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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1572, Sat Sep 16 22:06:45 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
4                    as 'N' (1-letter - Ok?)
5    
6            * tests/group-methods.R: add test for logical + NAs
7    
8            * R/dMatrix.R ("Compare"): fix to work with NA's
9    
10            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
11    
12            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
13                    which is implemented.
14    
15    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/chm_common.c: coerce logical <-> double instead of
18            typecasting;  needed for "l" matrix handling in cholmod.
19    
20            * tests/other-pkgs.R (graph): small extension in "graph" checks.
21    
22            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
23            (Tsp2grNEL): other fixes needed
24    
25    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
28                    Matrices, since "lMatrix", also "lsparseM" can have NA
29            * R/ndenseMatrix.R, etc: new source files
30            * man/nsparseMatrix-classes.Rd, etc: new help files
31            * tests/: adaptions
32            * src/chm_common.c (chm_dense_to_SEXP): and others:
33                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
34            * src/Csparse.c, etc: dito
35    
36    2006-09-11  Douglas Bates  <bates@R-project.org>
37    
38            * src/Mutils.[ch],init.c inst/include/*.h: Move the
39            alloc_d**Matrix functions to the lme4 package.
40    
41    2006-09-09  Douglas Bates  <bates@R-project.org>
42    
43            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
44            fixed
45    
46    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/lMatrix.R: new
49    
50            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
51    
52            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
53            * man/tcrossprod.Rd: dito
54    
55    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
58            for exported functions
59            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
60            Remove partitioning algorithms for sparse matrix reordering.  The
61            copyright on the Metis code was problematic and the methods were
62            rarely used.
63            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
64            operations are now done entirely in CHOLMOD code.
65    
66    2006-09-06  Douglas Bates  <bates@R-project.org>
67    
68            * src/Mutils.h: Remove functions that are no longer used.
69    
70    2006-09-04  Douglas Bates  <bates@R-project.org>
71    
72            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
73            * src/DEPS.mkf: update
74    
75    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * created branches/Matrix-for-R-2.3.x;  on trunk: do
78            * DESCRIPTION (Version): 0.9975-0
79            (Depends): R (>= 2.4.0)
80    
81    2006-09-01  Douglas Bates  <bates@R-project.org>
82    
83            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
84    
85    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
88            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
89    
90            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
91    
92    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
95            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
96            * R/dsparseMatrix.R: dito
97            * R/Csparse.R: dito
98    
99    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/dMatrix.R (Compare): improve availability of "<", etc
102            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
103    
104    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
107            of a 0-index which was used as 1-index (..hmm)
108    
109            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
110    
111            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
112            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
113            (.is.diagonal): dito
114    
115            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
116    
117            * R/Matrix.R (Matrix): also work for NA data
118    
119    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
122            in all cases.
123    
124    2006-08-27  Douglas Bates  <bates@R-project.org>
125    
126            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
127            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
128    
129    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
132            subclasses of "ddenseMatrix"
133            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
134            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
135            instead of half dozen specialized ones.
136    
137    2006-08-25  Douglas Bates  <bates@R-project.org>
138    
139            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
140            <tillard@cirad.fr> - ordering standard errors to match effects.
141    
142    2006-08-24  Douglas Bates  <bates@R-project.org>
143    
144            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
145            on R_ldl.
146            * R/lCholCMatrix.R,
147            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
148            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
149            * many files in ./R and ./src: Use more general version of
150            dup_mMatrix_as_dgeMatrix to simplify method definitions.
151            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
152            dtpMatrix, dspMatrix and dppMatrix conversions.
153    
154    
155    2006-08-23  Douglas Bates  <bates@R-project.org>
156    
157            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
158            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
159            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
160            dgeMatrix_crossprod (may need to do this in other places).
161            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
162            generic and method for dsCMatrix.  Use CHOLMOD for chol().
163    
164    2006-08-22  Douglas Bates  <bates@R-project.org>
165    
166            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
167            types of classed Matrices, matrices or numeric or logical vectors.
168            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
169            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
170            to Mutils.h (as an inline) and change name to Matrix_check_class;
171            fixes in as_cholmod_factor and chm_factor_to_SEXP.
172            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
173            dsCMatrix_matrix_solve.  Comment out vestigial functions.
174            * src/Csparse.c: use diag_P and uplo_P macros.
175    
176    2006-08-21  Douglas Bates  <bates@R-project.org>
177    
178            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
179            valgrind.
180            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
181            inverses.
182            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
183            -Wall warnings.
184            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
185            Use dup_mMatrix_as_dgeMatrix.
186    
187    2006-08-20  Douglas Bates  <bates@R-project.org>
188    
189            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
190            * tests/sparseQR.R: Added
191            * man/sparseQR-class.Rd: Document methods for qr.* generics
192            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
193    
194    2006-08-19  Douglas Bates  <bates@R-project.org>
195    
196            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
197            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
198            and qr.fitted.
199            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
200            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
201    
202    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
205            the base version has no "..." argument.
206    
207            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
208    
209            * R/Matrix.R: define and
210            * NAMESPACE: export as.numeric() and as.logical() methods.
211                    Let's hope these do not badly slow down something...
212            Finally export the zapsmall() method.
213    
214    2006-08-17  Douglas Bates  <bates@R-project.org>
215    
216            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
217            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
218            * src/dtCMatrix.c :Remove code that is no longer used
219            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
220    
221    2006-08-14  Douglas Bates  <bates@R-project.org>
222    
223            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
224            Csparse_to_logical and Csparse_symmetric_to_general.
225            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
226            coercion methods between CsparseMatrix and TsparseMatrix.
227    
228    2006-08-14  Douglas Bates  <bates@R-project.org>
229    
230            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
231            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
232            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
233            possible.
234    
235    2006-08-12  Douglas Bates  <bates@R-project.org>
236    
237            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
238              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
239              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
240              generalize conversions between TsparseMatrix, CsparseMatrix,
241              denseMatrix and matrix.  Preserve triangularity property and
242              propagate Dimnames in the easy cases.
243    
244    2006-08-10  Douglas Bates  <bates@R-project.org>
245    
246            * src/lmer.c: adjust checks in glmer_init for S4SXP
247            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
248            before S4SXP but for the wrong reasons.
249    
250    2006-08-08  Douglas Bates  <bates@R-project.org>
251    
252            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
253            Later modified to return the upper triangle only.
254            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
255    
256    2006-08-07  Douglas Bates  <bates@R-project.org>
257    
258            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
259            R-level conversion to a sparse symmetric class.
260            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
261            Remove conversion to sparse symmetric classes (now done in C code).
262    
263    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
266            * man/band.Rd:  adapt the \dontshow{} unit test.
267    
268    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.995-14  for CRAN
271    
272            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
273    
274            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
275            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
276    
277            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
278            * R/Tsparse.R (tril, triu, band): methods
279            * R/dgRMatrix.R (tril, ...):    ditto
280            * man/band.Rd:                  ditto
281    
282    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/Matrix.R (head, tail): directly use utils:::head.matrix
285                    to be up-to-date automatically.
286    
287    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
290    
291            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
292            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
293            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
294            such that the S4 objects are always created by the current version
295            of R and 'Matrix' class definitions.
296    
297    2006-08-01  Douglas Bates  <bates@R-project.org>
298    
299            * R/lmer.R (LMEoptimize method), tests/lmer.R,
300            inst/external/test3comp.rda: Added warnings for convergence on
301            boundary and test cases.
302    
303            * src/lmer.c (mer_postVar): Modified to return the variances that
304            are marginal to the fixed effects, not conditional on them (which
305            is what the bVar slot contents represent).
306    
307    2006-07-31  Douglas Bates  <bates@R-project.org>
308    
309            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
310            function which calls the C function mer_hat_trace2.
311    
312            * man/ranef.Rd: Include description of "postVar" argument and
313            producing a caterpillar plot.
314    
315    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * NAMESPACE:    change  "correlation" to "corMatrix"
318            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
319            * R/dpoMatrix.R: ditto
320            * R/lmer.R:      ditto
321    
322    2006-07-28  Douglas Bates  <bates@R-project.org>
323    
324            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
325            RZXinv slot's contents into a separate internal function that can
326            be used in mer_hat_trace.
327    
328    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
331            via new smart
332            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
333            utility functions.
334    
335    
336    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/Csparse.R (tril, triu, band): do return *triangular* classed
339            matrices when appropriate; band() even symmetric ones.
340            (replCmat): extend to potentially all "CsparseMatrix"
341            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
342            allow subassignment for special sparse matrices.
343    
344            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
345    
346            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
347            argument; in glmer_*(): print only if(verbose).
348    
349            speed-optimize a few places by moving REAL(.) out of loops.
350    
351            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
352    
353    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
356                    since that wrongly triggers also for M[ logi , ]
357    
358            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
359            a symmetric matrix that results in a non-symmetric one.
360            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
361    
362            * R/dMatrix.R: make round(M) work as round(M, 0)
363    
364            * R/dgTMatrix.R (image): coordinate system and axis now use
365            1-based indices, not 0-based ones.
366    
367            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
368            * tests/indexing.R: test it.
369    
370            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
371            * man/isSymmetric-methods.Rd: and document it.
372    
373            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
374            * man/SparseM-conv.Rd: docu them
375    
376            * tests/other-pkgs.R: renamed from tests/graph.R and add example
377                    for 'SparseM' conversions
378    
379    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
380    
381            * R/Matrix.R (head): added head() and tail() methods.
382    
383    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * DESCRIPTION (Version): 0.995-12 released to CRAN
386    
387    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * tests/simple.R: add check for correct dsT -> dgT coercion;
390                    add check for correct printing of symmetric sparse matrices.
391    
392            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
393            for sparse symmetric matrices.
394    
395            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
396            diagonal twice.
397    
398    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
399    
400            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
401            being applied to the x slot (detected by Brian Ripley).
402    
403    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
406    
407            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
408    
409    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * src/lgCMatrix.c (lgCMatrix_diag): new function
412            * R/lgCMatrix.R (diag): for new method
413    
414            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
415                 ==> construction of illegal "*gTMatrix" via new() should
416                 now be much less easy:
417            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
418    
419            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
420                    directly.
421            * man/Matrix.Rd: documents it.
422    
423    2006-07-06  Douglas Bates  <bates@R-project.org>
424    
425            * src/pedigree.c (pedigree_inbreeding): Correction in
426            initialization.  This function is not currently being used and is
427            not fully tested.
428    
429            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
430            Introduced the glmer class.  Added code for mcmcmsamp on glmer
431            objects.  Modified validity check on pedigree objects to account
432            for nonparallel patterns of missingness of parents.
433    
434            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
435            class.
436    
437    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/pMatrix.R: coercion pMatrix -> Tsparse
440    
441    2006-06-12  Douglas Bates  <bates@R-project.org>
442    
443            * DESCRIPTION (Version): 0.995-11 released to CRAN
444    
445            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
446            the output from mcmcsamp.
447    
448    2006-06-10  Douglas Bates  <bates@R-project.org>
449    
450            * R/lmer.R (simulestimate): added C code for calculating the trace
451            of the hat matrix.
452    
453    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
456            classes.
457            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
458    
459    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/dgTMatrix.R (colSums): etc. All four of
462            colSums(), rowSums(), colMeans(), rowMeans() now should work for
463            all "Matrices".
464    
465    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
466    
467            * R/lmer.R (panel.ci): Add a reference line at zero and a
468            background grid to the qqmath plot of ranef.lmer.
469    
470    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
471    
472            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
473            grouping factors to be specified in the formula as (1|foo/bar).
474    
475    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
476    
477            * R/lmer.R (findbars and others): Change check of is.numeric to
478            !is.language to resolve the bug reported by Jacob Wegelin.
479    
480            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
481            code to evaluate inbreeding coefficients without calculating T,
482            based on code in Sargolzaei and Iwaisaki's paper.
483    
484    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
485    
486            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
487            generic and mer methods for isNested and denomDF. This denomDF was
488            an attempt to emulate that in lme but I don't think that makes
489            sense.  Use the trace of the hat matrix instead.
490    
491    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
494            the C code depending on a slot structure that's no longer valid.
495            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
496    
497    
498    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
499    
500            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
501            of lowerTriMatrix generic and methods to tril (also upper to triu)
502            and added a general band extractor.
503    
504    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
505    
506            * R/pedigree.R (pedigree): Replace sire and dam values outside the
507            allowable range with NAs. Added a corresponding check in the
508            validity check for the pedigree class.
509    
510            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
511            crossprod methods now inherits from symmetricMatrix.
512    
513    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
516            generics lowerTriMatrix and upperTriMatrix along with methods for
517            the Csparse virtual class.  Also added a C function Csparse_band
518            that implements these methods by calling cholmod_band.
519    
520    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
523            erased when it was NULL.  This led to invalid subselections!
524    
525    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
526    
527            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
528            in method for "t" so as not to lose the unit diagonal property.
529    
530    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
531    
532            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
533            and methods.  This is now an option to the ranef method for the
534            mer class.
535    
536            * src/cs_utils.c: Ensure that the nz component is -1 for a
537            compressed column-oriented matrix.  Minor formatting cleanup.
538    
539            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
540            objects.
541    
542    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
545            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
546    
547    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
548    
549            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
550            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
551    
552            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
553            for the dtCMatrix class.
554    
555    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
556    
557            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
558            and methods for it.
559    
560    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
563            arguments, such that M %*% 1:6 now works
564            * Tests/matprod.R: test the above
565    
566    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
567    
568            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
569            the ranef.lmer class.
570    
571            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
572            methods to extract the posterior variances from the bVar slot.
573    
574    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
577            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
578    
579            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
580            * tests/simple: (extended)
581    
582            * R/sparseMatrix.R (isTriangular): now using much improved
583            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
584    
585    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
586    
587            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
588            (problem report from Franklin Parlamis).  This should be done
589            generally.
590    
591    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
592    
593            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
594            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
595            update the plot methods.
596    
597    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
598    
599            * R/lmer.R (resid and ranef methods):  Added methods for the
600            "residuals" and "resid" generic but only for linear mixed model
601            fits.  Changed the ranef method to return a list of data frames so
602            that the plot methods now work.
603    
604    2006-03-16  Douglas Bates  <bates@bates2>
605    
606            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
607            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
608    
609            * DESCRIPTION (Date): New release
610    
611    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
614    
615            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
616            * man/KNex.Rd: and other help files
617            * tests/*.R: several ones needed adaption
618            * inst/doc/Comparisons.Rnw: ditto
619    
620    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
623    
624            * tests/indexing.R: tests for new [<- methods for sparse matrices.
625    
626    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
629    
630            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
631    
632    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * R/dMatrix.R: enable things like  M [ M < 10 ]
635            * R/dgeMatrix.R: implement it
636    
637    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * R/AllClass.R: define "summary.mer" and "*.lmer"
640            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
641            * R/lmer.R (show): now works with summary()
642    
643    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
646            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
647                    support the above
648    
649    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
650    
651            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
652            Use glmFit$prior.weights for weights in a glmm.
653            Allow an option usePQL = FALSE to skip the PQL steps for the
654            Laplace method (and, in time, the AGQ method).
655    
656            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
657            into a separate function internal_mer_Xfactor to be able to call
658            it from internal_bhat.
659    
660    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * tests/Class+Meth.R (tstMatrixClass): function for much better
663            testing; now again of all actual classes.
664    
665            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
666                    use macros and define make_d_matrix_* and make_i_matrix_*
667                    where _i_ is for the ldense routines:
668    
669            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
670            * src/ldense.c (lsyMatrix_as_lgeMatrix):
671    
672            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
673    
674    
675    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
678                    many different kinds of matrices.
679            * R/*.R: quite a few new methods were needed for R CMD check with
680                    new Matrix().  Very good for users playing around.
681    
682    
683    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * src/dgeMatrix.c (dMatrix_validate): new
686            * src/Mutils.c (dense_nonpacked_validate): new
687    
688            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
689    
690    
691    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
692    
693            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
694    
695    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
696    
697            * DESCRIPTION (Version): 0.99-6 released to CRAN
698    
699            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
700            segfault in cases with multiple non-nested grouping factors.
701    
702    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
705                    (Depends): also on 'utils'
706    
707            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
708            * R/diagMatrix.R (Diagonal): constructor and methods for
709            diagonal matrices
710    
711            * R/ltTMatrix.R: new "minimal methods"
712    
713    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
716            all methods (and help files).
717    
718    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
721                    for case (dimn.  op  no_dimn.)
722    
723    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
724    
725            * DESCRIPTION (Version): 0.99-2  released to CRAN
726    
727    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
730            by Julian Faraway.
731    
732    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * R/Auxiliaries.R (try_as): new utility
735            * R/sparseMatrix.R: use try_as() in coercion to original class
736    
737    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
740    
741    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/Auxiliaries.R (dimNamesCheck): added
744    
745            * R/Matrix.R (as.array), (as.vector): new
746    
747    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
750                    default.
751            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
752                    "pMatrix" now contains "sparseMatrix"
753    
754    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * tests/Class+Meth.R: new tests; t(t(m)) == m
757    
758            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
759    
760            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
761            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
762    
763            * R/dspMatrix.R: typo in "t" method
764    
765    2005-09-18  Douglas Bates  <bates@wisc.edu>
766    
767            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
768            * R/Tsparse.R: instead of R/gTMatrix.R
769            * R/Csparse.R: new
770            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
771            * src/Tsparse.c: new; many trivial methods calling cholmod_()
772            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
773                            via cholmod
774    
775    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/Auxiliaries.R (non0ind): new function using new C code
778            * src/dgCMatrix.c (compressed_non_0_ij): new utility
779    
780    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
781    
782            * src/chm_common.h: header file required by all C sources that
783            call CHOLMOD functions.  It defines a cholmod_common structure
784            called 'c' whose address is passed as the last argument to
785            (virtually) every CHOLMOD function.
786    
787            * src/Pattern.c: Simple example of the use of CHOLMOD.
788    
789            * src/init.c: initialize and finalize the cholmod_common structure.
790    
791            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
792            LDL and CCOLAMD from the U. of Florida sparse matrix library.
793    
794    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * inst/test-tools.R: new file collecting the utility functions used
797                    in ./tests/*.R
798    
799            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
800            * R/Matrix.R (cbind2): methods for NULL and missing
801    
802    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * R/AllClass.R: new "index" class for "[" and "[<-":
805                    First cut at "symmetricMatrix" and "triangularMatrix"
806            * R/gTMatrix.R (.ind.prep): new function;
807                    Logical and character indexing now work too.
808            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
809            * tests/indexing.R: new, including *.Rout.save
810            * tests/dgTMatrix.R: new
811    
812    2005-08-29  Douglas Bates  <bates@wisc.edu>
813    
814            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
815            indicator pos not being updated.  Also enforced upper triangular
816            for symmetric case.  Need to coerce edges component of elements of
817            edge list - grr! (Why don't they define their classes cleanly?)
818    
819    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * R/Matrix.R:  added first "[<-" methods; not yet functional
822            * R/denseMatrix.R: ditto
823            * man/Subassign-methods.Rd: new help file for these
824    
825    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
826    
827            * DESCRIPTION (Version): 0.98-6
828    
829            * R/denseMatrix.R: new file for "[" fallback methods for all dense
830            matrices.
831    
832    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
835                    as( <logical>, "matrix")
836    
837            * R/pMatrix.R: coercion to "lgTMatrix"
838    
839            * R/gTMatrix.R: new virtual class to define "[" methods for.
840            * man/gTMatrix-class.Rd:
841            * General slight re-organization of where "[" methods are defined.
842              more to come.
843    
844    2005-08-18  Douglas Bates  <bates@wisc.edu>
845    
846            * DESCRIPTION (Version): 0.98-5  released to CRAN
847    
848            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
849            * .....
850    
851    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
852    
853            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
854            or glmer objects.
855    
856    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
859    
860    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
861    
862            * R/HBMM.R: finish re-writing R-only code.
863    
864    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
865    
866            * man/externalFormats.Rd: move documentation for writeHB and
867            writeMM here.
868    
869            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
870            (suggested by Paul Roecker).
871    
872            * tests/validObj.R (assertError): Comment out test that is failing
873            after recent changes in r-devel.
874    
875    
876    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * R/AllClass.R: intermediate virtual class "denseMatrix"
879            * man/denseMatrix-class.Rd
880            * NAMESPACE: export it, and also export
881            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
882    
883    2005-08-10  Douglas Bates  <bates@wisc.edu>
884    
885            * DESCRIPTION (Version): 0.98-3 to CRAN
886    
887            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
888            matrix_solve code (which was really, really wrong).
889    
890    2005-08-07  Douglas Bates  <bates@wisc.edu>
891    
892            * DESCRIPTION (Version): 0.98-2
893    
894            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
895    
896            * R/lmer.R (abbrvNms): new
897            * R/lmer.R (mcmcsamp): allow transformed parameters
898            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
899            for the Harwell-Boeing and the MatrixMarket formats.
900    
901    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * man/dtrMatrix-class.Rd: add examples
904            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
905    
906            * TODO: note the dtpMatrix (docu) bug
907    
908            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
909            in order to ensure that new as.matrix() is used by old functions,
910            e.g., svd(), qr(), eigen(), dist(),..;
911                  apply(), also matplot() or pairs().
912    
913    
914    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
917              add comments about 'control' / lmerControl() arguments
918    
919    2005-07-27  Douglas Bates  <bates@wisc.edu>
920    
921            * man/sleepstudy.Rd: Added the sleep data set.
922            * DESCRIPTION (Version): 0.98-1  released to CRAN
923    
924    2005-07-12  Douglas Bates  <bates@wisc.edu>
925            * man/sleepstudy.Rd: Added the sleep data set.
926    
927            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
928            .Call calls that were producing spurious output.
929    
930    2005-07-05  Douglas Bates  <bates@wisc.edu>
931    
932            * R/lmer.R (lmer): stored updated variance component estimates in
933            mer object for the generalized model.  (Bug reported by Renaud
934            Lancelot).
935    
936    2005-07-03  Douglas Bates  <bates@wisc.edu>
937    
938            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
939            unidimensional case.
940    
941    2005-06-08  Douglas Bates  <bates@wisc.edu>
942    
943            * DESCRIPTION (Version): 0.96-1
944    
945            * moved  lmer-class' R and C code moved from lme4 to here
946    
947    2005-06-04  Douglas Bates  <bates@wisc.edu>
948    
949            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
950            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
951    
952    2005-06-02  Douglas Bates  <bates@wisc.edu>
953    
954            * src/Makefile.win: Forgot to update this when Makefile changed.
955    
956    2005-05-11  Douglas Bates  <bates@wisc.edu>
957    
958            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
959            bug reported by Kurt Hornik and Michael Hahsler.
960    
961    2005-05-10  Douglas Bates  <bates@wisc.edu>
962    
963            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
964            logical sparse matrices.  These will also be used in the symbolic
965            analysis for lmer objects.
966    
967            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
968            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
969    
970    2005-05-06  Douglas Bates  <bates@wisc.edu>
971    
972            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
973            colMeans, colSums, rowMeans and rowSums.
974    
975    2005-04-18  Douglas Bates  <bates@wisc.edu>
976    
977            * src/lgCMatrix.[ch]: code for _validate method and stub for
978            multiplication operation.
979    
980            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
981            to dgetrs.
982    
983            * src/init.c: Fix cut-and-paste error in definition of
984            dgeMatrix_matrix_solve
985    
986            * src/{many files}: Tighten code by using ALLOC_SLOT.
987    
988    2005-04-15  Douglas Bates  <bates@wisc.edu>
989    
990            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
991    
992            * DESCRIPTION: Eliminate import of stats.
993    
994    
995    2005-04-06  Douglas Bates  <bates@wisc.edu>
996    
997            * R/AllClass.R : add logical sparse matrix classes
998    
999    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * R/dgTMatrix.R: add "[" method for triplet matrices
1002            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1003    
1004    2005-03-31  Douglas Bates  <bates@wisc.edu>
1005    
1006            * DESCRIPTION (Version): release 0.95-5 to CRAN
1007    
1008            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1009            * R/sparseMatrix.R: %*%, crossprod()
1010            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1011            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1012            * src/lmer.c (lmer_fitted): fix thinko
1013    
1014    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/AllClass.R: add two virtual sparse classes ``on top''
1017    
1018    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1021                    correspondingly fix examples and tests/ since new()
1022                    doesn't work for virtual classes.
1023    
1024    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1025    
1026            * R/Matrix.R (as.matrix): method and one for unname()
1027            * tests/dpoMatrix.R: tests should now be less platform dependent;
1028              also run for R 2.1.0; using as.matrix()
1029    
1030    2005-03-15  Douglas Bates  <bates@wisc.edu>
1031    
1032            * R/pMatrix.R: "pMatrix" class added
1033            * ....
1034    
1035    2005-03-14  Douglas Bates  <bates@wisc.edu>
1036    
1037            * R/dtpMatrix.R: Add unpack method and an example.
1038    
1039            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1040            of general symmetric matrices and associated S4 methods.
1041    
1042    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1043            +
1044    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1045    
1046            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1047              crossprod() and "%*%" methods added; tests, too.
1048            * tests/matprod.R: new, for testing these
1049    
1050    2005-03-03  Douglas Bates  <bates@wisc.edu>
1051    
1052            * src/lmer.c (lmer_fitted): Added.
1053    
1054    2005-03-02  Douglas Bates  <bates@wisc.edu>
1055    
1056            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1057    
1058    2005-02-28  Douglas Bates  <bates@wisc.edu>
1059    
1060            * src/*.c,po/,inst/po: Internationalization and localization of
1061            the package.
1062    
1063            * src/ldl.[ch]: Removed these as their contents are referenced in the
1064            R_ldl.c file.
1065    
1066            * src/flame.[ch]: Removed these source files.
1067    
1068            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1069    
1070            * src/LU.[ch],src/init.c: absorb in factorizations
1071    
1072            * src/Mutils.h: prepare for internationalization
1073    
1074            * src/cblas.h: move the enum definitions to Mutils.h and remove
1075            this file
1076    
1077    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1078    
1079            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1080    
1081            * R/dtrMatrix.R: fix t() method
1082    
1083            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1084            * NAMESPACE: export them (and import generics from "methods")
1085            * tests/group-methods.R : and test them.
1086    
1087            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1088            border case
1089    
1090    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1091    
1092            * DESCRIPTION (Version): 0.95-2  released to CRAN
1093    
1094            * src/dgBCMatrix.c:
1095            * src/lmer.c: many changes
1096            * ...
1097    
1098    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1099    
1100            * R/Matrix.R: add more sophisticated show() method.
1101    
1102    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1103    
1104            * */* : almost complete reorganization of classes.
1105    
1106    2005-01-26  Douglas Bates  <bates@wisc.edu>
1107    
1108            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1109            for the geMatrix class.
1110    
1111    2005-01-24  Douglas Bates  <bates@wisc.edu>
1112    
1113            * src/Makefile (clean): Remove *.a and *.so
1114    
1115            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1116    
1117    2005-01-23  Douglas Bates  <bates@wisc.edu>
1118    
1119            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1120            had an effect in cases with more than 2 grouping factors.
1121    
1122    2005-01-03  Douglas Bates  <bates@wisc.edu>
1123    
1124            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1125    
1126    2004-12-23  Douglas Bates  <bates@wisc.edu>
1127    
1128            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1129            and R_useDynamicSymbols (suggested by B.D.Ripley).
1130    
1131    2004-12-14  Douglas Bates  <bates@wisc.edu>
1132    
1133            * R/sscMatrix.R: Add determinant methods
1134    
1135            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1136            for tripletMatrix to matrix.
1137    
1138    2004-12-13  Douglas Bates  <bates@wisc.edu>
1139    
1140            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1141            no longer used.
1142    
1143            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1144            with dynamic allocation of scratch arrays.
1145    
1146            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1147            for multivariate random effects with multiple grouping factors.
1148            Fixes part but not all of #15.
1149    
1150    2004-12-03  Douglas Bates  <bates@wisc.edu>
1151    
1152            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1153            scalar grouping factors corrected.
1154    
1155    2004-11-29  Douglas Bates  <bates@wisc.edu>
1156    
1157            * src/bCrosstab.c: remove diag_update which is no longer used
1158    
1159    2004-11-16  Douglas Bates  <bates@wisc.edu>
1160    
1161          * 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
1162          .h file can be included.          .h file can be included.
1163    
1164  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1165    
1166          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1167          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1168    
1169          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1170    
1171  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1172    
1173          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1174    
1175  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1176    
1177          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1178    
1179  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1180    
1181          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1182    
1183  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1184    
1185          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1186    
1187  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1188    
1189          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1190          routines.          routines.
1191    
1192  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1193    
1194          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1195    
1196  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1197    
1198          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1199    

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