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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1595, Thu Sep 28 22:32:23 2006 UTC
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1    2006-09-28  Douglas Bates  <bates@R-project.org>
2    
3            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
4            included.
5    
6            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
7            Export C-callable functions used in Zt_create in lme4.
8    
9    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * DESCRIPTION (Version): 0.9975-1
12    
13            * tests/simple.R: less checks fail; using NA, found that our
14                    kronecker() is not base-compatible with NA's.
15    
16            * R/dMatrix.R: "Compare" method now implemented for all cases
17    
18            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
19    
20            * man/dtpMatrix-class.Rd: mention length of 'x' slot
21    
22            * src/dtpMatrix.c (dtpMatrix_validate): fix check
23            * src/dspMatrix.c (dspMatrix_validate): ditto
24    
25            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
26              including coercion to [nl]tTMatrix.
27    
28            * R/diagMatrix.R (show): print a header line as for other classes.
29    
30    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * src/Makefile.win (SUBDIRS): fix typo
33    
34    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
37    
38    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
41            symmetric and y missing in R code using %*% (cholmod_aat doesn't
42            accept a symmetric matrix).
43            * tests/group-methods.R: Uncomment test of crossprod applied to
44            lsCMatrix objects.
45    
46    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/AllClass.R (symmetricMatrix): add validity method (available
49            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
50    
51            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
52    
53            * tests/indexing.Rout.save:
54            * tests/indexing.R: additions, mainly for 'lsparse'
55    
56            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
57            case.
58    
59            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
60    
61    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
64                    as 'N' (1-letter - Ok?)
65    
66            * tests/group-methods.R: add test for logical + NAs
67    
68            * R/dMatrix.R ("Compare"): fix to work with NA's
69    
70            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
71    
72            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
73                    which is implemented.
74    
75    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/chm_common.c: coerce logical <-> double instead of
78            typecasting;  needed for "l" matrix handling in cholmod.
79    
80            * tests/other-pkgs.R (graph): small extension in "graph" checks.
81    
82            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
83            (Tsp2grNEL): other fixes needed
84    
85    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
88                    Matrices, since "lMatrix", also "lsparseM" can have NA
89            * R/ndenseMatrix.R, etc: new source files
90            * man/nsparseMatrix-classes.Rd, etc: new help files
91            * tests/: adaptions
92            * src/chm_common.c (chm_dense_to_SEXP): and others:
93                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
94            * src/Csparse.c, etc: ditto
95    
96    2006-09-11  Douglas Bates  <bates@R-project.org>
97    
98            * src/Mutils.[ch],init.c inst/include/*.h: Move the
99            alloc_d**Matrix functions to the lme4 package.
100    
101    2006-09-09  Douglas Bates  <bates@R-project.org>
102    
103            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
104            fixed
105    
106    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/lMatrix.R: new
109    
110            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
111    
112            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
113            * man/tcrossprod.Rd: ditto
114    
115    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
118            for exported functions
119            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
120            Remove partitioning algorithms for sparse matrix reordering.  The
121            copyright on the Metis code was problematic and the methods were
122            rarely used.
123            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
124            operations are now done entirely in CHOLMOD code.
125    
126    2006-09-06  Douglas Bates  <bates@R-project.org>
127    
128            * src/Mutils.h: Remove functions that are no longer used.
129    
130    2006-09-04  Douglas Bates  <bates@R-project.org>
131    
132            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
133            * src/DEPS.mkf: update
134    
135    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * created branches/Matrix-for-R-2.3.x;  on trunk: do
138            * DESCRIPTION (Version): 0.9975-0
139            (Depends): R (>= 2.4.0)
140    
141    2006-09-01  Douglas Bates  <bates@R-project.org>
142    
143            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
144    
145    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
148            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
149    
150            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
151    
152    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
155            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
156            * R/dsparseMatrix.R: ditto
157            * R/Csparse.R: ditto
158    
159    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/dMatrix.R (Compare): improve availability of "<", etc
162            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
163    
164    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
167            of a 0-index which was used as 1-index (..hmm)
168    
169            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
170    
171            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
172            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
173            (.is.diagonal): ditto
174    
175            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
176    
177            * R/Matrix.R (Matrix): also work for NA data
178    
179    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
182            in all cases.
183    
184    2006-08-27  Douglas Bates  <bates@R-project.org>
185    
186            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
187            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
188    
189    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
192            subclasses of "ddenseMatrix"
193            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
194            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
195            instead of half dozen specialized ones.
196    
197    2006-08-25  Douglas Bates  <bates@R-project.org>
198    
199            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
200            <tillard@cirad.fr> - ordering standard errors to match effects.
201    
202    2006-08-24  Douglas Bates  <bates@R-project.org>
203    
204            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
205            on R_ldl.
206            * R/lCholCMatrix.R,
207            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
208            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
209            * many files in ./R and ./src: Use more general version of
210            dup_mMatrix_as_dgeMatrix to simplify method definitions.
211            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
212            dtpMatrix, dspMatrix and dppMatrix conversions.
213    
214    
215    2006-08-23  Douglas Bates  <bates@R-project.org>
216    
217            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
218            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
219            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
220            dgeMatrix_crossprod (may need to do this in other places).
221            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
222            generic and method for dsCMatrix.  Use CHOLMOD for chol().
223    
224    2006-08-22  Douglas Bates  <bates@R-project.org>
225    
226            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
227            types of classed Matrices, matrices or numeric or logical vectors.
228            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
229            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
230            to Mutils.h (as an inline) and change name to Matrix_check_class;
231            fixes in as_cholmod_factor and chm_factor_to_SEXP.
232            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
233            dsCMatrix_matrix_solve.  Comment out vestigial functions.
234            * src/Csparse.c: use diag_P and uplo_P macros.
235    
236    2006-08-21  Douglas Bates  <bates@R-project.org>
237    
238            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
239            valgrind.
240            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
241            inverses.
242            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
243            -Wall warnings.
244            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
245            Use dup_mMatrix_as_dgeMatrix.
246    
247    2006-08-20  Douglas Bates  <bates@R-project.org>
248    
249            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
250            * tests/sparseQR.R: Added
251            * man/sparseQR-class.Rd: Document methods for qr.* generics
252            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
253    
254    2006-08-19  Douglas Bates  <bates@R-project.org>
255    
256            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
257            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
258            and qr.fitted.
259            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
260            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
261    
262    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
265            the base version has no "..." argument.
266    
267            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
268    
269            * R/Matrix.R: define and
270            * NAMESPACE: export as.numeric() and as.logical() methods.
271                    Let's hope these do not badly slow down something...
272            Finally export the zapsmall() method.
273    
274    2006-08-17  Douglas Bates  <bates@R-project.org>
275    
276            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
277            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
278            * src/dtCMatrix.c :Remove code that is no longer used
279            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
280    
281    2006-08-14  Douglas Bates  <bates@R-project.org>
282    
283            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
284            Csparse_to_logical and Csparse_symmetric_to_general.
285            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
286            coercion methods between CsparseMatrix and TsparseMatrix.
287    
288    2006-08-14  Douglas Bates  <bates@R-project.org>
289    
290            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
291            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
292            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
293            possible.
294    
295    2006-08-12  Douglas Bates  <bates@R-project.org>
296    
297            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
298              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
299              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
300              generalize conversions between TsparseMatrix, CsparseMatrix,
301              denseMatrix and matrix.  Preserve triangularity property and
302              propagate Dimnames in the easy cases.
303    
304    2006-08-10  Douglas Bates  <bates@R-project.org>
305    
306            * src/lmer.c: adjust checks in glmer_init for S4SXP
307            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
308            before S4SXP but for the wrong reasons.
309    
310    2006-08-08  Douglas Bates  <bates@R-project.org>
311    
312            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
313            Later modified to return the upper triangle only.
314            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
315    
316    2006-08-07  Douglas Bates  <bates@R-project.org>
317    
318            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
319            R-level conversion to a sparse symmetric class.
320            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
321            Remove conversion to sparse symmetric classes (now done in C code).
322    
323    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
326            * man/band.Rd:  adapt the \dontshow{} unit test.
327    
328    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * DESCRIPTION (Version): 0.995-14  for CRAN
331    
332            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
333    
334            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
335            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
336    
337            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
338            * R/Tsparse.R (tril, triu, band): methods
339            * R/dgRMatrix.R (tril, ...):    ditto
340            * man/band.Rd:                  ditto
341    
342    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Matrix.R (head, tail): directly use utils:::head.matrix
345                    to be up-to-date automatically.
346    
347    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
350    
351            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
352            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
353            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
354            such that the S4 objects are always created by the current version
355            of R and 'Matrix' class definitions.
356    
357    2006-08-01  Douglas Bates  <bates@R-project.org>
358    
359            * R/lmer.R (LMEoptimize method), tests/lmer.R,
360            inst/external/test3comp.rda: Added warnings for convergence on
361            boundary and test cases.
362    
363            * src/lmer.c (mer_postVar): Modified to return the variances that
364            are marginal to the fixed effects, not conditional on them (which
365            is what the bVar slot contents represent).
366    
367    2006-07-31  Douglas Bates  <bates@R-project.org>
368    
369            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
370            function which calls the C function mer_hat_trace2.
371    
372            * man/ranef.Rd: Include description of "postVar" argument and
373            producing a caterpillar plot.
374    
375    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * NAMESPACE:    change  "correlation" to "corMatrix"
378            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
379            * R/dpoMatrix.R: ditto
380            * R/lmer.R:      ditto
381    
382    2006-07-28  Douglas Bates  <bates@R-project.org>
383    
384            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
385            RZXinv slot's contents into a separate internal function that can
386            be used in mer_hat_trace.
387    
388    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
391            via new smart
392            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
393            utility functions.
394    
395    
396    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/Csparse.R (tril, triu, band): do return *triangular* classed
399            matrices when appropriate; band() even symmetric ones.
400            (replCmat): extend to potentially all "CsparseMatrix"
401            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
402            allow subassignment for special sparse matrices.
403    
404            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
405    
406            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
407            argument; in glmer_*(): print only if(verbose).
408    
409            speed-optimize a few places by moving REAL(.) out of loops.
410    
411            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
412    
413    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
416                    since that wrongly triggers also for M[ logi , ]
417    
418            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
419            a symmetric matrix that results in a non-symmetric one.
420            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
421    
422            * R/dMatrix.R: make round(M) work as round(M, 0)
423    
424            * R/dgTMatrix.R (image): coordinate system and axis now use
425            1-based indices, not 0-based ones.
426    
427            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
428            * tests/indexing.R: test it.
429    
430            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
431            * man/isSymmetric-methods.Rd: and document it.
432    
433            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
434            * man/SparseM-conv.Rd: docu them
435    
436            * tests/other-pkgs.R: renamed from tests/graph.R and add example
437                    for 'SparseM' conversions
438    
439    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
440    
441            * R/Matrix.R (head): added head() and tail() methods.
442    
443    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * DESCRIPTION (Version): 0.995-12 released to CRAN
446    
447    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * tests/simple.R: add check for correct dsT -> dgT coercion;
450                    add check for correct printing of symmetric sparse matrices.
451    
452            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
453            for sparse symmetric matrices.
454    
455            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
456            diagonal twice.
457    
458    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
459    
460            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
461            being applied to the x slot (detected by Brian Ripley).
462    
463    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
466    
467            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
468    
469    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * src/lgCMatrix.c (lgCMatrix_diag): new function
472            * R/lgCMatrix.R (diag): for new method
473    
474            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
475                 ==> construction of illegal "*gTMatrix" via new() should
476                 now be much less easy:
477            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
478    
479            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
480                    directly.
481            * man/Matrix.Rd: documents it.
482    
483    2006-07-06  Douglas Bates  <bates@R-project.org>
484    
485            * src/pedigree.c (pedigree_inbreeding): Correction in
486            initialization.  This function is not currently being used and is
487            not fully tested.
488    
489            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
490            Introduced the glmer class.  Added code for mcmcmsamp on glmer
491            objects.  Modified validity check on pedigree objects to account
492            for nonparallel patterns of missingness of parents.
493    
494            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
495            class.
496    
497    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * R/pMatrix.R: coercion pMatrix -> Tsparse
500    
501    2006-06-12  Douglas Bates  <bates@R-project.org>
502    
503            * DESCRIPTION (Version): 0.995-11 released to CRAN
504    
505            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
506            the output from mcmcsamp.
507    
508    2006-06-10  Douglas Bates  <bates@R-project.org>
509    
510            * R/lmer.R (simulestimate): added C code for calculating the trace
511            of the hat matrix.
512    
513    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
516            classes.
517            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
518    
519    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/dgTMatrix.R (colSums): etc. All four of
522            colSums(), rowSums(), colMeans(), rowMeans() now should work for
523            all "Matrices".
524    
525    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
526    
527            * R/lmer.R (panel.ci): Add a reference line at zero and a
528            background grid to the qqmath plot of ranef.lmer.
529    
530    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
531    
532            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
533            grouping factors to be specified in the formula as (1|foo/bar).
534    
535    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
536    
537            * R/lmer.R (findbars and others): Change check of is.numeric to
538            !is.language to resolve the bug reported by Jacob Wegelin.
539    
540            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
541            code to evaluate inbreeding coefficients without calculating T,
542            based on code in Sargolzaei and Iwaisaki's paper.
543    
544    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
545    
546            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
547            generic and mer methods for isNested and denomDF. This denomDF was
548            an attempt to emulate that in lme but I don't think that makes
549            sense.  Use the trace of the hat matrix instead.
550    
551    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
554            the C code depending on a slot structure that's no longer valid.
555            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
556    
557    
558    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
559    
560            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
561            of lowerTriMatrix generic and methods to tril (also upper to triu)
562            and added a general band extractor.
563    
564    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
565    
566            * R/pedigree.R (pedigree): Replace sire and dam values outside the
567            allowable range with NAs. Added a corresponding check in the
568            validity check for the pedigree class.
569    
570            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
571            crossprod methods now inherits from symmetricMatrix.
572    
573    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
574    
575            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
576            generics lowerTriMatrix and upperTriMatrix along with methods for
577            the Csparse virtual class.  Also added a C function Csparse_band
578            that implements these methods by calling cholmod_band.
579    
580    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
583            erased when it was NULL.  This led to invalid subselections!
584    
585    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
586    
587            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
588            in method for "t" so as not to lose the unit diagonal property.
589    
590    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
591    
592            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
593            and methods.  This is now an option to the ranef method for the
594            mer class.
595    
596            * src/cs_utils.c: Ensure that the nz component is -1 for a
597            compressed column-oriented matrix.  Minor formatting cleanup.
598    
599            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
600            objects.
601    
602    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
605            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
606    
607    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
608    
609            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
610            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
611    
612            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
613            for the dtCMatrix class.
614    
615    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
616    
617            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
618            and methods for it.
619    
620    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
623            arguments, such that M %*% 1:6 now works
624            * Tests/matprod.R: test the above
625    
626    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
627    
628            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
629            the ranef.lmer class.
630    
631            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
632            methods to extract the posterior variances from the bVar slot.
633    
634    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
637            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
638    
639            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
640            * tests/simple: (extended)
641    
642            * R/sparseMatrix.R (isTriangular): now using much improved
643            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
644    
645    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
646    
647            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
648            (problem report from Franklin Parlamis).  This should be done
649            generally.
650    
651    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
652    
653            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
654            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
655            update the plot methods.
656    
657    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
658    
659            * R/lmer.R (resid and ranef methods):  Added methods for the
660            "residuals" and "resid" generic but only for linear mixed model
661            fits.  Changed the ranef method to return a list of data frames so
662            that the plot methods now work.
663    
664    2006-03-16  Douglas Bates  <bates@bates2>
665    
666            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
667            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
668    
669            * DESCRIPTION (Date): New release
670    
671    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
674    
675            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
676            * man/KNex.Rd: and other help files
677            * tests/*.R: several ones needed adaption
678            * inst/doc/Comparisons.Rnw: ditto
679    
680    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
683    
684            * tests/indexing.R: tests for new [<- methods for sparse matrices.
685    
686    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
689    
690            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
691    
692    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/dMatrix.R: enable things like  M [ M < 10 ]
695            * R/dgeMatrix.R: implement it
696    
697    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/AllClass.R: define "summary.mer" and "*.lmer"
700            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
701            * R/lmer.R (show): now works with summary()
702    
703    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
706            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
707                    support the above
708    
709    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
710    
711            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
712            Use glmFit$prior.weights for weights in a glmm.
713            Allow an option usePQL = FALSE to skip the PQL steps for the
714            Laplace method (and, in time, the AGQ method).
715    
716            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
717            into a separate function internal_mer_Xfactor to be able to call
718            it from internal_bhat.
719    
720    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * tests/Class+Meth.R (tstMatrixClass): function for much better
723            testing; now again of all actual classes.
724    
725            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
726                    use macros and define make_d_matrix_* and make_i_matrix_*
727                    where _i_ is for the ldense routines:
728    
729            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
730            * src/ldense.c (lsyMatrix_as_lgeMatrix):
731    
732            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
733    
734    
735    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
738                    many different kinds of matrices.
739            * R/*.R: quite a few new methods were needed for R CMD check with
740                    new Matrix().  Very good for users playing around.
741    
742    
743    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * src/dgeMatrix.c (dMatrix_validate): new
746            * src/Mutils.c (dense_nonpacked_validate): new
747    
748            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
749    
750    
751    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
752    
753            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
754    
755    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
756    
757            * DESCRIPTION (Version): 0.99-6 released to CRAN
758    
759            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
760            segfault in cases with multiple non-nested grouping factors.
761    
762    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
765                    (Depends): also on 'utils'
766    
767            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
768            * R/diagMatrix.R (Diagonal): constructor and methods for
769            diagonal matrices
770    
771            * R/ltTMatrix.R: new "minimal methods"
772    
773    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
776            all methods (and help files).
777    
778    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
781                    for case (dimn.  op  no_dimn.)
782    
783    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
784    
785            * DESCRIPTION (Version): 0.99-2  released to CRAN
786    
787    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
788    
789            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
790            by Julian Faraway.
791    
792    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
793    
794            * R/Auxiliaries.R (try_as): new utility
795            * R/sparseMatrix.R: use try_as() in coercion to original class
796    
797    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
800    
801    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * R/Auxiliaries.R (dimNamesCheck): added
804    
805            * R/Matrix.R (as.array), (as.vector): new
806    
807    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
810                    default.
811            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
812                    "pMatrix" now contains "sparseMatrix"
813    
814    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
815    
816            * tests/Class+Meth.R: new tests; t(t(m)) == m
817    
818            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
819    
820            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
821            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
822    
823            * R/dspMatrix.R: typo in "t" method
824    
825    2005-09-18  Douglas Bates  <bates@wisc.edu>
826    
827            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
828            * R/Tsparse.R: instead of R/gTMatrix.R
829            * R/Csparse.R: new
830            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
831            * src/Tsparse.c: new; many trivial methods calling cholmod_()
832            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
833                            via cholmod
834    
835    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * R/Auxiliaries.R (non0ind): new function using new C code
838            * src/dgCMatrix.c (compressed_non_0_ij): new utility
839    
840    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
841    
842            * src/chm_common.h: header file required by all C sources that
843            call CHOLMOD functions.  It defines a cholmod_common structure
844            called 'c' whose address is passed as the last argument to
845            (virtually) every CHOLMOD function.
846    
847            * src/Pattern.c: Simple example of the use of CHOLMOD.
848    
849            * src/init.c: initialize and finalize the cholmod_common structure.
850    
851            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
852            LDL and CCOLAMD from the U. of Florida sparse matrix library.
853    
854    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * inst/test-tools.R: new file collecting the utility functions used
857                    in ./tests/*.R
858    
859            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
860            * R/Matrix.R (cbind2): methods for NULL and missing
861    
862    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/AllClass.R: new "index" class for "[" and "[<-":
865                    First cut at "symmetricMatrix" and "triangularMatrix"
866            * R/gTMatrix.R (.ind.prep): new function;
867                    Logical and character indexing now work too.
868            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
869            * tests/indexing.R: new, including *.Rout.save
870            * tests/dgTMatrix.R: new
871    
872  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
873    
874          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 879 
879  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
882          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
883          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
884    
885  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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