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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1611, Mon Oct 2 17:07:16 2006 UTC
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1    2006-10-02  Douglas Bates  <bates@R-project.org>
2    
3            * tests/dg_Matrix.R: Simplify test taking into account new code.
4    
5    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
8    
9            * R/lsTMatrix.R: new files w/ missing methods
10            * R/nsTMatrix.R:  "  'for completeness'
11    
12            * tests/Class+Meth.R: a bit less 'not.ok.classes'
13    
14            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
15    
16    
17    2006-09-28  Douglas Bates  <bates@R-project.org>
18    
19            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
20            included.
21    
22            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
23            Export C-callable functions used in Zt_create in lme4.
24    
25    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * DESCRIPTION (Version): 0.9975-1
28    
29            * tests/simple.R: less checks fail; using NA, found that our
30                    kronecker() is not base-compatible with NA's.
31    
32            * R/dMatrix.R: "Compare" method now implemented for all cases
33    
34            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
35    
36            * man/dtpMatrix-class.Rd: mention length of 'x' slot
37    
38            * src/dtpMatrix.c (dtpMatrix_validate): fix check
39            * src/dspMatrix.c (dspMatrix_validate): ditto
40    
41            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
42              including coercion to [nl]tTMatrix.
43    
44            * R/diagMatrix.R (show): print a header line as for other classes.
45    
46    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * src/Makefile.win (SUBDIRS): fix typo
49    
50    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
53    
54    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
57            symmetric and y missing in R code using %*% (cholmod_aat doesn't
58            accept a symmetric matrix).
59            * tests/group-methods.R: Uncomment test of crossprod applied to
60            lsCMatrix objects.
61    
62    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (symmetricMatrix): add validity method (available
65            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
66    
67            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
68    
69            * tests/indexing.Rout.save:
70            * tests/indexing.R: additions, mainly for 'lsparse'
71    
72            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
73            case.
74    
75            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
76    
77    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
80                    as 'N' (1-letter - Ok?)
81    
82            * tests/group-methods.R: add test for logical + NAs
83    
84            * R/dMatrix.R ("Compare"): fix to work with NA's
85    
86            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
87    
88            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
89                    which is implemented.
90    
91    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * src/chm_common.c: coerce logical <-> double instead of
94            typecasting;  needed for "l" matrix handling in cholmod.
95    
96            * tests/other-pkgs.R (graph): small extension in "graph" checks.
97    
98            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
99            (Tsp2grNEL): other fixes needed
100    
101    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
104                    Matrices, since "lMatrix", also "lsparseM" can have NA
105            * R/ndenseMatrix.R, etc: new source files
106            * man/nsparseMatrix-classes.Rd, etc: new help files
107            * tests/: adaptions
108            * src/chm_common.c (chm_dense_to_SEXP): and others:
109                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
110            * src/Csparse.c, etc: ditto
111    
112    2006-09-11  Douglas Bates  <bates@R-project.org>
113    
114            * src/Mutils.[ch],init.c inst/include/*.h: Move the
115            alloc_d**Matrix functions to the lme4 package.
116    
117    2006-09-09  Douglas Bates  <bates@R-project.org>
118    
119            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
120            fixed
121    
122    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/lMatrix.R: new
125    
126            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
127    
128            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
129            * man/tcrossprod.Rd: ditto
130    
131    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
134            for exported functions
135            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
136            Remove partitioning algorithms for sparse matrix reordering.  The
137            copyright on the Metis code was problematic and the methods were
138            rarely used.
139            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
140            operations are now done entirely in CHOLMOD code.
141    
142    2006-09-06  Douglas Bates  <bates@R-project.org>
143    
144            * src/Mutils.h: Remove functions that are no longer used.
145    
146    2006-09-04  Douglas Bates  <bates@R-project.org>
147    
148            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
149            * src/DEPS.mkf: update
150    
151    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * created branches/Matrix-for-R-2.3.x;  on trunk: do
154            * DESCRIPTION (Version): 0.9975-0
155            (Depends): R (>= 2.4.0)
156    
157    2006-09-01  Douglas Bates  <bates@R-project.org>
158    
159            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
160    
161    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
164            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
165    
166            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
167    
168    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
171            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
172            * R/dsparseMatrix.R: ditto
173            * R/Csparse.R: ditto
174    
175    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/dMatrix.R (Compare): improve availability of "<", etc
178            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
179    
180    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
183            of a 0-index which was used as 1-index (..hmm)
184    
185            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
186    
187            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
188            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
189            (.is.diagonal): ditto
190    
191            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
192    
193            * R/Matrix.R (Matrix): also work for NA data
194    
195    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
198            in all cases.
199    
200    2006-08-27  Douglas Bates  <bates@R-project.org>
201    
202            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
203            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
204    
205    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
208            subclasses of "ddenseMatrix"
209            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
210            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
211            instead of half dozen specialized ones.
212    
213    2006-08-25  Douglas Bates  <bates@R-project.org>
214    
215            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
216            <tillard@cirad.fr> - ordering standard errors to match effects.
217    
218    2006-08-24  Douglas Bates  <bates@R-project.org>
219    
220            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
221            on R_ldl.
222            * R/lCholCMatrix.R,
223            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
224            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
225            * many files in ./R and ./src: Use more general version of
226            dup_mMatrix_as_dgeMatrix to simplify method definitions.
227            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
228            dtpMatrix, dspMatrix and dppMatrix conversions.
229    
230    
231    2006-08-23  Douglas Bates  <bates@R-project.org>
232    
233            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
234            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
235            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
236            dgeMatrix_crossprod (may need to do this in other places).
237            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
238            generic and method for dsCMatrix.  Use CHOLMOD for chol().
239    
240    2006-08-22  Douglas Bates  <bates@R-project.org>
241    
242            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
243            types of classed Matrices, matrices or numeric or logical vectors.
244            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
245            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
246            to Mutils.h (as an inline) and change name to Matrix_check_class;
247            fixes in as_cholmod_factor and chm_factor_to_SEXP.
248            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
249            dsCMatrix_matrix_solve.  Comment out vestigial functions.
250            * src/Csparse.c: use diag_P and uplo_P macros.
251    
252    2006-08-21  Douglas Bates  <bates@R-project.org>
253    
254            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
255            valgrind.
256            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
257            inverses.
258            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
259            -Wall warnings.
260            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
261            Use dup_mMatrix_as_dgeMatrix.
262    
263    2006-08-20  Douglas Bates  <bates@R-project.org>
264    
265            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
266            * tests/sparseQR.R: Added
267            * man/sparseQR-class.Rd: Document methods for qr.* generics
268            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
269    
270    2006-08-19  Douglas Bates  <bates@R-project.org>
271    
272            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
273            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
274            and qr.fitted.
275            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
276            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
277    
278    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
281            the base version has no "..." argument.
282    
283            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
284    
285            * R/Matrix.R: define and
286            * NAMESPACE: export as.numeric() and as.logical() methods.
287                    Let's hope these do not badly slow down something...
288            Finally export the zapsmall() method.
289    
290    2006-08-17  Douglas Bates  <bates@R-project.org>
291    
292            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
293            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
294            * src/dtCMatrix.c :Remove code that is no longer used
295            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
296    
297    2006-08-14  Douglas Bates  <bates@R-project.org>
298    
299            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
300            Csparse_to_logical and Csparse_symmetric_to_general.
301            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
302            coercion methods between CsparseMatrix and TsparseMatrix.
303    
304    2006-08-14  Douglas Bates  <bates@R-project.org>
305    
306            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
307            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
308            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
309            possible.
310    
311    2006-08-12  Douglas Bates  <bates@R-project.org>
312    
313            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
314              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
315              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
316              generalize conversions between TsparseMatrix, CsparseMatrix,
317              denseMatrix and matrix.  Preserve triangularity property and
318              propagate Dimnames in the easy cases.
319    
320    2006-08-10  Douglas Bates  <bates@R-project.org>
321    
322            * src/lmer.c: adjust checks in glmer_init for S4SXP
323            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
324            before S4SXP but for the wrong reasons.
325    
326    2006-08-08  Douglas Bates  <bates@R-project.org>
327    
328            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
329            Later modified to return the upper triangle only.
330            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
331    
332    2006-08-07  Douglas Bates  <bates@R-project.org>
333    
334            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
335            R-level conversion to a sparse symmetric class.
336            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
337            Remove conversion to sparse symmetric classes (now done in C code).
338    
339    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
342            * man/band.Rd:  adapt the \dontshow{} unit test.
343    
344    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.995-14  for CRAN
347    
348            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
349    
350            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
351            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
352    
353            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
354            * R/Tsparse.R (tril, triu, band): methods
355            * R/dgRMatrix.R (tril, ...):    ditto
356            * man/band.Rd:                  ditto
357    
358    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Matrix.R (head, tail): directly use utils:::head.matrix
361                    to be up-to-date automatically.
362    
363    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
366    
367            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
368            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
369            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
370            such that the S4 objects are always created by the current version
371            of R and 'Matrix' class definitions.
372    
373    2006-08-01  Douglas Bates  <bates@R-project.org>
374    
375            * R/lmer.R (LMEoptimize method), tests/lmer.R,
376            inst/external/test3comp.rda: Added warnings for convergence on
377            boundary and test cases.
378    
379            * src/lmer.c (mer_postVar): Modified to return the variances that
380            are marginal to the fixed effects, not conditional on them (which
381            is what the bVar slot contents represent).
382    
383    2006-07-31  Douglas Bates  <bates@R-project.org>
384    
385            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
386            function which calls the C function mer_hat_trace2.
387    
388            * man/ranef.Rd: Include description of "postVar" argument and
389            producing a caterpillar plot.
390    
391    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * NAMESPACE:    change  "correlation" to "corMatrix"
394            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
395            * R/dpoMatrix.R: ditto
396            * R/lmer.R:      ditto
397    
398    2006-07-28  Douglas Bates  <bates@R-project.org>
399    
400            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
401            RZXinv slot's contents into a separate internal function that can
402            be used in mer_hat_trace.
403    
404    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
407            via new smart
408            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
409            utility functions.
410    
411    
412    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/Csparse.R (tril, triu, band): do return *triangular* classed
415            matrices when appropriate; band() even symmetric ones.
416            (replCmat): extend to potentially all "CsparseMatrix"
417            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
418            allow subassignment for special sparse matrices.
419    
420            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
421    
422            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
423            argument; in glmer_*(): print only if(verbose).
424    
425            speed-optimize a few places by moving REAL(.) out of loops.
426    
427            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
428    
429    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
432                    since that wrongly triggers also for M[ logi , ]
433    
434            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
435            a symmetric matrix that results in a non-symmetric one.
436            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
437    
438            * R/dMatrix.R: make round(M) work as round(M, 0)
439    
440            * R/dgTMatrix.R (image): coordinate system and axis now use
441            1-based indices, not 0-based ones.
442    
443            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
444            * tests/indexing.R: test it.
445    
446            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
447            * man/isSymmetric-methods.Rd: and document it.
448    
449            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
450            * man/SparseM-conv.Rd: docu them
451    
452            * tests/other-pkgs.R: renamed from tests/graph.R and add example
453                    for 'SparseM' conversions
454    
455    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
456    
457            * R/Matrix.R (head): added head() and tail() methods.
458    
459    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * DESCRIPTION (Version): 0.995-12 released to CRAN
462    
463    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * tests/simple.R: add check for correct dsT -> dgT coercion;
466                    add check for correct printing of symmetric sparse matrices.
467    
468            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
469            for sparse symmetric matrices.
470    
471            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
472            diagonal twice.
473    
474    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
475    
476            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
477            being applied to the x slot (detected by Brian Ripley).
478    
479    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
482    
483            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
484    
485    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * src/lgCMatrix.c (lgCMatrix_diag): new function
488            * R/lgCMatrix.R (diag): for new method
489    
490            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
491                 ==> construction of illegal "*gTMatrix" via new() should
492                 now be much less easy:
493            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
494    
495            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
496                    directly.
497            * man/Matrix.Rd: documents it.
498    
499    2006-07-06  Douglas Bates  <bates@R-project.org>
500    
501            * src/pedigree.c (pedigree_inbreeding): Correction in
502            initialization.  This function is not currently being used and is
503            not fully tested.
504    
505            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
506            Introduced the glmer class.  Added code for mcmcmsamp on glmer
507            objects.  Modified validity check on pedigree objects to account
508            for nonparallel patterns of missingness of parents.
509    
510            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
511            class.
512    
513    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/pMatrix.R: coercion pMatrix -> Tsparse
516    
517    2006-06-12  Douglas Bates  <bates@R-project.org>
518    
519            * DESCRIPTION (Version): 0.995-11 released to CRAN
520    
521            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
522            the output from mcmcsamp.
523    
524    2006-06-10  Douglas Bates  <bates@R-project.org>
525    
526            * R/lmer.R (simulestimate): added C code for calculating the trace
527            of the hat matrix.
528    
529    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
532            classes.
533            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
534    
535    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/dgTMatrix.R (colSums): etc. All four of
538            colSums(), rowSums(), colMeans(), rowMeans() now should work for
539            all "Matrices".
540    
541    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
542    
543            * R/lmer.R (panel.ci): Add a reference line at zero and a
544            background grid to the qqmath plot of ranef.lmer.
545    
546    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
547    
548            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
549            grouping factors to be specified in the formula as (1|foo/bar).
550    
551    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
552    
553            * R/lmer.R (findbars and others): Change check of is.numeric to
554            !is.language to resolve the bug reported by Jacob Wegelin.
555    
556            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
557            code to evaluate inbreeding coefficients without calculating T,
558            based on code in Sargolzaei and Iwaisaki's paper.
559    
560    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
561    
562            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
563            generic and mer methods for isNested and denomDF. This denomDF was
564            an attempt to emulate that in lme but I don't think that makes
565            sense.  Use the trace of the hat matrix instead.
566    
567    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
570            the C code depending on a slot structure that's no longer valid.
571            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
572    
573    
574    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
575    
576            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
577            of lowerTriMatrix generic and methods to tril (also upper to triu)
578            and added a general band extractor.
579    
580    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
581    
582            * R/pedigree.R (pedigree): Replace sire and dam values outside the
583            allowable range with NAs. Added a corresponding check in the
584            validity check for the pedigree class.
585    
586            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
587            crossprod methods now inherits from symmetricMatrix.
588    
589    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
590    
591            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
592            generics lowerTriMatrix and upperTriMatrix along with methods for
593            the Csparse virtual class.  Also added a C function Csparse_band
594            that implements these methods by calling cholmod_band.
595    
596    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
599            erased when it was NULL.  This led to invalid subselections!
600    
601    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
604            in method for "t" so as not to lose the unit diagonal property.
605    
606    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
607    
608            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
609            and methods.  This is now an option to the ranef method for the
610            mer class.
611    
612            * src/cs_utils.c: Ensure that the nz component is -1 for a
613            compressed column-oriented matrix.  Minor formatting cleanup.
614    
615            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
616            objects.
617    
618    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
621            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
622    
623    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
624    
625            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
626            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
627    
628            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
629            for the dtCMatrix class.
630    
631    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
632    
633            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
634            and methods for it.
635    
636    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
639            arguments, such that M %*% 1:6 now works
640            * Tests/matprod.R: test the above
641    
642    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
643    
644            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
645            the ranef.lmer class.
646    
647            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
648            methods to extract the posterior variances from the bVar slot.
649    
650    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
653            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
654    
655            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
656            * tests/simple: (extended)
657    
658            * R/sparseMatrix.R (isTriangular): now using much improved
659            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
660    
661    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
662    
663            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
664            (problem report from Franklin Parlamis).  This should be done
665            generally.
666    
667    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
670            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
671            update the plot methods.
672    
673    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
674    
675            * R/lmer.R (resid and ranef methods):  Added methods for the
676            "residuals" and "resid" generic but only for linear mixed model
677            fits.  Changed the ranef method to return a list of data frames so
678            that the plot methods now work.
679    
680    2006-03-16  Douglas Bates  <bates@bates2>
681    
682            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
683            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
684    
685            * DESCRIPTION (Date): New release
686    
687    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
690    
691            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
692            * man/KNex.Rd: and other help files
693            * tests/*.R: several ones needed adaption
694            * inst/doc/Comparisons.Rnw: ditto
695    
696    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
699    
700            * tests/indexing.R: tests for new [<- methods for sparse matrices.
701    
702    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
705    
706            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
707    
708    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/dMatrix.R: enable things like  M [ M < 10 ]
711            * R/dgeMatrix.R: implement it
712    
713    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/AllClass.R: define "summary.mer" and "*.lmer"
716            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
717            * R/lmer.R (show): now works with summary()
718    
719    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
722            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
723                    support the above
724    
725  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
726    
727          * 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 895 
895  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
898          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
899          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
900    
901  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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