix.R (Compare): improve availability of "<", etc
237            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
238    
239    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
242            of a 0-index which was used as 1-index (..hmm)
243    
244            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
245    
246            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
247            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
248            (.is.diagonal): ditto
249    
250            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
251    
252            * R/Matrix.R (Matrix): also work for NA data
253    
254    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
257            in all cases.
258    
259    2006-08-27  Douglas Bates  <bates@R-project.org>
260    
261            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
262            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
263    
264    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
267            subclasses of "ddenseMatrix"
268            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
269            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
270            instead of half dozen specialized ones.
271    
272    2006-08-25  Douglas Bates  <bates@R-project.org>
273    
274            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
275            <tillard@cirad.fr> - ordering standard errors to match effects.
276    
277    2006-08-24  Douglas Bates  <bates@R-project.org>
278    
279            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
280            on R_ldl.
281            * R/lCholCMatrix.R,
282            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
283            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
284            * many files in ./R and ./src: Use more general version of
285            dup_mMatrix_as_dgeMatrix to simplify method definitions.
286            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
287            dtpMatrix, dspMatrix and dppMatrix conversions.
288    
289    
290    2006-08-23  Douglas Bates  <bates@R-project.org>
291    
292            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
293            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
294            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
295            dgeMatrix_crossprod (may need to do this in other places).
296            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
297            generic and method for dsCMatrix.  Use CHOLMOD for chol().
298    
299    2006-08-22  Douglas Bates  <bates@R-project.org>
300    
301            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
302            types of classed Matrices, matrices or numeric or logical vectors.
303            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
304            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
305            to Mutils.h (as an inline) and change name to Matrix_check_class;
306            fixes in as_cholmod_factor and chm_factor_to_SEXP.
307            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
308            dsCMatrix_matrix_solve.  Comment out vestigial functions.
309            * src/Csparse.c: use diag_P and uplo_P macros.
310    
311    2006-08-21  Douglas Bates  <bates@R-project.org>
312    
313            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
314            valgrind.
315            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
316            inverses.
317            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
318            -Wall warnings.
319            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
320            Use dup_mMatrix_as_dgeMatrix.
321    
322    2006-08-20  Douglas Bates  <bates@R-project.org>
323    
324            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
325            * tests/sparseQR.R: Added
326            * man/sparseQR-class.Rd: Document methods for qr.* generics
327            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
328    
329    2006-08-19  Douglas Bates  <bates@R-project.org>
330    
331            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
332            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
333            and qr.fitted.
334            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
335            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
336    
337    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
340            the base version has no "..." argument.
341    
342            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
343    
344            * R/Matrix.R: define and
345            * NAMESPACE: export as.numeric() and as.logical() methods.
346                    Let's hope these do not badly slow down something...
347            Finally export the zapsmall() method.
348    
349    2006-08-17  Douglas Bates  <bates@R-project.org>
350    
351            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
352            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
353            * src/dtCMatrix.c :Remove code that is no longer used
354            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
355    
356    2006-08-14  Douglas Bates  <bates@R-project.org>
357    
358            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
359            Csparse_to_logical and Csparse_symmetric_to_general.
360            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
361            coercion methods between CsparseMatrix and TsparseMatrix.
362    
363    2006-08-14  Douglas Bates  <bates@R-project.org>
364    
365            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
366            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
367            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
368            possible.
369    
370    2006-08-12  Douglas Bates  <bates@R-project.org>
371    
372            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
373              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
374              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
375              generalize conversions between TsparseMatrix, CsparseMatrix,
376              denseMatrix and matrix.  Preserve triangularity property and
377              propagate Dimnames in the easy cases.
378    
379    2006-08-10  Douglas Bates  <bates@R-project.org>
380    
381            * src/lmer.c: adjust checks in glmer_init for S4SXP
382            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
383            before S4SXP but for the wrong reasons.
384    
385    2006-08-08  Douglas Bates  <bates@R-project.org>
386    
387            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
388            Later modified to return the upper triangle only.
389            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
390    
391    2006-08-07  Douglas Bates  <bates@R-project.org>
392    
393            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
394            R-level conversion to a sparse symmetric class.
395            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
396            Remove conversion to sparse symmetric classes (now done in C code).
397    
398    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
401            * man/band.Rd:  adapt the \dontshow{} unit test.
402    
403    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version): 0.995-14  for CRAN
406    
407            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
408    
409            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
410            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
411    
412            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
413            * R/Tsparse.R (tril, triu, band): methods
414            * R/dgRMatrix.R (tril, ...):    ditto
415            * man/band.Rd:                  ditto
416    
417    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/Matrix.R (head, tail): directly use utils:::head.matrix
420                    to be up-to-date automatically.
421    
422    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
425    
426            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
427            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
428            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
429            such that the S4 objects are always created by the current version
430            of R and 'Matrix' class definitions.
431    
432    2006-08-01  Douglas Bates  <bates@R-project.org>
433    
434            * R/lmer.R (LMEoptimize method), tests/lmer.R,
435            inst/external/test3comp.rda: Added warnings for convergence on
436            boundary and test cases.
437    
438            * src/lmer.c (mer_postVar): Modified to return the variances that
439            are marginal to the fixed effects, not conditional on them (which
440            is what the bVar slot contents represent).
441    
442    2006-07-31  Douglas Bates  <bates@R-project.org>
443    
444            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
445            function which calls the C function mer_hat_trace2.
446    
447            * man/ranef.Rd: Include description of "postVar" argument and
448            producing a caterpillar plot.
449    
450    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * NAMESPACE:    change  "correlation" to "corMatrix"
453            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
454            * R/dpoMatrix.R: ditto
455            * R/lmer.R:      ditto
456    
457    2006-07-28  Douglas Bates  <bates@R-project.org>
458    
459            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
460            RZXinv slot's contents into a separate internal function that can
461            be used in mer_hat_trace.
462    
463    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
466            via new smart
467            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
468            utility functions.
469    
470    
471    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/Csparse.R (tril, triu, band): do return *triangular* classed
474            matrices when appropriate; band() even symmetric ones.
475            (replCmat): extend to potentially all "CsparseMatrix"
476            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
477            allow subassignment for special sparse matrices.
478    
479            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
480    
481            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
482            argument; in glmer_*(): print only if(verbose).
483    
484            speed-optimize a few places by moving REAL(.) out of loops.
485    
486            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
487    
488    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
491                    since that wrongly triggers also for M[ logi , ]
492    
493            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
494            a symmetric matrix that results in a non-symmetric one.
495            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
496    
497            * R/dMatrix.R: make round(M) work as round(M, 0)
498    
499            * R/dgTMatrix.R (image): coordinate system and axis now use
500            1-based indices, not 0-based ones.
501    
502            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
503            * tests/indexing.R: test it.
504    
505            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
506            * man/isSymmetric-methods.Rd: and document it.
507    
508            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
509            * man/SparseM-conv.Rd: docu them
510    
511            * tests/other-pkgs.R: renamed from tests/graph.R and add example
512                    for 'SparseM' conversions
513    
514    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
515    
516            * R/Matrix.R (head): added head() and tail() methods.
517    
518    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * DESCRIPTION (Version): 0.995-12 released to CRAN
521    
522    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * tests/simple.R: add check for correct dsT -> dgT coercion;
525                    add check for correct printing of symmetric sparse matrices.
526    
527            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
528            for sparse symmetric matrices.
529    
530            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
531            diagonal twice.
532    
533    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
534    
535            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
536            being applied to the x slot (detected by Brian Ripley).
537    
538    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
541    
542            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
543    
544    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * src/lgCMatrix.c (lgCMatrix_diag): new function
547            * R/lgCMatrix.R (diag): for new method
548    
549            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
550                 ==> construction of illegal "*gTMatrix" via new() should
551                 now be much less easy:
552            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
553    
554            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
555                    directly.
556            * man/Matrix.Rd: documents it.
557    
558    2006-07-06  Douglas Bates  <bates@R-project.org>
559    
560            * src/pedigree.c (pedigree_inbreeding): Correction in
561            initialization.  This function is not currently being used and is
562            not fully tested.
563    
564            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
565            Introduced the glmer class.  Added code for mcmcmsamp on glmer
566            objects.  Modified validity check on pedigree objects to account
567            for nonparallel patterns of missingness of parents.
568    
569            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
570            class.
571    
572    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/pMatrix.R: coercion pMatrix -> Tsparse
575    
576    2006-06-12  Douglas Bates  <bates@R-project.org>
577    
578            * DESCRIPTION (Version): 0.995-11 released to CRAN
579    
580            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
581            the output from mcmcsamp.
582    
583    2006-06-10  Douglas Bates  <bates@R-project.org>
584    
585            * R/lmer.R (simulestimate): added C code for calculating the trace
586            of the hat matrix.
587    
588    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
591            classes.
592            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
593    
594    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/dgTMatrix.R (colSums): etc. All four of
597            colSums(), rowSums(), colMeans(), rowMeans() now should work for
598            all "Matrices".
599    
600    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * R/lmer.R (panel.ci): Add a reference line at zero and a
603            background grid to the qqmath plot of ranef.lmer.
604    
605    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
606    
607            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
608            grouping factors to be specified in the formula as (1|foo/bar).
609    
610    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
611    
612            * R/lmer.R (findbars and others): Change check of is.numeric to
613            !is.language to resolve the bug reported by Jacob Wegelin.
614    
615            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
616            code to evaluate inbreeding coefficients without calculating T,
617            based on code in Sargolzaei and Iwaisaki's paper.
618    
619    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
620    
621            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
622            generic and mer methods for isNested and denomDF. This denomDF was
623            an attempt to emulate that in lme but I don't think that makes
624            sense.  Use the trace of the hat matrix instead.
625    
626    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
629            the C code depending on a slot structure that's no longer valid.
630            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
631    
632    
633    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
634    
635            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
636            of lowerTriMatrix generic and methods to tril (also upper to triu)
637            and added a general band extractor.
638    
639    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * R/pedigree.R (pedigree): Replace sire and dam values outside the
642            allowable range with NAs. Added a corresponding check in the
643            validity check for the pedigree class.
644    
645            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
646            crossprod methods now inherits from symmetricMatrix.
647    
648    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
649    
650            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
651            generics lowerTriMatrix and upperTriMatrix along with methods for
652            the Csparse virtual class.  Also added a C function Csparse_band
653            that implements these methods by calling cholmod_band.
654    
655    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
658            erased when it was NULL.  This led to invalid subselections!
659    
660    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
661    
662            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
663            in method for "t" so as not to lose the unit diagonal property.
664    
665    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
666    
667            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
668            and methods.  This is now an option to the ranef method for the
669            mer class.
670    
671            * src/cs_utils.c: Ensure that the nz component is -1 for a
672            compressed column-oriented matrix.  Minor formatting cleanup.
673    
674            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
675            objects.
676    
677    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
680            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
681    
682    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
683    
684            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
685            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
686    
687            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
688            for the dtCMatrix class.
689    
690    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
691    
692            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
693            and methods for it.
694    
695    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
698            arguments, such that M %*% 1:6 now works
699            * Tests/matprod.R: test the above
700    
701    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
702    
703            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
704            the ranef.lmer class.
705    
706            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
707            methods to extract the posterior variances from the bVar slot.
708    
709    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
712            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
713    
714            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
715            * tests/simple: (extended)
716    
717            * R/sparseMatrix.R (isTriangular): now using much improved
718            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
719    
720    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
721    
722            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
723            (problem report from Franklin Parlamis).  This should be done
724            generally.
725    
726    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
727    
728            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
729            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
730            update the plot methods.
731    
732    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
733    
734            * R/lmer.R (resid and ranef methods):  Added methods for the
735            "residuals" and "resid" generic but only for linear mixed model
736            fits.  Changed the ranef method to return a list of data frames so
737            that the plot methods now work.
738    
739    2006-03-16  Douglas Bates  <bates@bates2>
740    
741            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
742            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
743    
744            * DESCRIPTION (Date): New release
745    
746    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
749    
750            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
751            * man/KNex.Rd: and other help files
752            * tests/*.R: several ones needed adaption
753            * inst/doc/Comparisons.Rnw: ditto
754    
755    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
758    
759            * tests/indexing.R: tests for new [<- methods for sparse matrices.
760    
761    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
764    
765            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
766    
767    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/dMatrix.R: enable things like  M [ M < 10 ]
770            * R/dgeMatrix.R: implement it
771    
772    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/AllClass.R: define "summary.mer" and "*.lmer"
775            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
776            * R/lmer.R (show): now works with summary()
777    
778    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
781            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
782                    support the above
783    
784    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
785    
786            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
787            Use glmFit$prior.weights for weights in a glmm.
788            Allow an option usePQL = FALSE to skip the PQL steps for the
789            Laplace method (and, in time, the AGQ method).
790    
791            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
792            into a separate function internal_mer_Xfactor to be able to call
793            it from internal_bhat.
794    
795    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * tests/Class+Meth.R (tstMatrixClass): function for much better
798            testing; now again of all actual classes.
799    
800            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
801                    use macros and define make_d_matrix_* and make_i_matrix_*
802                    where _i_ is for the ldense routines:
803    
804            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
805            * src/ldense.c (lsyMatrix_as_lgeMatrix):
806    
807            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
808    
809    
810    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
813                    many different kinds of matrices.
814            * R/*.R: quite a few new methods were needed for R CMD check with
815                    new Matrix().  Very good for users playing around.
816    
817    
818  2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820          * src/dgeMatrix.c (dMatrix_validate): new          * src/dgeMatrix.c (dMatrix_validate): new
# Line 137  Line 954 
954  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
957          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
958          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
959    
960  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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