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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1641, Fri Oct 20 15:04:40 2006 UTC
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1    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
4            use Rprintf and R's error handling.
5    
6    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
9            * tests/matprod.R: add tests for the bug fixed.
10    
11    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
14            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
15    
16    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
17    
18            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
19    
20    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.9975-3
23    
24            * R/diagMatrix.R (bdiag): new function constructing block diagonal
25            (sparse) matrices.
26            * man/bdiag.Rd: docu + examples
27    
28            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
29    
30            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
31            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
32    
33            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
34            that result is sparse or diagonal (and not dense).
35    
36            * man/Subassign-methods.Rd: fix examples
37    
38            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
39            should always return a sparse (and not sometimes a diagonal) matrix.
40    
41    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
44    
45    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
46    
47            * DESCRIPTION (Version): 0.9975-2
48    
49            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
50    
51    2006-10-02  Douglas Bates  <bates@R-project.org>
52    
53            * tests/dg_Matrix.R: Simplify test taking into account new code.
54    
55    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
58    
59            * R/lsTMatrix.R: new files w/ missing methods
60            * R/nsTMatrix.R:  "  'for completeness'
61    
62            * tests/Class+Meth.R: a bit less 'not.ok.classes'
63    
64            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
65    
66    
67    2006-09-28  Douglas Bates  <bates@R-project.org>
68    
69            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
70            included.
71    
72            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
73            Export C-callable functions used in Zt_create in lme4.
74    
75    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * DESCRIPTION (Version): 0.9975-1
78    
79            * tests/simple.R: less checks fail; using NA, found that our
80                    kronecker() is not base-compatible with NA's.
81    
82            * R/dMatrix.R: "Compare" method now implemented for all cases
83    
84            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
85    
86            * man/dtpMatrix-class.Rd: mention length of 'x' slot
87    
88            * src/dtpMatrix.c (dtpMatrix_validate): fix check
89            * src/dspMatrix.c (dspMatrix_validate): ditto
90    
91            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
92              including coercion to [nl]tTMatrix.
93    
94            * R/diagMatrix.R (show): print a header line as for other classes.
95    
96    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/Makefile.win (SUBDIRS): fix typo
99    
100    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
103    
104    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
105    
106            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
107            symmetric and y missing in R code using %*% (cholmod_aat doesn't
108            accept a symmetric matrix).
109            * tests/group-methods.R: Uncomment test of crossprod applied to
110            lsCMatrix objects.
111    
112    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/AllClass.R (symmetricMatrix): add validity method (available
115            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
116    
117            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
118    
119            * tests/indexing.Rout.save:
120            * tests/indexing.R: additions, mainly for 'lsparse'
121    
122            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
123            case.
124    
125            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
126    
127    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
130                    as 'N' (1-letter - Ok?)
131    
132            * tests/group-methods.R: add test for logical + NAs
133    
134            * R/dMatrix.R ("Compare"): fix to work with NA's
135    
136            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
137    
138            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
139                    which is implemented.
140    
141    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/chm_common.c: coerce logical <-> double instead of
144            typecasting;  needed for "l" matrix handling in cholmod.
145    
146            * tests/other-pkgs.R (graph): small extension in "graph" checks.
147    
148            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
149            (Tsp2grNEL): other fixes needed
150    
151    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
154                    Matrices, since "lMatrix", also "lsparseM" can have NA
155            * R/ndenseMatrix.R, etc: new source files
156            * man/nsparseMatrix-classes.Rd, etc: new help files
157            * tests/: adaptions
158            * src/chm_common.c (chm_dense_to_SEXP): and others:
159                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
160            * src/Csparse.c, etc: ditto
161    
162    2006-09-11  Douglas Bates  <bates@R-project.org>
163    
164            * src/Mutils.[ch],init.c inst/include/*.h: Move the
165            alloc_d**Matrix functions to the lme4 package.
166    
167    2006-09-09  Douglas Bates  <bates@R-project.org>
168    
169            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
170            fixed
171    
172    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/lMatrix.R: new
175    
176            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
177    
178            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
179            * man/tcrossprod.Rd: ditto
180    
181    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
182    
183            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
184            for exported functions
185            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
186            Remove partitioning algorithms for sparse matrix reordering.  The
187            copyright on the Metis code was problematic and the methods were
188            rarely used.
189            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
190            operations are now done entirely in CHOLMOD code.
191    
192    2006-09-06  Douglas Bates  <bates@R-project.org>
193    
194            * src/Mutils.h: Remove functions that are no longer used.
195    
196    2006-09-04  Douglas Bates  <bates@R-project.org>
197    
198            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
199            * src/DEPS.mkf: update
200    
201    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * created branches/Matrix-for-R-2.3.x;  on trunk: do
204            * DESCRIPTION (Version): 0.9975-0
205            (Depends): R (>= 2.4.0)
206    
207    2006-09-01  Douglas Bates  <bates@R-project.org>
208    
209            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
210    
211    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
214            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
215    
216            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
217    
218    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
221            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
222            * R/dsparseMatrix.R: ditto
223            * R/Csparse.R: ditto
224    
225    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dMatrix.R (Compare): improve availability of "<", etc
228            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
229    
230    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
233            of a 0-index which was used as 1-index (..hmm)
234    
235            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
236    
237            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
238            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
239            (.is.diagonal): ditto
240    
241            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
242    
243            * R/Matrix.R (Matrix): also work for NA data
244    
245    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
248            in all cases.
249    
250    2006-08-27  Douglas Bates  <bates@R-project.org>
251    
252            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
253            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
254    
255    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
258            subclasses of "ddenseMatrix"
259            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
260            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
261            instead of half dozen specialized ones.
262    
263    2006-08-25  Douglas Bates  <bates@R-project.org>
264    
265            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
266            <tillard@cirad.fr> - ordering standard errors to match effects.
267    
268    2006-08-24  Douglas Bates  <bates@R-project.org>
269    
270            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
271            on R_ldl.
272            * R/lCholCMatrix.R,
273            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
274            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
275            * many files in ./R and ./src: Use more general version of
276            dup_mMatrix_as_dgeMatrix to simplify method definitions.
277            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
278            dtpMatrix, dspMatrix and dppMatrix conversions.
279    
280    
281    2006-08-23  Douglas Bates  <bates@R-project.org>
282    
283            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
284            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
285            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
286            dgeMatrix_crossprod (may need to do this in other places).
287            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
288            generic and method for dsCMatrix.  Use CHOLMOD for chol().
289    
290    2006-08-22  Douglas Bates  <bates@R-project.org>
291    
292            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
293            types of classed Matrices, matrices or numeric or logical vectors.
294            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
295            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
296            to Mutils.h (as an inline) and change name to Matrix_check_class;
297            fixes in as_cholmod_factor and chm_factor_to_SEXP.
298            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
299            dsCMatrix_matrix_solve.  Comment out vestigial functions.
300            * src/Csparse.c: use diag_P and uplo_P macros.
301    
302    2006-08-21  Douglas Bates  <bates@R-project.org>
303    
304            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
305            valgrind.
306            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
307            inverses.
308            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
309            -Wall warnings.
310            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
311            Use dup_mMatrix_as_dgeMatrix.
312    
313    2006-08-20  Douglas Bates  <bates@R-project.org>
314    
315            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
316            * tests/sparseQR.R: Added
317            * man/sparseQR-class.Rd: Document methods for qr.* generics
318            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
319    
320    2006-08-19  Douglas Bates  <bates@R-project.org>
321    
322            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
323            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
324            and qr.fitted.
325            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
326            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
327    
328    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
331            the base version has no "..." argument.
332    
333            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
334    
335            * R/Matrix.R: define and
336            * NAMESPACE: export as.numeric() and as.logical() methods.
337                    Let's hope these do not badly slow down something...
338            Finally export the zapsmall() method.
339    
340    2006-08-17  Douglas Bates  <bates@R-project.org>
341    
342            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
343            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
344            * src/dtCMatrix.c :Remove code that is no longer used
345            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
346    
347    2006-08-14  Douglas Bates  <bates@R-project.org>
348    
349            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
350            Csparse_to_logical and Csparse_symmetric_to_general.
351            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
352            coercion methods between CsparseMatrix and TsparseMatrix.
353    
354    2006-08-14  Douglas Bates  <bates@R-project.org>
355    
356            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
357            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
358            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
359            possible.
360    
361    2006-08-12  Douglas Bates  <bates@R-project.org>
362    
363            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
364              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
365              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
366              generalize conversions between TsparseMatrix, CsparseMatrix,
367              denseMatrix and matrix.  Preserve triangularity property and
368              propagate Dimnames in the easy cases.
369    
370    2006-08-10  Douglas Bates  <bates@R-project.org>
371    
372            * src/lmer.c: adjust checks in glmer_init for S4SXP
373            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
374            before S4SXP but for the wrong reasons.
375    
376    2006-08-08  Douglas Bates  <bates@R-project.org>
377    
378            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
379            Later modified to return the upper triangle only.
380            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
381    
382    2006-08-07  Douglas Bates  <bates@R-project.org>
383    
384            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
385            R-level conversion to a sparse symmetric class.
386            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
387            Remove conversion to sparse symmetric classes (now done in C code).
388    
389    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
392            * man/band.Rd:  adapt the \dontshow{} unit test.
393    
394    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * DESCRIPTION (Version): 0.995-14  for CRAN
397    
398            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
399    
400            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
401            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
402    
403            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
404            * R/Tsparse.R (tril, triu, band): methods
405            * R/dgRMatrix.R (tril, ...):    ditto
406            * man/band.Rd:                  ditto
407    
408    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Matrix.R (head, tail): directly use utils:::head.matrix
411                    to be up-to-date automatically.
412    
413    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
416    
417            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
418            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
419            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
420            such that the S4 objects are always created by the current version
421            of R and 'Matrix' class definitions.
422    
423    2006-08-01  Douglas Bates  <bates@R-project.org>
424    
425            * R/lmer.R (LMEoptimize method), tests/lmer.R,
426            inst/external/test3comp.rda: Added warnings for convergence on
427            boundary and test cases.
428    
429            * src/lmer.c (mer_postVar): Modified to return the variances that
430            are marginal to the fixed effects, not conditional on them (which
431            is what the bVar slot contents represent).
432    
433    2006-07-31  Douglas Bates  <bates@R-project.org>
434    
435            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
436            function which calls the C function mer_hat_trace2.
437    
438            * man/ranef.Rd: Include description of "postVar" argument and
439            producing a caterpillar plot.
440    
441    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * NAMESPACE:    change  "correlation" to "corMatrix"
444            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
445            * R/dpoMatrix.R: ditto
446            * R/lmer.R:      ditto
447    
448    2006-07-28  Douglas Bates  <bates@R-project.org>
449    
450            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
451            RZXinv slot's contents into a separate internal function that can
452            be used in mer_hat_trace.
453    
454    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
457            via new smart
458            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
459            utility functions.
460    
461    
462    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/Csparse.R (tril, triu, band): do return *triangular* classed
465            matrices when appropriate; band() even symmetric ones.
466            (replCmat): extend to potentially all "CsparseMatrix"
467            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
468            allow subassignment for special sparse matrices.
469    
470            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
471    
472            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
473            argument; in glmer_*(): print only if(verbose).
474    
475            speed-optimize a few places by moving REAL(.) out of loops.
476    
477            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
478    
479    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
482                    since that wrongly triggers also for M[ logi , ]
483    
484            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
485            a symmetric matrix that results in a non-symmetric one.
486            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
487    
488            * R/dMatrix.R: make round(M) work as round(M, 0)
489    
490            * R/dgTMatrix.R (image): coordinate system and axis now use
491            1-based indices, not 0-based ones.
492    
493            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
494            * tests/indexing.R: test it.
495    
496            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
497            * man/isSymmetric-methods.Rd: and document it.
498    
499            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
500            * man/SparseM-conv.Rd: docu them
501    
502            * tests/other-pkgs.R: renamed from tests/graph.R and add example
503                    for 'SparseM' conversions
504    
505    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
506    
507            * R/Matrix.R (head): added head() and tail() methods.
508    
509    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * DESCRIPTION (Version): 0.995-12 released to CRAN
512    
513    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * tests/simple.R: add check for correct dsT -> dgT coercion;
516                    add check for correct printing of symmetric sparse matrices.
517    
518            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
519            for sparse symmetric matrices.
520    
521            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
522            diagonal twice.
523    
524    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
525    
526            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
527            being applied to the x slot (detected by Brian Ripley).
528    
529    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
532    
533            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
534    
535    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * src/lgCMatrix.c (lgCMatrix_diag): new function
538            * R/lgCMatrix.R (diag): for new method
539    
540            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
541                 ==> construction of illegal "*gTMatrix" via new() should
542                 now be much less easy:
543            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
544    
545            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
546                    directly.
547            * man/Matrix.Rd: documents it.
548    
549    2006-07-06  Douglas Bates  <bates@R-project.org>
550    
551            * src/pedigree.c (pedigree_inbreeding): Correction in
552            initialization.  This function is not currently being used and is
553            not fully tested.
554    
555            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
556            Introduced the glmer class.  Added code for mcmcmsamp on glmer
557            objects.  Modified validity check on pedigree objects to account
558            for nonparallel patterns of missingness of parents.
559    
560            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
561            class.
562    
563    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/pMatrix.R: coercion pMatrix -> Tsparse
566    
567    2006-06-12  Douglas Bates  <bates@R-project.org>
568    
569            * DESCRIPTION (Version): 0.995-11 released to CRAN
570    
571            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
572            the output from mcmcsamp.
573    
574    2006-06-10  Douglas Bates  <bates@R-project.org>
575    
576            * R/lmer.R (simulestimate): added C code for calculating the trace
577            of the hat matrix.
578    
579    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
582            classes.
583            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
584    
585    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/dgTMatrix.R (colSums): etc. All four of
588            colSums(), rowSums(), colMeans(), rowMeans() now should work for
589            all "Matrices".
590    
591    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
592    
593            * R/lmer.R (panel.ci): Add a reference line at zero and a
594            background grid to the qqmath plot of ranef.lmer.
595    
596    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
597    
598            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
599            grouping factors to be specified in the formula as (1|foo/bar).
600    
601    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * R/lmer.R (findbars and others): Change check of is.numeric to
604            !is.language to resolve the bug reported by Jacob Wegelin.
605    
606            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
607            code to evaluate inbreeding coefficients without calculating T,
608            based on code in Sargolzaei and Iwaisaki's paper.
609    
610    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
611    
612            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
613            generic and mer methods for isNested and denomDF. This denomDF was
614            an attempt to emulate that in lme but I don't think that makes
615            sense.  Use the trace of the hat matrix instead.
616    
617    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
620            the C code depending on a slot structure that's no longer valid.
621            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
622    
623    
624    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
625    
626            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
627            of lowerTriMatrix generic and methods to tril (also upper to triu)
628            and added a general band extractor.
629    
630    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
631    
632            * R/pedigree.R (pedigree): Replace sire and dam values outside the
633            allowable range with NAs. Added a corresponding check in the
634            validity check for the pedigree class.
635    
636            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
637            crossprod methods now inherits from symmetricMatrix.
638    
639    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
642            generics lowerTriMatrix and upperTriMatrix along with methods for
643            the Csparse virtual class.  Also added a C function Csparse_band
644            that implements these methods by calling cholmod_band.
645    
646    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
649            erased when it was NULL.  This led to invalid subselections!
650    
651    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
652    
653            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
654            in method for "t" so as not to lose the unit diagonal property.
655    
656    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
657    
658            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
659            and methods.  This is now an option to the ranef method for the
660            mer class.
661    
662            * src/cs_utils.c: Ensure that the nz component is -1 for a
663            compressed column-oriented matrix.  Minor formatting cleanup.
664    
665            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
666            objects.
667    
668    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
671            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
672    
673    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
674    
675            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
676            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
677    
678            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
679            for the dtCMatrix class.
680    
681    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
684            and methods for it.
685    
686    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
689            arguments, such that M %*% 1:6 now works
690            * Tests/matprod.R: test the above
691    
692    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
693    
694            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
695            the ranef.lmer class.
696    
697            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
698            methods to extract the posterior variances from the bVar slot.
699    
700    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
703            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
704    
705            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
706            * tests/simple: (extended)
707    
708            * R/sparseMatrix.R (isTriangular): now using much improved
709            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
710    
711    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
712    
713            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
714            (problem report from Franklin Parlamis).  This should be done
715            generally.
716    
717    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
718    
719            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
720            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
721            update the plot methods.
722    
723    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
724    
725            * R/lmer.R (resid and ranef methods):  Added methods for the
726            "residuals" and "resid" generic but only for linear mixed model
727            fits.  Changed the ranef method to return a list of data frames so
728            that the plot methods now work.
729    
730    2006-03-16  Douglas Bates  <bates@bates2>
731    
732            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
733            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
734    
735            * DESCRIPTION (Date): New release
736    
737    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
740    
741            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
742            * man/KNex.Rd: and other help files
743            * tests/*.R: several ones needed adaption
744            * inst/doc/Comparisons.Rnw: ditto
745    
746    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
749    
750            * tests/indexing.R: tests for new [<- methods for sparse matrices.
751    
752    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
755    
756            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
757    
758    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/dMatrix.R: enable things like  M [ M < 10 ]
761            * R/dgeMatrix.R: implement it
762    
763    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/AllClass.R: define "summary.mer" and "*.lmer"
766            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
767            * R/lmer.R (show): now works with summary()
768    
769    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
772            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
773                    support the above
774    
775  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
776    
777          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 945 
945  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
948          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
949          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
950    
951  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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