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revision 726, Thu May 12 14:59:04 2005 UTC revision 1635, Tue Oct 17 21:21:44 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
4            * tests/matprod.R: add tests for the bug fixed.
5    
6    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
9            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
10    
11    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
14    
15    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Version): 0.9975-3
18    
19            * R/diagMatrix.R (bdiag): new function constructing block diagonal
20            (sparse) matrices.
21            * man/bdiag.Rd: docu + examples
22    
23            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
24    
25            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
26            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
27    
28            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
29            that result is sparse or diagonal (and not dense).
30    
31            * man/Subassign-methods.Rd: fix examples
32    
33            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
34            should always return a sparse (and not sometimes a diagonal) matrix.
35    
36    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
39    
40    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * DESCRIPTION (Version): 0.9975-2
43    
44            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
45    
46    2006-10-02  Douglas Bates  <bates@R-project.org>
47    
48            * tests/dg_Matrix.R: Simplify test taking into account new code.
49    
50    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
53    
54            * R/lsTMatrix.R: new files w/ missing methods
55            * R/nsTMatrix.R:  "  'for completeness'
56    
57            * tests/Class+Meth.R: a bit less 'not.ok.classes'
58    
59            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
60    
61    
62    2006-09-28  Douglas Bates  <bates@R-project.org>
63    
64            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
65            included.
66    
67            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
68            Export C-callable functions used in Zt_create in lme4.
69    
70    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Version): 0.9975-1
73    
74            * tests/simple.R: less checks fail; using NA, found that our
75                    kronecker() is not base-compatible with NA's.
76    
77            * R/dMatrix.R: "Compare" method now implemented for all cases
78    
79            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
80    
81            * man/dtpMatrix-class.Rd: mention length of 'x' slot
82    
83            * src/dtpMatrix.c (dtpMatrix_validate): fix check
84            * src/dspMatrix.c (dspMatrix_validate): ditto
85    
86            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
87              including coercion to [nl]tTMatrix.
88    
89            * R/diagMatrix.R (show): print a header line as for other classes.
90    
91    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * src/Makefile.win (SUBDIRS): fix typo
94    
95    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
98    
99    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
100    
101            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
102            symmetric and y missing in R code using %*% (cholmod_aat doesn't
103            accept a symmetric matrix).
104            * tests/group-methods.R: Uncomment test of crossprod applied to
105            lsCMatrix objects.
106    
107    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/AllClass.R (symmetricMatrix): add validity method (available
110            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
111    
112            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
113    
114            * tests/indexing.Rout.save:
115            * tests/indexing.R: additions, mainly for 'lsparse'
116    
117            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
118            case.
119    
120            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
121    
122    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
125                    as 'N' (1-letter - Ok?)
126    
127            * tests/group-methods.R: add test for logical + NAs
128    
129            * R/dMatrix.R ("Compare"): fix to work with NA's
130    
131            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
132    
133            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
134                    which is implemented.
135    
136    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/chm_common.c: coerce logical <-> double instead of
139            typecasting;  needed for "l" matrix handling in cholmod.
140    
141            * tests/other-pkgs.R (graph): small extension in "graph" checks.
142    
143            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
144            (Tsp2grNEL): other fixes needed
145    
146    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
149                    Matrices, since "lMatrix", also "lsparseM" can have NA
150            * R/ndenseMatrix.R, etc: new source files
151            * man/nsparseMatrix-classes.Rd, etc: new help files
152            * tests/: adaptions
153            * src/chm_common.c (chm_dense_to_SEXP): and others:
154                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
155            * src/Csparse.c, etc: ditto
156    
157    2006-09-11  Douglas Bates  <bates@R-project.org>
158    
159            * src/Mutils.[ch],init.c inst/include/*.h: Move the
160            alloc_d**Matrix functions to the lme4 package.
161    
162    2006-09-09  Douglas Bates  <bates@R-project.org>
163    
164            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
165            fixed
166    
167    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/lMatrix.R: new
170    
171            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
172    
173            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
174            * man/tcrossprod.Rd: ditto
175    
176    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
177    
178            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
179            for exported functions
180            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
181            Remove partitioning algorithms for sparse matrix reordering.  The
182            copyright on the Metis code was problematic and the methods were
183            rarely used.
184            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
185            operations are now done entirely in CHOLMOD code.
186    
187    2006-09-06  Douglas Bates  <bates@R-project.org>
188    
189            * src/Mutils.h: Remove functions that are no longer used.
190    
191    2006-09-04  Douglas Bates  <bates@R-project.org>
192    
193            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
194            * src/DEPS.mkf: update
195    
196    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * created branches/Matrix-for-R-2.3.x;  on trunk: do
199            * DESCRIPTION (Version): 0.9975-0
200            (Depends): R (>= 2.4.0)
201    
202    2006-09-01  Douglas Bates  <bates@R-project.org>
203    
204            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
205    
206    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
209            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
210    
211            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
212    
213    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
216            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
217            * R/dsparseMatrix.R: ditto
218            * R/Csparse.R: ditto
219    
220    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/dMatrix.R (Compare): improve availability of "<", etc
223            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
224    
225    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
228            of a 0-index which was used as 1-index (..hmm)
229    
230            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
231    
232            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
233            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
234            (.is.diagonal): ditto
235    
236            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
237    
238            * R/Matrix.R (Matrix): also work for NA data
239    
240    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
243            in all cases.
244    
245    2006-08-27  Douglas Bates  <bates@R-project.org>
246    
247            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
248            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
249    
250    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
253            subclasses of "ddenseMatrix"
254            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
255            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
256            instead of half dozen specialized ones.
257    
258    2006-08-25  Douglas Bates  <bates@R-project.org>
259    
260            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
261            <tillard@cirad.fr> - ordering standard errors to match effects.
262    
263    2006-08-24  Douglas Bates  <bates@R-project.org>
264    
265            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
266            on R_ldl.
267            * R/lCholCMatrix.R,
268            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
269            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
270            * many files in ./R and ./src: Use more general version of
271            dup_mMatrix_as_dgeMatrix to simplify method definitions.
272            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
273            dtpMatrix, dspMatrix and dppMatrix conversions.
274    
275    
276    2006-08-23  Douglas Bates  <bates@R-project.org>
277    
278            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
279            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
280            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
281            dgeMatrix_crossprod (may need to do this in other places).
282            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
283            generic and method for dsCMatrix.  Use CHOLMOD for chol().
284    
285    2006-08-22  Douglas Bates  <bates@R-project.org>
286    
287            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
288            types of classed Matrices, matrices or numeric or logical vectors.
289            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
290            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
291            to Mutils.h (as an inline) and change name to Matrix_check_class;
292            fixes in as_cholmod_factor and chm_factor_to_SEXP.
293            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
294            dsCMatrix_matrix_solve.  Comment out vestigial functions.
295            * src/Csparse.c: use diag_P and uplo_P macros.
296    
297    2006-08-21  Douglas Bates  <bates@R-project.org>
298    
299            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
300            valgrind.
301            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
302            inverses.
303            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
304            -Wall warnings.
305            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
306            Use dup_mMatrix_as_dgeMatrix.
307    
308    2006-08-20  Douglas Bates  <bates@R-project.org>
309    
310            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
311            * tests/sparseQR.R: Added
312            * man/sparseQR-class.Rd: Document methods for qr.* generics
313            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
314    
315    2006-08-19  Douglas Bates  <bates@R-project.org>
316    
317            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
318            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
319            and qr.fitted.
320            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
321            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
322    
323    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
326            the base version has no "..." argument.
327    
328            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
329    
330            * R/Matrix.R: define and
331            * NAMESPACE: export as.numeric() and as.logical() methods.
332                    Let's hope these do not badly slow down something...
333            Finally export the zapsmall() method.
334    
335    2006-08-17  Douglas Bates  <bates@R-project.org>
336    
337            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
338            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
339            * src/dtCMatrix.c :Remove code that is no longer used
340            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
341    
342    2006-08-14  Douglas Bates  <bates@R-project.org>
343    
344            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
345            Csparse_to_logical and Csparse_symmetric_to_general.
346            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
347            coercion methods between CsparseMatrix and TsparseMatrix.
348    
349    2006-08-14  Douglas Bates  <bates@R-project.org>
350    
351            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
352            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
353            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
354            possible.
355    
356    2006-08-12  Douglas Bates  <bates@R-project.org>
357    
358            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
359              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
360              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
361              generalize conversions between TsparseMatrix, CsparseMatrix,
362              denseMatrix and matrix.  Preserve triangularity property and
363              propagate Dimnames in the easy cases.
364    
365    2006-08-10  Douglas Bates  <bates@R-project.org>
366    
367            * src/lmer.c: adjust checks in glmer_init for S4SXP
368            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
369            before S4SXP but for the wrong reasons.
370    
371    2006-08-08  Douglas Bates  <bates@R-project.org>
372    
373            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
374            Later modified to return the upper triangle only.
375            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
376    
377    2006-08-07  Douglas Bates  <bates@R-project.org>
378    
379            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
380            R-level conversion to a sparse symmetric class.
381            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
382            Remove conversion to sparse symmetric classes (now done in C code).
383    
384    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
387            * man/band.Rd:  adapt the \dontshow{} unit test.
388    
389    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * DESCRIPTION (Version): 0.995-14  for CRAN
392    
393            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
394    
395            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
396            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
397    
398            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
399            * R/Tsparse.R (tril, triu, band): methods
400            * R/dgRMatrix.R (tril, ...):    ditto
401            * man/band.Rd:                  ditto
402    
403    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/Matrix.R (head, tail): directly use utils:::head.matrix
406                    to be up-to-date automatically.
407    
408    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
411    
412            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
413            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
414            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
415            such that the S4 objects are always created by the current version
416            of R and 'Matrix' class definitions.
417    
418    2006-08-01  Douglas Bates  <bates@R-project.org>
419    
420            * R/lmer.R (LMEoptimize method), tests/lmer.R,
421            inst/external/test3comp.rda: Added warnings for convergence on
422            boundary and test cases.
423    
424            * src/lmer.c (mer_postVar): Modified to return the variances that
425            are marginal to the fixed effects, not conditional on them (which
426            is what the bVar slot contents represent).
427    
428    2006-07-31  Douglas Bates  <bates@R-project.org>
429    
430            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
431            function which calls the C function mer_hat_trace2.
432    
433            * man/ranef.Rd: Include description of "postVar" argument and
434            producing a caterpillar plot.
435    
436    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * NAMESPACE:    change  "correlation" to "corMatrix"
439            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
440            * R/dpoMatrix.R: ditto
441            * R/lmer.R:      ditto
442    
443    2006-07-28  Douglas Bates  <bates@R-project.org>
444    
445            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
446            RZXinv slot's contents into a separate internal function that can
447            be used in mer_hat_trace.
448    
449    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
452            via new smart
453            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
454            utility functions.
455    
456    
457    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/Csparse.R (tril, triu, band): do return *triangular* classed
460            matrices when appropriate; band() even symmetric ones.
461            (replCmat): extend to potentially all "CsparseMatrix"
462            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
463            allow subassignment for special sparse matrices.
464    
465            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
466    
467            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
468            argument; in glmer_*(): print only if(verbose).
469    
470            speed-optimize a few places by moving REAL(.) out of loops.
471    
472            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
473    
474    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
477                    since that wrongly triggers also for M[ logi , ]
478    
479            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
480            a symmetric matrix that results in a non-symmetric one.
481            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
482    
483            * R/dMatrix.R: make round(M) work as round(M, 0)
484    
485            * R/dgTMatrix.R (image): coordinate system and axis now use
486            1-based indices, not 0-based ones.
487    
488            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
489            * tests/indexing.R: test it.
490    
491            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
492            * man/isSymmetric-methods.Rd: and document it.
493    
494            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
495            * man/SparseM-conv.Rd: docu them
496    
497            * tests/other-pkgs.R: renamed from tests/graph.R and add example
498                    for 'SparseM' conversions
499    
500    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
501    
502            * R/Matrix.R (head): added head() and tail() methods.
503    
504    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * DESCRIPTION (Version): 0.995-12 released to CRAN
507    
508    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * tests/simple.R: add check for correct dsT -> dgT coercion;
511                    add check for correct printing of symmetric sparse matrices.
512    
513            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
514            for sparse symmetric matrices.
515    
516            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
517            diagonal twice.
518    
519    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
520    
521            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
522            being applied to the x slot (detected by Brian Ripley).
523    
524    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
527    
528            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
529    
530    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * src/lgCMatrix.c (lgCMatrix_diag): new function
533            * R/lgCMatrix.R (diag): for new method
534    
535            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
536                 ==> construction of illegal "*gTMatrix" via new() should
537                 now be much less easy:
538            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
539    
540            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
541                    directly.
542            * man/Matrix.Rd: documents it.
543    
544    2006-07-06  Douglas Bates  <bates@R-project.org>
545    
546            * src/pedigree.c (pedigree_inbreeding): Correction in
547            initialization.  This function is not currently being used and is
548            not fully tested.
549    
550            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
551            Introduced the glmer class.  Added code for mcmcmsamp on glmer
552            objects.  Modified validity check on pedigree objects to account
553            for nonparallel patterns of missingness of parents.
554    
555            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
556            class.
557    
558    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/pMatrix.R: coercion pMatrix -> Tsparse
561    
562    2006-06-12  Douglas Bates  <bates@R-project.org>
563    
564            * DESCRIPTION (Version): 0.995-11 released to CRAN
565    
566            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
567            the output from mcmcsamp.
568    
569    2006-06-10  Douglas Bates  <bates@R-project.org>
570    
571            * R/lmer.R (simulestimate): added C code for calculating the trace
572            of the hat matrix.
573    
574    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
577            classes.
578            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
579    
580    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/dgTMatrix.R (colSums): etc. All four of
583            colSums(), rowSums(), colMeans(), rowMeans() now should work for
584            all "Matrices".
585    
586    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
587    
588            * R/lmer.R (panel.ci): Add a reference line at zero and a
589            background grid to the qqmath plot of ranef.lmer.
590    
591    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
592    
593            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
594            grouping factors to be specified in the formula as (1|foo/bar).
595    
596    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
597    
598            * R/lmer.R (findbars and others): Change check of is.numeric to
599            !is.language to resolve the bug reported by Jacob Wegelin.
600    
601            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
602            code to evaluate inbreeding coefficients without calculating T,
603            based on code in Sargolzaei and Iwaisaki's paper.
604    
605    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
606    
607            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
608            generic and mer methods for isNested and denomDF. This denomDF was
609            an attempt to emulate that in lme but I don't think that makes
610            sense.  Use the trace of the hat matrix instead.
611    
612    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
615            the C code depending on a slot structure that's no longer valid.
616            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
617    
618    
619    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
620    
621            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
622            of lowerTriMatrix generic and methods to tril (also upper to triu)
623            and added a general band extractor.
624    
625    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
626    
627            * R/pedigree.R (pedigree): Replace sire and dam values outside the
628            allowable range with NAs. Added a corresponding check in the
629            validity check for the pedigree class.
630    
631            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
632            crossprod methods now inherits from symmetricMatrix.
633    
634    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
637            generics lowerTriMatrix and upperTriMatrix along with methods for
638            the Csparse virtual class.  Also added a C function Csparse_band
639            that implements these methods by calling cholmod_band.
640    
641    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
644            erased when it was NULL.  This led to invalid subselections!
645    
646    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
649            in method for "t" so as not to lose the unit diagonal property.
650    
651    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
652    
653            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
654            and methods.  This is now an option to the ranef method for the
655            mer class.
656    
657            * src/cs_utils.c: Ensure that the nz component is -1 for a
658            compressed column-oriented matrix.  Minor formatting cleanup.
659    
660            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
661            objects.
662    
663    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
666            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
667    
668    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
669    
670            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
671            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
672    
673            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
674            for the dtCMatrix class.
675    
676    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
677    
678            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
679            and methods for it.
680    
681    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
684            arguments, such that M %*% 1:6 now works
685            * Tests/matprod.R: test the above
686    
687    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
688    
689            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
690            the ranef.lmer class.
691    
692            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
693            methods to extract the posterior variances from the bVar slot.
694    
695    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
698            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
699    
700            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
701            * tests/simple: (extended)
702    
703            * R/sparseMatrix.R (isTriangular): now using much improved
704            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
705    
706    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
709            (problem report from Franklin Parlamis).  This should be done
710            generally.
711    
712    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
713    
714            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
715            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
716            update the plot methods.
717    
718    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
719    
720            * R/lmer.R (resid and ranef methods):  Added methods for the
721            "residuals" and "resid" generic but only for linear mixed model
722            fits.  Changed the ranef method to return a list of data frames so
723            that the plot methods now work.
724    
725    2006-03-16  Douglas Bates  <bates@bates2>
726    
727            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
728            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
729    
730            * DESCRIPTION (Date): New release
731    
732    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
735    
736            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
737            * man/KNex.Rd: and other help files
738            * tests/*.R: several ones needed adaption
739            * inst/doc/Comparisons.Rnw: ditto
740    
741    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
744    
745            * tests/indexing.R: tests for new [<- methods for sparse matrices.
746    
747    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
750    
751            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
752    
753    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/dMatrix.R: enable things like  M [ M < 10 ]
756            * R/dgeMatrix.R: implement it
757    
758    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/AllClass.R: define "summary.mer" and "*.lmer"
761            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
762            * R/lmer.R (show): now works with summary()
763    
764    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
767            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
768                    support the above
769    
770    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
771    
772            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
773            Use glmFit$prior.weights for weights in a glmm.
774            Allow an option usePQL = FALSE to skip the PQL steps for the
775            Laplace method (and, in time, the AGQ method).
776    
777            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
778            into a separate function internal_mer_Xfactor to be able to call
779            it from internal_bhat.
780    
781    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * tests/Class+Meth.R (tstMatrixClass): function for much better
784            testing; now again of all actual classes.
785    
786            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
787                    use macros and define make_d_matrix_* and make_i_matrix_*
788                    where _i_ is for the ldense routines:
789    
790            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
791            * src/ldense.c (lsyMatrix_as_lgeMatrix):
792    
793            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
794    
795    
796    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
799                    many different kinds of matrices.
800            * R/*.R: quite a few new methods were needed for R CMD check with
801                    new Matrix().  Very good for users playing around.
802    
803    
804    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * src/dgeMatrix.c (dMatrix_validate): new
807            * src/Mutils.c (dense_nonpacked_validate): new
808    
809            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
810    
811    
812    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
813    
814            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
815    
816    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
817    
818            * DESCRIPTION (Version): 0.99-6 released to CRAN
819    
820            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
821            segfault in cases with multiple non-nested grouping factors.
822    
823    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
826                    (Depends): also on 'utils'
827    
828            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
829            * R/diagMatrix.R (Diagonal): constructor and methods for
830            diagonal matrices
831    
832            * R/ltTMatrix.R: new "minimal methods"
833    
834    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
837            all methods (and help files).
838    
839    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
842                    for case (dimn.  op  no_dimn.)
843    
844    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
845    
846            * DESCRIPTION (Version): 0.99-2  released to CRAN
847    
848    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
849    
850            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
851            by Julian Faraway.
852    
853    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * R/Auxiliaries.R (try_as): new utility
856            * R/sparseMatrix.R: use try_as() in coercion to original class
857    
858    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
861    
862    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/Auxiliaries.R (dimNamesCheck): added
865    
866            * R/Matrix.R (as.array), (as.vector): new
867    
868    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
871                    default.
872            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
873                    "pMatrix" now contains "sparseMatrix"
874    
875    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * tests/Class+Meth.R: new tests; t(t(m)) == m
878    
879            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
880    
881            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
882            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
883    
884            * R/dspMatrix.R: typo in "t" method
885    
886    2005-09-18  Douglas Bates  <bates@wisc.edu>
887    
888            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
889            * R/Tsparse.R: instead of R/gTMatrix.R
890            * R/Csparse.R: new
891            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
892            * src/Tsparse.c: new; many trivial methods calling cholmod_()
893            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
894                            via cholmod
895    
896    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
897    
898            * R/Auxiliaries.R (non0ind): new function using new C code
899            * src/dgCMatrix.c (compressed_non_0_ij): new utility
900    
901    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
902    
903            * src/chm_common.h: header file required by all C sources that
904            call CHOLMOD functions.  It defines a cholmod_common structure
905            called 'c' whose address is passed as the last argument to
906            (virtually) every CHOLMOD function.
907    
908            * src/Pattern.c: Simple example of the use of CHOLMOD.
909    
910            * src/init.c: initialize and finalize the cholmod_common structure.
911    
912            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
913            LDL and CCOLAMD from the U. of Florida sparse matrix library.
914    
915    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * inst/test-tools.R: new file collecting the utility functions used
918                    in ./tests/*.R
919    
920            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
921            * R/Matrix.R (cbind2): methods for NULL and missing
922    
923    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * R/AllClass.R: new "index" class for "[" and "[<-":
926                    First cut at "symmetricMatrix" and "triangularMatrix"
927            * R/gTMatrix.R (.ind.prep): new function;
928                    Logical and character indexing now work too.
929            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
930            * tests/indexing.R: new, including *.Rout.save
931            * tests/dgTMatrix.R: new
932    
933    2005-08-29  Douglas Bates  <bates@wisc.edu>
934    
935            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
936            indicator pos not being updated.  Also enforced upper triangular
937            for symmetric case.  Need to coerce edges component of elements of
938            edge list - grr! (Why don't they define their classes cleanly?)
939    
940    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942            * R/Matrix.R:  added first "[<-" methods; not yet functional
943            * R/denseMatrix.R: ditto
944            * man/Subassign-methods.Rd: new help file for these
945    
946    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * DESCRIPTION (Version): 0.98-6
949    
950            * R/denseMatrix.R: new file for "[" fallback methods for all dense
951            matrices.
952    
953    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
956                    as( <logical>, "matrix")
957    
958            * R/pMatrix.R: coercion to "lgTMatrix"
959    
960            * R/gTMatrix.R: new virtual class to define "[" methods for.
961            * man/gTMatrix-class.Rd:
962            * General slight re-organization of where "[" methods are defined.
963              more to come.
964    
965    2005-08-18  Douglas Bates  <bates@wisc.edu>
966    
967            * DESCRIPTION (Version): 0.98-5  released to CRAN
968    
969            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
970            * .....
971    
972    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
973    
974            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
975            or glmer objects.
976    
977    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
980    
981    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
982    
983            * R/HBMM.R: finish re-writing R-only code.
984    
985    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
986    
987            * man/externalFormats.Rd: move documentation for writeHB and
988            writeMM here.
989    
990            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
991            (suggested by Paul Roecker).
992    
993            * tests/validObj.R (assertError): Comment out test that is failing
994            after recent changes in r-devel.
995    
996    
997    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * R/AllClass.R: intermediate virtual class "denseMatrix"
1000            * man/denseMatrix-class.Rd
1001            * NAMESPACE: export it, and also export
1002            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1003    
1004    2005-08-10  Douglas Bates  <bates@wisc.edu>
1005    
1006            * DESCRIPTION (Version): 0.98-3 to CRAN
1007    
1008            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1009            matrix_solve code (which was really, really wrong).
1010    
1011    2005-08-07  Douglas Bates  <bates@wisc.edu>
1012    
1013            * DESCRIPTION (Version): 0.98-2
1014    
1015            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1016    
1017            * R/lmer.R (abbrvNms): new
1018            * R/lmer.R (mcmcsamp): allow transformed parameters
1019            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1020            for the Harwell-Boeing and the MatrixMarket formats.
1021    
1022    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * man/dtrMatrix-class.Rd: add examples
1025            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1026    
1027            * TODO: note the dtpMatrix (docu) bug
1028    
1029            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1030            in order to ensure that new as.matrix() is used by old functions,
1031            e.g., svd(), qr(), eigen(), dist(),..;
1032                  apply(), also matplot() or pairs().
1033    
1034    
1035    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1038              add comments about 'control' / lmerControl() arguments
1039    
1040    2005-07-27  Douglas Bates  <bates@wisc.edu>
1041    
1042            * man/sleepstudy.Rd: Added the sleep data set.
1043            * DESCRIPTION (Version): 0.98-1  released to CRAN
1044    
1045    2005-07-12  Douglas Bates  <bates@wisc.edu>
1046            * man/sleepstudy.Rd: Added the sleep data set.
1047    
1048            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1049            .Call calls that were producing spurious output.
1050    
1051    2005-07-05  Douglas Bates  <bates@wisc.edu>
1052    
1053            * R/lmer.R (lmer): stored updated variance component estimates in
1054            mer object for the generalized model.  (Bug reported by Renaud
1055            Lancelot).
1056    
1057    2005-07-03  Douglas Bates  <bates@wisc.edu>
1058    
1059            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1060            unidimensional case.
1061    
1062    2005-06-08  Douglas Bates  <bates@wisc.edu>
1063    
1064            * DESCRIPTION (Version): 0.96-1
1065    
1066            * moved  lmer-class' R and C code moved from lme4 to here
1067    
1068    2005-06-04  Douglas Bates  <bates@wisc.edu>
1069    
1070            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1071            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1072    
1073    2005-06-02  Douglas Bates  <bates@wisc.edu>
1074    
1075            * src/Makefile.win: Forgot to update this when Makefile changed.
1076    
1077    2005-05-11  Douglas Bates  <bates@wisc.edu>
1078    
1079          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1080          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1081    
1082  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1083    
1084          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1085          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 1088 
1088          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1089          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1090    
1091  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1092    
1093          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1094          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1095    
1096  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1097    
1098          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1099          multiplication operation.          multiplication operation.
# Line 30  Line 1106 
1106    
1107          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1108    
1109  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1110    
1111          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1112    
1113          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1114    
1115    
1116  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1117    
1118          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1119    
# Line 46  Line 1122 
1122          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1123          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1124    
1125  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1126    
1127          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1128    
# Line 72  Line 1148 
1148          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1149            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1150    
1151  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1152    
1153          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1154          * ....          * ....
1155    
1156  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1157    
1158          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1159    
# Line 92  Line 1168 
1168            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1169          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1170    
1171  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1172    
1173          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1174    
1175  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1176    
1177          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1178    
1179  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1180    
1181          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1182          the package.          the package.
# Line 148  Line 1224 
1224    
1225          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1226    
1227  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1228    
1229          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1230          for the geMatrix class.          for the geMatrix class.
1231    
1232  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1233    
1234          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1235    
1236          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1237    
1238  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1239    
1240          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1241          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1242    
1243  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1244    
1245          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1246    
1247  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1248    
1249          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1250          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1251    
1252  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1253    
1254          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1255    
1256          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1257          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1258    
1259  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1260    
1261          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1262          no longer used.          no longer used.
# Line 192  Line 1268 
1268          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1269          Fixes part but not all of #15.          Fixes part but not all of #15.
1270    
1271  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1272    
1273          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1274          scalar grouping factors corrected.          scalar grouping factors corrected.
1275    
1276  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1277    
1278          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1279    
1280  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1281    
1282          * 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
1283          .h file can be included.          .h file can be included.
1284    
1285  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1286    
1287          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1288          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1289    
1290          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1291    
1292  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1293    
1294          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1295    
1296  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1297    
1298          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1299    
1300  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1301    
1302          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1303    
1304  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1305    
1306          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1307    
1308  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1309    
1310          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1311          routines.          routines.
1312    
1313  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1314    
1315          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1316    
1317  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1318    
1319          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1320    

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