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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1582, Tue Sep 19 08:03:10 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
4            symmetric and y missing in R code using %*% (cholmod_aat doesn't
5            accept a symmetric matrix).
6            * tests/group-methods.R: Uncomment test of crossprod applied to
7            lsCMatrix objects.
8    
9    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R (symmetricMatrix): add validity method (available
12            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
13    
14            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
15    
16            * tests/indexing.Rout.save:
17            * tests/indexing.R: additions, mainly for 'lsparse'
18    
19            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
20            case.
21    
22            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
23    
24    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
27                    as 'N' (1-letter - Ok?)
28    
29            * tests/group-methods.R: add test for logical + NAs
30    
31            * R/dMatrix.R ("Compare"): fix to work with NA's
32    
33            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
34    
35            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
36                    which is implemented.
37    
38    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * src/chm_common.c: coerce logical <-> double instead of
41            typecasting;  needed for "l" matrix handling in cholmod.
42    
43            * tests/other-pkgs.R (graph): small extension in "graph" checks.
44    
45            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
46            (Tsp2grNEL): other fixes needed
47    
48    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
51                    Matrices, since "lMatrix", also "lsparseM" can have NA
52            * R/ndenseMatrix.R, etc: new source files
53            * man/nsparseMatrix-classes.Rd, etc: new help files
54            * tests/: adaptions
55            * src/chm_common.c (chm_dense_to_SEXP): and others:
56                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
57            * src/Csparse.c, etc: ditto
58    
59    2006-09-11  Douglas Bates  <bates@R-project.org>
60    
61            * src/Mutils.[ch],init.c inst/include/*.h: Move the
62            alloc_d**Matrix functions to the lme4 package.
63    
64    2006-09-09  Douglas Bates  <bates@R-project.org>
65    
66            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
67            fixed
68    
69    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/lMatrix.R: new
72    
73            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
74    
75            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
76            * man/tcrossprod.Rd: ditto
77    
78    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
81            for exported functions
82            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
83            Remove partitioning algorithms for sparse matrix reordering.  The
84            copyright on the Metis code was problematic and the methods were
85            rarely used.
86            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
87            operations are now done entirely in CHOLMOD code.
88    
89    2006-09-06  Douglas Bates  <bates@R-project.org>
90    
91            * src/Mutils.h: Remove functions that are no longer used.
92    
93    2006-09-04  Douglas Bates  <bates@R-project.org>
94    
95            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
96            * src/DEPS.mkf: update
97    
98    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * created branches/Matrix-for-R-2.3.x;  on trunk: do
101            * DESCRIPTION (Version): 0.9975-0
102            (Depends): R (>= 2.4.0)
103    
104    2006-09-01  Douglas Bates  <bates@R-project.org>
105    
106            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
107    
108    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
111            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
112    
113            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
114    
115    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
118            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
119            * R/dsparseMatrix.R: ditto
120            * R/Csparse.R: ditto
121    
122    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dMatrix.R (Compare): improve availability of "<", etc
125            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
126    
127    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
130            of a 0-index which was used as 1-index (..hmm)
131    
132            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
133    
134            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
135            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
136            (.is.diagonal): ditto
137    
138            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
139    
140            * R/Matrix.R (Matrix): also work for NA data
141    
142    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
145            in all cases.
146    
147    2006-08-27  Douglas Bates  <bates@R-project.org>
148    
149            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
150            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
151    
152    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
155            subclasses of "ddenseMatrix"
156            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
157            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
158            instead of half dozen specialized ones.
159    
160    2006-08-25  Douglas Bates  <bates@R-project.org>
161    
162            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
163            <tillard@cirad.fr> - ordering standard errors to match effects.
164    
165    2006-08-24  Douglas Bates  <bates@R-project.org>
166    
167            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
168            on R_ldl.
169            * R/lCholCMatrix.R,
170            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
171            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
172            * many files in ./R and ./src: Use more general version of
173            dup_mMatrix_as_dgeMatrix to simplify method definitions.
174            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
175            dtpMatrix, dspMatrix and dppMatrix conversions.
176    
177    
178    2006-08-23  Douglas Bates  <bates@R-project.org>
179    
180            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
181            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
182            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
183            dgeMatrix_crossprod (may need to do this in other places).
184            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
185            generic and method for dsCMatrix.  Use CHOLMOD for chol().
186    
187    2006-08-22  Douglas Bates  <bates@R-project.org>
188    
189            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
190            types of classed Matrices, matrices or numeric or logical vectors.
191            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
192            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
193            to Mutils.h (as an inline) and change name to Matrix_check_class;
194            fixes in as_cholmod_factor and chm_factor_to_SEXP.
195            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
196            dsCMatrix_matrix_solve.  Comment out vestigial functions.
197            * src/Csparse.c: use diag_P and uplo_P macros.
198    
199    2006-08-21  Douglas Bates  <bates@R-project.org>
200    
201            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
202            valgrind.
203            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
204            inverses.
205            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
206            -Wall warnings.
207            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
208            Use dup_mMatrix_as_dgeMatrix.
209    
210    2006-08-20  Douglas Bates  <bates@R-project.org>
211    
212            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
213            * tests/sparseQR.R: Added
214            * man/sparseQR-class.Rd: Document methods for qr.* generics
215            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
216    
217    2006-08-19  Douglas Bates  <bates@R-project.org>
218    
219            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
220            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
221            and qr.fitted.
222            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
223            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
224    
225    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
228            the base version has no "..." argument.
229    
230            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
231    
232            * R/Matrix.R: define and
233            * NAMESPACE: export as.numeric() and as.logical() methods.
234                    Let's hope these do not badly slow down something...
235            Finally export the zapsmall() method.
236    
237    2006-08-17  Douglas Bates  <bates@R-project.org>
238    
239            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
240            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
241            * src/dtCMatrix.c :Remove code that is no longer used
242            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
243    
244    2006-08-14  Douglas Bates  <bates@R-project.org>
245    
246            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
247            Csparse_to_logical and Csparse_symmetric_to_general.
248            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
249            coercion methods between CsparseMatrix and TsparseMatrix.
250    
251    2006-08-14  Douglas Bates  <bates@R-project.org>
252    
253            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
254            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
255            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
256            possible.
257    
258    2006-08-12  Douglas Bates  <bates@R-project.org>
259    
260            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
261              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
262              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
263              generalize conversions between TsparseMatrix, CsparseMatrix,
264              denseMatrix and matrix.  Preserve triangularity property and
265              propagate Dimnames in the easy cases.
266    
267    2006-08-10  Douglas Bates  <bates@R-project.org>
268    
269            * src/lmer.c: adjust checks in glmer_init for S4SXP
270            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
271            before S4SXP but for the wrong reasons.
272    
273    2006-08-08  Douglas Bates  <bates@R-project.org>
274    
275            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
276            Later modified to return the upper triangle only.
277            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
278    
279    2006-08-07  Douglas Bates  <bates@R-project.org>
280    
281            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
282            R-level conversion to a sparse symmetric class.
283            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
284            Remove conversion to sparse symmetric classes (now done in C code).
285    
286    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
289            * man/band.Rd:  adapt the \dontshow{} unit test.
290    
291    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * DESCRIPTION (Version): 0.995-14  for CRAN
294    
295            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
296    
297            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
298            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
299    
300            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
301            * R/Tsparse.R (tril, triu, band): methods
302            * R/dgRMatrix.R (tril, ...):    ditto
303            * man/band.Rd:                  ditto
304    
305    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Matrix.R (head, tail): directly use utils:::head.matrix
308                    to be up-to-date automatically.
309    
310    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
313    
314            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
315            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
316            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
317            such that the S4 objects are always created by the current version
318            of R and 'Matrix' class definitions.
319    
320    2006-08-01  Douglas Bates  <bates@R-project.org>
321    
322            * R/lmer.R (LMEoptimize method), tests/lmer.R,
323            inst/external/test3comp.rda: Added warnings for convergence on
324            boundary and test cases.
325    
326            * src/lmer.c (mer_postVar): Modified to return the variances that
327            are marginal to the fixed effects, not conditional on them (which
328            is what the bVar slot contents represent).
329    
330    2006-07-31  Douglas Bates  <bates@R-project.org>
331    
332            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
333            function which calls the C function mer_hat_trace2.
334    
335            * man/ranef.Rd: Include description of "postVar" argument and
336            producing a caterpillar plot.
337    
338    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * NAMESPACE:    change  "correlation" to "corMatrix"
341            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
342            * R/dpoMatrix.R: ditto
343            * R/lmer.R:      ditto
344    
345    2006-07-28  Douglas Bates  <bates@R-project.org>
346    
347            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
348            RZXinv slot's contents into a separate internal function that can
349            be used in mer_hat_trace.
350    
351    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
354            via new smart
355            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
356            utility functions.
357    
358    
359    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Csparse.R (tril, triu, band): do return *triangular* classed
362            matrices when appropriate; band() even symmetric ones.
363            (replCmat): extend to potentially all "CsparseMatrix"
364            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
365            allow subassignment for special sparse matrices.
366    
367            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
368    
369            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
370            argument; in glmer_*(): print only if(verbose).
371    
372            speed-optimize a few places by moving REAL(.) out of loops.
373    
374            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
375    
376    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
379                    since that wrongly triggers also for M[ logi , ]
380    
381            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
382            a symmetric matrix that results in a non-symmetric one.
383            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
384    
385            * R/dMatrix.R: make round(M) work as round(M, 0)
386    
387            * R/dgTMatrix.R (image): coordinate system and axis now use
388            1-based indices, not 0-based ones.
389    
390            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
391            * tests/indexing.R: test it.
392    
393            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
394            * man/isSymmetric-methods.Rd: and document it.
395    
396            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
397            * man/SparseM-conv.Rd: docu them
398    
399            * tests/other-pkgs.R: renamed from tests/graph.R and add example
400                    for 'SparseM' conversions
401    
402    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
403    
404            * R/Matrix.R (head): added head() and tail() methods.
405    
406    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * DESCRIPTION (Version): 0.995-12 released to CRAN
409    
410    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * tests/simple.R: add check for correct dsT -> dgT coercion;
413                    add check for correct printing of symmetric sparse matrices.
414    
415            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
416            for sparse symmetric matrices.
417    
418            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
419            diagonal twice.
420    
421    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
422    
423            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
424            being applied to the x slot (detected by Brian Ripley).
425    
426    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
429    
430            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
431    
432    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * src/lgCMatrix.c (lgCMatrix_diag): new function
435            * R/lgCMatrix.R (diag): for new method
436    
437            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
438                 ==> construction of illegal "*gTMatrix" via new() should
439                 now be much less easy:
440            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
441    
442            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
443                    directly.
444            * man/Matrix.Rd: documents it.
445    
446    2006-07-06  Douglas Bates  <bates@R-project.org>
447    
448            * src/pedigree.c (pedigree_inbreeding): Correction in
449            initialization.  This function is not currently being used and is
450            not fully tested.
451    
452            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
453            Introduced the glmer class.  Added code for mcmcmsamp on glmer
454            objects.  Modified validity check on pedigree objects to account
455            for nonparallel patterns of missingness of parents.
456    
457            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
458            class.
459    
460    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/pMatrix.R: coercion pMatrix -> Tsparse
463    
464    2006-06-12  Douglas Bates  <bates@R-project.org>
465    
466            * DESCRIPTION (Version): 0.995-11 released to CRAN
467    
468            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
469            the output from mcmcsamp.
470    
471    2006-06-10  Douglas Bates  <bates@R-project.org>
472    
473            * R/lmer.R (simulestimate): added C code for calculating the trace
474            of the hat matrix.
475    
476    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
479            classes.
480            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
481    
482    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/dgTMatrix.R (colSums): etc. All four of
485            colSums(), rowSums(), colMeans(), rowMeans() now should work for
486            all "Matrices".
487    
488    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * R/lmer.R (panel.ci): Add a reference line at zero and a
491            background grid to the qqmath plot of ranef.lmer.
492    
493    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
496            grouping factors to be specified in the formula as (1|foo/bar).
497    
498    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
499    
500            * R/lmer.R (findbars and others): Change check of is.numeric to
501            !is.language to resolve the bug reported by Jacob Wegelin.
502    
503            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
504            code to evaluate inbreeding coefficients without calculating T,
505            based on code in Sargolzaei and Iwaisaki's paper.
506    
507    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
508    
509            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
510            generic and mer methods for isNested and denomDF. This denomDF was
511            an attempt to emulate that in lme but I don't think that makes
512            sense.  Use the trace of the hat matrix instead.
513    
514    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
517            the C code depending on a slot structure that's no longer valid.
518            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
519    
520    
521    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
522    
523            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
524            of lowerTriMatrix generic and methods to tril (also upper to triu)
525            and added a general band extractor.
526    
527    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
528    
529            * R/pedigree.R (pedigree): Replace sire and dam values outside the
530            allowable range with NAs. Added a corresponding check in the
531            validity check for the pedigree class.
532    
533            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
534            crossprod methods now inherits from symmetricMatrix.
535    
536    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
537    
538            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
539            generics lowerTriMatrix and upperTriMatrix along with methods for
540            the Csparse virtual class.  Also added a C function Csparse_band
541            that implements these methods by calling cholmod_band.
542    
543    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
546            erased when it was NULL.  This led to invalid subselections!
547    
548    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
549    
550            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
551            in method for "t" so as not to lose the unit diagonal property.
552    
553    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
554    
555            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
556            and methods.  This is now an option to the ranef method for the
557            mer class.
558    
559            * src/cs_utils.c: Ensure that the nz component is -1 for a
560            compressed column-oriented matrix.  Minor formatting cleanup.
561    
562            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
563            objects.
564    
565    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
568            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
569    
570    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
571    
572            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
573            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
574    
575            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
576            for the dtCMatrix class.
577    
578    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
579    
580            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
581            and methods for it.
582    
583    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
586            arguments, such that M %*% 1:6 now works
587            * Tests/matprod.R: test the above
588    
589    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
590    
591            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
592            the ranef.lmer class.
593    
594            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
595            methods to extract the posterior variances from the bVar slot.
596    
597    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
600            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
601    
602            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
603            * tests/simple: (extended)
604    
605            * R/sparseMatrix.R (isTriangular): now using much improved
606            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
607    
608    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
609    
610            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
611            (problem report from Franklin Parlamis).  This should be done
612            generally.
613    
614    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
615    
616            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
617            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
618            update the plot methods.
619    
620    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * R/lmer.R (resid and ranef methods):  Added methods for the
623            "residuals" and "resid" generic but only for linear mixed model
624            fits.  Changed the ranef method to return a list of data frames so
625            that the plot methods now work.
626    
627    2006-03-16  Douglas Bates  <bates@bates2>
628    
629            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
630            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
631    
632            * DESCRIPTION (Date): New release
633    
634    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
637    
638            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
639            * man/KNex.Rd: and other help files
640            * tests/*.R: several ones needed adaption
641            * inst/doc/Comparisons.Rnw: ditto
642    
643    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
646    
647            * tests/indexing.R: tests for new [<- methods for sparse matrices.
648    
649    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
652    
653            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
654    
655    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/dMatrix.R: enable things like  M [ M < 10 ]
658            * R/dgeMatrix.R: implement it
659    
660    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/AllClass.R: define "summary.mer" and "*.lmer"
663            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
664            * R/lmer.R (show): now works with summary()
665    
666    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
669            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
670                    support the above
671    
672    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
673    
674            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
675            Use glmFit$prior.weights for weights in a glmm.
676            Allow an option usePQL = FALSE to skip the PQL steps for the
677            Laplace method (and, in time, the AGQ method).
678    
679            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
680            into a separate function internal_mer_Xfactor to be able to call
681            it from internal_bhat.
682    
683    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * tests/Class+Meth.R (tstMatrixClass): function for much better
686            testing; now again of all actual classes.
687    
688            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
689                    use macros and define make_d_matrix_* and make_i_matrix_*
690                    where _i_ is for the ldense routines:
691    
692            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
693            * src/ldense.c (lsyMatrix_as_lgeMatrix):
694    
695            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
696    
697    
698    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
701                    many different kinds of matrices.
702            * R/*.R: quite a few new methods were needed for R CMD check with
703                    new Matrix().  Very good for users playing around.
704    
705    
706    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * src/dgeMatrix.c (dMatrix_validate): new
709            * src/Mutils.c (dense_nonpacked_validate): new
710    
711            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
712    
713    
714    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
715    
716            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
717    
718    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
719    
720            * DESCRIPTION (Version): 0.99-6 released to CRAN
721    
722            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
723            segfault in cases with multiple non-nested grouping factors.
724    
725    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
728                    (Depends): also on 'utils'
729    
730            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
731            * R/diagMatrix.R (Diagonal): constructor and methods for
732            diagonal matrices
733    
734            * R/ltTMatrix.R: new "minimal methods"
735    
736    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
739            all methods (and help files).
740    
741    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
744                    for case (dimn.  op  no_dimn.)
745    
746    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
747    
748            * DESCRIPTION (Version): 0.99-2  released to CRAN
749    
750    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
751    
752            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
753            by Julian Faraway.
754    
755    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * R/Auxiliaries.R (try_as): new utility
758            * R/sparseMatrix.R: use try_as() in coercion to original class
759    
760    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
763    
764    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * R/Auxiliaries.R (dimNamesCheck): added
767    
768            * R/Matrix.R (as.array), (as.vector): new
769    
770    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
773                    default.
774            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
775                    "pMatrix" now contains "sparseMatrix"
776    
777    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * tests/Class+Meth.R: new tests; t(t(m)) == m
780    
781            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
782    
783            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
784            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
785    
786            * R/dspMatrix.R: typo in "t" method
787    
788    2005-09-18  Douglas Bates  <bates@wisc.edu>
789    
790            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
791            * R/Tsparse.R: instead of R/gTMatrix.R
792            * R/Csparse.R: new
793            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
794            * src/Tsparse.c: new; many trivial methods calling cholmod_()
795            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
796                            via cholmod
797    
798    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Auxiliaries.R (non0ind): new function using new C code
801            * src/dgCMatrix.c (compressed_non_0_ij): new utility
802    
803    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
804    
805            * src/chm_common.h: header file required by all C sources that
806            call CHOLMOD functions.  It defines a cholmod_common structure
807            called 'c' whose address is passed as the last argument to
808            (virtually) every CHOLMOD function.
809    
810            * src/Pattern.c: Simple example of the use of CHOLMOD.
811    
812            * src/init.c: initialize and finalize the cholmod_common structure.
813    
814            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
815            LDL and CCOLAMD from the U. of Florida sparse matrix library.
816    
817    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * inst/test-tools.R: new file collecting the utility functions used
820                    in ./tests/*.R
821    
822            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
823            * R/Matrix.R (cbind2): methods for NULL and missing
824    
825    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
826    
827            * R/AllClass.R: new "index" class for "[" and "[<-":
828                    First cut at "symmetricMatrix" and "triangularMatrix"
829            * R/gTMatrix.R (.ind.prep): new function;
830                    Logical and character indexing now work too.
831            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
832            * tests/indexing.R: new, including *.Rout.save
833            * tests/dgTMatrix.R: new
834    
835    2005-08-29  Douglas Bates  <bates@wisc.edu>
836    
837            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
838            indicator pos not being updated.  Also enforced upper triangular
839            for symmetric case.  Need to coerce edges component of elements of
840            edge list - grr! (Why don't they define their classes cleanly?)
841    
842    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/Matrix.R:  added first "[<-" methods; not yet functional
845            * R/denseMatrix.R: ditto
846            * man/Subassign-methods.Rd: new help file for these
847    
848    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * DESCRIPTION (Version): 0.98-6
851    
852            * R/denseMatrix.R: new file for "[" fallback methods for all dense
853            matrices.
854    
855    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
858                    as( <logical>, "matrix")
859    
860            * R/pMatrix.R: coercion to "lgTMatrix"
861    
862            * R/gTMatrix.R: new virtual class to define "[" methods for.
863            * man/gTMatrix-class.Rd:
864            * General slight re-organization of where "[" methods are defined.
865              more to come.
866    
867    2005-08-18  Douglas Bates  <bates@wisc.edu>
868    
869            * DESCRIPTION (Version): 0.98-5  released to CRAN
870    
871            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
872            * .....
873    
874    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
875    
876            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
877            or glmer objects.
878    
879    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
882    
883    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
884    
885            * R/HBMM.R: finish re-writing R-only code.
886    
887    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
888    
889            * man/externalFormats.Rd: move documentation for writeHB and
890            writeMM here.
891    
892            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
893            (suggested by Paul Roecker).
894    
895            * tests/validObj.R (assertError): Comment out test that is failing
896            after recent changes in r-devel.
897    
898    
899    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/AllClass.R: intermediate virtual class "denseMatrix"
902            * man/denseMatrix-class.Rd
903            * NAMESPACE: export it, and also export
904            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
905    
906    2005-08-10  Douglas Bates  <bates@wisc.edu>
907    
908            * DESCRIPTION (Version): 0.98-3 to CRAN
909    
910            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
911            matrix_solve code (which was really, really wrong).
912    
913    2005-08-07  Douglas Bates  <bates@wisc.edu>
914    
915            * DESCRIPTION (Version): 0.98-2
916    
917            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
918    
919            * R/lmer.R (abbrvNms): new
920            * R/lmer.R (mcmcsamp): allow transformed parameters
921            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
922            for the Harwell-Boeing and the MatrixMarket formats.
923    
924    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * man/dtrMatrix-class.Rd: add examples
927            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
928    
929            * TODO: note the dtpMatrix (docu) bug
930    
931            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
932            in order to ensure that new as.matrix() is used by old functions,
933            e.g., svd(), qr(), eigen(), dist(),..;
934                  apply(), also matplot() or pairs().
935    
936    
937    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
940              add comments about 'control' / lmerControl() arguments
941    
942    2005-07-27  Douglas Bates  <bates@wisc.edu>
943    
944            * man/sleepstudy.Rd: Added the sleep data set.
945            * DESCRIPTION (Version): 0.98-1  released to CRAN
946    
947    2005-07-12  Douglas Bates  <bates@wisc.edu>
948            * man/sleepstudy.Rd: Added the sleep data set.
949    
950            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
951            .Call calls that were producing spurious output.
952    
953    2005-07-05  Douglas Bates  <bates@wisc.edu>
954    
955            * R/lmer.R (lmer): stored updated variance component estimates in
956            mer object for the generalized model.  (Bug reported by Renaud
957            Lancelot).
958    
959    2005-07-03  Douglas Bates  <bates@wisc.edu>
960    
961            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
962            unidimensional case.
963    
964    2005-06-08  Douglas Bates  <bates@wisc.edu>
965    
966            * DESCRIPTION (Version): 0.96-1
967    
968            * moved  lmer-class' R and C code moved from lme4 to here
969    
970    2005-06-04  Douglas Bates  <bates@wisc.edu>
971    
972            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
973            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
974    
975    2005-06-02  Douglas Bates  <bates@wisc.edu>
976    
977            * src/Makefile.win: Forgot to update this when Makefile changed.
978    
979    2005-05-11  Douglas Bates  <bates@wisc.edu>
980    
981            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
982            bug reported by Kurt Hornik and Michael Hahsler.
983    
984    2005-05-10  Douglas Bates  <bates@wisc.edu>
985    
986            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
987            logical sparse matrices.  These will also be used in the symbolic
988            analysis for lmer objects.
989    
990            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
991            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
992    
993    2005-05-06  Douglas Bates  <bates@wisc.edu>
994    
995            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
996            colMeans, colSums, rowMeans and rowSums.
997    
998    2005-04-18  Douglas Bates  <bates@wisc.edu>
999    
1000            * src/lgCMatrix.[ch]: code for _validate method and stub for
1001            multiplication operation.
1002    
1003            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1004            to dgetrs.
1005    
1006            * src/init.c: Fix cut-and-paste error in definition of
1007            dgeMatrix_matrix_solve
1008    
1009            * src/{many files}: Tighten code by using ALLOC_SLOT.
1010    
1011    2005-04-15  Douglas Bates  <bates@wisc.edu>
1012    
1013            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1014    
1015            * DESCRIPTION: Eliminate import of stats.
1016    
1017    
1018    2005-04-06  Douglas Bates  <bates@wisc.edu>
1019    
1020            * R/AllClass.R : add logical sparse matrix classes
1021    
1022    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * R/dgTMatrix.R: add "[" method for triplet matrices
1025            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1026    
1027    2005-03-31  Douglas Bates  <bates@wisc.edu>
1028    
1029            * DESCRIPTION (Version): release 0.95-5 to CRAN
1030    
1031            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1032            * R/sparseMatrix.R: %*%, crossprod()
1033            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1034            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1035            * src/lmer.c (lmer_fitted): fix thinko
1036    
1037    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1038    
1039            * R/AllClass.R: add two virtual sparse classes ``on top''
1040    
1041    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1042    
1043            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1044                    correspondingly fix examples and tests/ since new()
1045                    doesn't work for virtual classes.
1046    
1047    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * R/Matrix.R (as.matrix): method and one for unname()
1050            * tests/dpoMatrix.R: tests should now be less platform dependent;
1051              also run for R 2.1.0; using as.matrix()
1052    
1053    2005-03-15  Douglas Bates  <bates@wisc.edu>
1054    
1055            * R/pMatrix.R: "pMatrix" class added
1056            * ....
1057    
1058    2005-03-14  Douglas Bates  <bates@wisc.edu>
1059    
1060            * R/dtpMatrix.R: Add unpack method and an example.
1061    
1062            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1063            of general symmetric matrices and associated S4 methods.
1064    
1065    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1066            +
1067    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1070              crossprod() and "%*%" methods added; tests, too.
1071            * tests/matprod.R: new, for testing these
1072    
1073    2005-03-03  Douglas Bates  <bates@wisc.edu>
1074    
1075            * src/lmer.c (lmer_fitted): Added.
1076    
1077    2005-03-02  Douglas Bates  <bates@wisc.edu>
1078    
1079            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1080    
1081    2005-02-28  Douglas Bates  <bates@wisc.edu>
1082    
1083            * src/*.c,po/,inst/po: Internationalization and localization of
1084            the package.
1085    
1086            * src/ldl.[ch]: Removed these as their contents are referenced in the
1087            R_ldl.c file.
1088    
1089            * src/flame.[ch]: Removed these source files.
1090    
1091            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1092    
1093            * src/LU.[ch],src/init.c: absorb in factorizations
1094    
1095            * src/Mutils.h: prepare for internationalization
1096    
1097            * src/cblas.h: move the enum definitions to Mutils.h and remove
1098            this file
1099    
1100    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1103    
1104            * R/dtrMatrix.R: fix t() method
1105    
1106            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1107            * NAMESPACE: export them (and import generics from "methods")
1108            * tests/group-methods.R : and test them.
1109    
1110            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1111            border case
1112    
1113    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1114    
1115            * DESCRIPTION (Version): 0.95-2  released to CRAN
1116    
1117            * src/dgBCMatrix.c:
1118            * src/lmer.c: many changes
1119            * ...
1120    
1121    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/Matrix.R: add more sophisticated show() method.
1124    
1125    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1126    
1127            * */* : almost complete reorganization of classes.
1128    
1129    2005-01-26  Douglas Bates  <bates@wisc.edu>
1130    
1131            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1132            for the geMatrix class.
1133    
1134    2005-01-24  Douglas Bates  <bates@wisc.edu>
1135    
1136            * src/Makefile (clean): Remove *.a and *.so
1137    
1138            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1139    
1140    2005-01-23  Douglas Bates  <bates@wisc.edu>
1141    
1142            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1143            had an effect in cases with more than 2 grouping factors.
1144    
1145    2005-01-03  Douglas Bates  <bates@wisc.edu>
1146    
1147            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1148    
1149    2004-12-23  Douglas Bates  <bates@wisc.edu>
1150    
1151            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1152            and R_useDynamicSymbols (suggested by B.D.Ripley).
1153    
1154    2004-12-14  Douglas Bates  <bates@wisc.edu>
1155    
1156            * R/sscMatrix.R: Add determinant methods
1157    
1158            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1159            for tripletMatrix to matrix.
1160    
1161    2004-12-13  Douglas Bates  <bates@wisc.edu>
1162    
1163            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1164            no longer used.
1165    
1166          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1167          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1170 
1170          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1171          Fixes part but not all of #15.          Fixes part but not all of #15.
1172    
1173  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1174    
1175          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1176          scalar grouping factors corrected.          scalar grouping factors corrected.
1177    
1178  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1179    
1180          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1181    
1182  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1183    
1184          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1185          .h file can be included.          .h file can be included.
1186    
1187  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1188    
1189          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1190          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1191    
1192          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1193    
1194  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1195    
1196          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1197    
1198  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1199    
1200          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1201    
1202  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1203    
1204          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1205    
1206  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1207    
1208          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1209    
1210  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1211    
1212          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1213          routines.          routines.
1214    
1215  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1216    
1217          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1218    
1219  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1220    
1221          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1222    

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