SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1600, Fri Sep 29 13:37:25 2006 UTC
# Line 1  Line 1 
1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
4    
5            * R/lsTMatrix.R: new files w/ missing methods
6            * R/nsTMatrix.R:  "  'for completeness'
7    
8            * tests/Class+Meth.R: a bit less 'not.ok.classes'
9    
10            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
11    
12    
13    2006-09-28  Douglas Bates  <bates@R-project.org>
14    
15            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
16            included.
17    
18            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
19            Export C-callable functions used in Zt_create in lme4.
20    
21    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * DESCRIPTION (Version): 0.9975-1
24    
25            * tests/simple.R: less checks fail; using NA, found that our
26                    kronecker() is not base-compatible with NA's.
27    
28            * R/dMatrix.R: "Compare" method now implemented for all cases
29    
30            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
31    
32            * man/dtpMatrix-class.Rd: mention length of 'x' slot
33    
34            * src/dtpMatrix.c (dtpMatrix_validate): fix check
35            * src/dspMatrix.c (dspMatrix_validate): ditto
36    
37            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
38              including coercion to [nl]tTMatrix.
39    
40            * R/diagMatrix.R (show): print a header line as for other classes.
41    
42    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/Makefile.win (SUBDIRS): fix typo
45    
46    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
49    
50    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
53            symmetric and y missing in R code using %*% (cholmod_aat doesn't
54            accept a symmetric matrix).
55            * tests/group-methods.R: Uncomment test of crossprod applied to
56            lsCMatrix objects.
57    
58    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/AllClass.R (symmetricMatrix): add validity method (available
61            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
62    
63            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
64    
65            * tests/indexing.Rout.save:
66            * tests/indexing.R: additions, mainly for 'lsparse'
67    
68            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
69            case.
70    
71            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
72    
73    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
76                    as 'N' (1-letter - Ok?)
77    
78            * tests/group-methods.R: add test for logical + NAs
79    
80            * R/dMatrix.R ("Compare"): fix to work with NA's
81    
82            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
83    
84            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
85                    which is implemented.
86    
87    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/chm_common.c: coerce logical <-> double instead of
90            typecasting;  needed for "l" matrix handling in cholmod.
91    
92            * tests/other-pkgs.R (graph): small extension in "graph" checks.
93    
94            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
95            (Tsp2grNEL): other fixes needed
96    
97    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
100                    Matrices, since "lMatrix", also "lsparseM" can have NA
101            * R/ndenseMatrix.R, etc: new source files
102            * man/nsparseMatrix-classes.Rd, etc: new help files
103            * tests/: adaptions
104            * src/chm_common.c (chm_dense_to_SEXP): and others:
105                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
106            * src/Csparse.c, etc: ditto
107    
108    2006-09-11  Douglas Bates  <bates@R-project.org>
109    
110            * src/Mutils.[ch],init.c inst/include/*.h: Move the
111            alloc_d**Matrix functions to the lme4 package.
112    
113    2006-09-09  Douglas Bates  <bates@R-project.org>
114    
115            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
116            fixed
117    
118    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/lMatrix.R: new
121    
122            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
123    
124            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
125            * man/tcrossprod.Rd: ditto
126    
127    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
130            for exported functions
131            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
132            Remove partitioning algorithms for sparse matrix reordering.  The
133            copyright on the Metis code was problematic and the methods were
134            rarely used.
135            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
136            operations are now done entirely in CHOLMOD code.
137    
138    2006-09-06  Douglas Bates  <bates@R-project.org>
139    
140            * src/Mutils.h: Remove functions that are no longer used.
141    
142    2006-09-04  Douglas Bates  <bates@R-project.org>
143    
144            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
145            * src/DEPS.mkf: update
146    
147    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * created branches/Matrix-for-R-2.3.x;  on trunk: do
150            * DESCRIPTION (Version): 0.9975-0
151            (Depends): R (>= 2.4.0)
152    
153    2006-09-01  Douglas Bates  <bates@R-project.org>
154    
155            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
156    
157    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
160            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
161    
162            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
163    
164    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
167            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
168            * R/dsparseMatrix.R: ditto
169            * R/Csparse.R: ditto
170    
171    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dMatrix.R (Compare): improve availability of "<", etc
174            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
175    
176    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
179            of a 0-index which was used as 1-index (..hmm)
180    
181            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
182    
183            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
184            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
185            (.is.diagonal): ditto
186    
187            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
188    
189            * R/Matrix.R (Matrix): also work for NA data
190    
191    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
194            in all cases.
195    
196    2006-08-27  Douglas Bates  <bates@R-project.org>
197    
198            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
199            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
200    
201    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
204            subclasses of "ddenseMatrix"
205            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
206            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
207            instead of half dozen specialized ones.
208    
209    2006-08-25  Douglas Bates  <bates@R-project.org>
210    
211            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
212            <tillard@cirad.fr> - ordering standard errors to match effects.
213    
214    2006-08-24  Douglas Bates  <bates@R-project.org>
215    
216            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
217            on R_ldl.
218            * R/lCholCMatrix.R,
219            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
220            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
221            * many files in ./R and ./src: Use more general version of
222            dup_mMatrix_as_dgeMatrix to simplify method definitions.
223            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
224            dtpMatrix, dspMatrix and dppMatrix conversions.
225    
226    
227    2006-08-23  Douglas Bates  <bates@R-project.org>
228    
229            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
230            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
231            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
232            dgeMatrix_crossprod (may need to do this in other places).
233            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
234            generic and method for dsCMatrix.  Use CHOLMOD for chol().
235    
236    2006-08-22  Douglas Bates  <bates@R-project.org>
237    
238            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
239            types of classed Matrices, matrices or numeric or logical vectors.
240            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
241            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
242            to Mutils.h (as an inline) and change name to Matrix_check_class;
243            fixes in as_cholmod_factor and chm_factor_to_SEXP.
244            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
245            dsCMatrix_matrix_solve.  Comment out vestigial functions.
246            * src/Csparse.c: use diag_P and uplo_P macros.
247    
248    2006-08-21  Douglas Bates  <bates@R-project.org>
249    
250            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
251            valgrind.
252            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
253            inverses.
254            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
255            -Wall warnings.
256            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
257            Use dup_mMatrix_as_dgeMatrix.
258    
259    2006-08-20  Douglas Bates  <bates@R-project.org>
260    
261            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
262            * tests/sparseQR.R: Added
263            * man/sparseQR-class.Rd: Document methods for qr.* generics
264            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
265    
266    2006-08-19  Douglas Bates  <bates@R-project.org>
267    
268            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
269            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
270            and qr.fitted.
271            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
272            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
273    
274    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
277            the base version has no "..." argument.
278    
279            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
280    
281            * R/Matrix.R: define and
282            * NAMESPACE: export as.numeric() and as.logical() methods.
283                    Let's hope these do not badly slow down something...
284            Finally export the zapsmall() method.
285    
286    2006-08-17  Douglas Bates  <bates@R-project.org>
287    
288            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
289            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
290            * src/dtCMatrix.c :Remove code that is no longer used
291            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
292    
293    2006-08-14  Douglas Bates  <bates@R-project.org>
294    
295            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
296            Csparse_to_logical and Csparse_symmetric_to_general.
297            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
298            coercion methods between CsparseMatrix and TsparseMatrix.
299    
300    2006-08-14  Douglas Bates  <bates@R-project.org>
301    
302            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
303            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
304            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
305            possible.
306    
307    2006-08-12  Douglas Bates  <bates@R-project.org>
308    
309            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
310              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
311              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
312              generalize conversions between TsparseMatrix, CsparseMatrix,
313              denseMatrix and matrix.  Preserve triangularity property and
314              propagate Dimnames in the easy cases.
315    
316    2006-08-10  Douglas Bates  <bates@R-project.org>
317    
318            * src/lmer.c: adjust checks in glmer_init for S4SXP
319            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
320            before S4SXP but for the wrong reasons.
321    
322    2006-08-08  Douglas Bates  <bates@R-project.org>
323    
324            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
325            Later modified to return the upper triangle only.
326            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
327    
328    2006-08-07  Douglas Bates  <bates@R-project.org>
329    
330            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
331            R-level conversion to a sparse symmetric class.
332            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
333            Remove conversion to sparse symmetric classes (now done in C code).
334    
335    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
338            * man/band.Rd:  adapt the \dontshow{} unit test.
339    
340    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * DESCRIPTION (Version): 0.995-14  for CRAN
343    
344            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
345    
346            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
347            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
348    
349            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
350            * R/Tsparse.R (tril, triu, band): methods
351            * R/dgRMatrix.R (tril, ...):    ditto
352            * man/band.Rd:                  ditto
353    
354    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Matrix.R (head, tail): directly use utils:::head.matrix
357                    to be up-to-date automatically.
358    
359    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
362    
363            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
364            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
365            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
366            such that the S4 objects are always created by the current version
367            of R and 'Matrix' class definitions.
368    
369    2006-08-01  Douglas Bates  <bates@R-project.org>
370    
371            * R/lmer.R (LMEoptimize method), tests/lmer.R,
372            inst/external/test3comp.rda: Added warnings for convergence on
373            boundary and test cases.
374    
375            * src/lmer.c (mer_postVar): Modified to return the variances that
376            are marginal to the fixed effects, not conditional on them (which
377            is what the bVar slot contents represent).
378    
379    2006-07-31  Douglas Bates  <bates@R-project.org>
380    
381            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
382            function which calls the C function mer_hat_trace2.
383    
384            * man/ranef.Rd: Include description of "postVar" argument and
385            producing a caterpillar plot.
386    
387    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * NAMESPACE:    change  "correlation" to "corMatrix"
390            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
391            * R/dpoMatrix.R: ditto
392            * R/lmer.R:      ditto
393    
394    2006-07-28  Douglas Bates  <bates@R-project.org>
395    
396            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
397            RZXinv slot's contents into a separate internal function that can
398            be used in mer_hat_trace.
399    
400    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
403            via new smart
404            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
405            utility functions.
406    
407    
408    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Csparse.R (tril, triu, band): do return *triangular* classed
411            matrices when appropriate; band() even symmetric ones.
412            (replCmat): extend to potentially all "CsparseMatrix"
413            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
414            allow subassignment for special sparse matrices.
415    
416            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
417    
418            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
419            argument; in glmer_*(): print only if(verbose).
420    
421            speed-optimize a few places by moving REAL(.) out of loops.
422    
423            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
424    
425    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
428                    since that wrongly triggers also for M[ logi , ]
429    
430            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
431            a symmetric matrix that results in a non-symmetric one.
432            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
433    
434            * R/dMatrix.R: make round(M) work as round(M, 0)
435    
436            * R/dgTMatrix.R (image): coordinate system and axis now use
437            1-based indices, not 0-based ones.
438    
439            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
440            * tests/indexing.R: test it.
441    
442            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
443            * man/isSymmetric-methods.Rd: and document it.
444    
445            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
446            * man/SparseM-conv.Rd: docu them
447    
448            * tests/other-pkgs.R: renamed from tests/graph.R and add example
449                    for 'SparseM' conversions
450    
451    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
452    
453            * R/Matrix.R (head): added head() and tail() methods.
454    
455    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * DESCRIPTION (Version): 0.995-12 released to CRAN
458    
459    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * tests/simple.R: add check for correct dsT -> dgT coercion;
462                    add check for correct printing of symmetric sparse matrices.
463    
464            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
465            for sparse symmetric matrices.
466    
467            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
468            diagonal twice.
469    
470    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
471    
472            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
473            being applied to the x slot (detected by Brian Ripley).
474    
475    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
478    
479            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
480    
481    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * src/lgCMatrix.c (lgCMatrix_diag): new function
484            * R/lgCMatrix.R (diag): for new method
485    
486            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
487                 ==> construction of illegal "*gTMatrix" via new() should
488                 now be much less easy:
489            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
490    
491            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
492                    directly.
493            * man/Matrix.Rd: documents it.
494    
495    2006-07-06  Douglas Bates  <bates@R-project.org>
496    
497            * src/pedigree.c (pedigree_inbreeding): Correction in
498            initialization.  This function is not currently being used and is
499            not fully tested.
500    
501            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
502            Introduced the glmer class.  Added code for mcmcmsamp on glmer
503            objects.  Modified validity check on pedigree objects to account
504            for nonparallel patterns of missingness of parents.
505    
506            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
507            class.
508    
509    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/pMatrix.R: coercion pMatrix -> Tsparse
512    
513    2006-06-12  Douglas Bates  <bates@R-project.org>
514    
515            * DESCRIPTION (Version): 0.995-11 released to CRAN
516    
517            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
518            the output from mcmcsamp.
519    
520    2006-06-10  Douglas Bates  <bates@R-project.org>
521    
522            * R/lmer.R (simulestimate): added C code for calculating the trace
523            of the hat matrix.
524    
525    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
528            classes.
529            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
530    
531    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/dgTMatrix.R (colSums): etc. All four of
534            colSums(), rowSums(), colMeans(), rowMeans() now should work for
535            all "Matrices".
536    
537    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
538    
539            * R/lmer.R (panel.ci): Add a reference line at zero and a
540            background grid to the qqmath plot of ranef.lmer.
541    
542    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
543    
544            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
545            grouping factors to be specified in the formula as (1|foo/bar).
546    
547    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
548    
549            * R/lmer.R (findbars and others): Change check of is.numeric to
550            !is.language to resolve the bug reported by Jacob Wegelin.
551    
552            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
553            code to evaluate inbreeding coefficients without calculating T,
554            based on code in Sargolzaei and Iwaisaki's paper.
555    
556    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
557    
558            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
559            generic and mer methods for isNested and denomDF. This denomDF was
560            an attempt to emulate that in lme but I don't think that makes
561            sense.  Use the trace of the hat matrix instead.
562    
563    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
566            the C code depending on a slot structure that's no longer valid.
567            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
568    
569    
570    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
571    
572            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
573            of lowerTriMatrix generic and methods to tril (also upper to triu)
574            and added a general band extractor.
575    
576    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
577    
578            * R/pedigree.R (pedigree): Replace sire and dam values outside the
579            allowable range with NAs. Added a corresponding check in the
580            validity check for the pedigree class.
581    
582            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
583            crossprod methods now inherits from symmetricMatrix.
584    
585    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
586    
587            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
588            generics lowerTriMatrix and upperTriMatrix along with methods for
589            the Csparse virtual class.  Also added a C function Csparse_band
590            that implements these methods by calling cholmod_band.
591    
592    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
595            erased when it was NULL.  This led to invalid subselections!
596    
597    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
598    
599            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
600            in method for "t" so as not to lose the unit diagonal property.
601    
602    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
603    
604            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
605            and methods.  This is now an option to the ranef method for the
606            mer class.
607    
608            * src/cs_utils.c: Ensure that the nz component is -1 for a
609            compressed column-oriented matrix.  Minor formatting cleanup.
610    
611            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
612            objects.
613    
614    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
617            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
618    
619    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
620    
621            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
622            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
623    
624            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
625            for the dtCMatrix class.
626    
627    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
628    
629            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
630            and methods for it.
631    
632    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
635            arguments, such that M %*% 1:6 now works
636            * Tests/matprod.R: test the above
637    
638    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
639    
640            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
641            the ranef.lmer class.
642    
643            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
644            methods to extract the posterior variances from the bVar slot.
645    
646    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
649            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
650    
651            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
652            * tests/simple: (extended)
653    
654            * R/sparseMatrix.R (isTriangular): now using much improved
655            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
656    
657    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
658    
659            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
660            (problem report from Franklin Parlamis).  This should be done
661            generally.
662    
663    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
664    
665            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
666            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
667            update the plot methods.
668    
669    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
670    
671            * R/lmer.R (resid and ranef methods):  Added methods for the
672            "residuals" and "resid" generic but only for linear mixed model
673            fits.  Changed the ranef method to return a list of data frames so
674            that the plot methods now work.
675    
676    2006-03-16  Douglas Bates  <bates@bates2>
677    
678            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
679            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
680    
681            * DESCRIPTION (Date): New release
682    
683    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
686    
687            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
688            * man/KNex.Rd: and other help files
689            * tests/*.R: several ones needed adaption
690            * inst/doc/Comparisons.Rnw: ditto
691    
692    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
695    
696            * tests/indexing.R: tests for new [<- methods for sparse matrices.
697    
698    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
701    
702            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
703    
704    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * R/dMatrix.R: enable things like  M [ M < 10 ]
707            * R/dgeMatrix.R: implement it
708    
709    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/AllClass.R: define "summary.mer" and "*.lmer"
712            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
713            * R/lmer.R (show): now works with summary()
714    
715    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
718            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
719                    support the above
720    
721    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
722    
723            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
724            Use glmFit$prior.weights for weights in a glmm.
725            Allow an option usePQL = FALSE to skip the PQL steps for the
726            Laplace method (and, in time, the AGQ method).
727    
728            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
729            into a separate function internal_mer_Xfactor to be able to call
730            it from internal_bhat.
731    
732    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * tests/Class+Meth.R (tstMatrixClass): function for much better
735            testing; now again of all actual classes.
736    
737            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
738                    use macros and define make_d_matrix_* and make_i_matrix_*
739                    where _i_ is for the ldense routines:
740    
741            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
742            * src/ldense.c (lsyMatrix_as_lgeMatrix):
743    
744            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
745    
746    
747    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
750                    many different kinds of matrices.
751            * R/*.R: quite a few new methods were needed for R CMD check with
752                    new Matrix().  Very good for users playing around.
753    
754    
755    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * src/dgeMatrix.c (dMatrix_validate): new
758            * src/Mutils.c (dense_nonpacked_validate): new
759    
760            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
761    
762    
763    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
764    
765            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
766    
767    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
768    
769            * DESCRIPTION (Version): 0.99-6 released to CRAN
770    
771            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
772            segfault in cases with multiple non-nested grouping factors.
773    
774    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
777                    (Depends): also on 'utils'
778    
779            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
780            * R/diagMatrix.R (Diagonal): constructor and methods for
781            diagonal matrices
782    
783            * R/ltTMatrix.R: new "minimal methods"
784    
785    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
788            all methods (and help files).
789    
790    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
793                    for case (dimn.  op  no_dimn.)
794    
795    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
796    
797            * DESCRIPTION (Version): 0.99-2  released to CRAN
798    
799    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
800    
801            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
802            by Julian Faraway.
803    
804    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/Auxiliaries.R (try_as): new utility
807            * R/sparseMatrix.R: use try_as() in coercion to original class
808    
809    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
812    
813    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * R/Auxiliaries.R (dimNamesCheck): added
816    
817            * R/Matrix.R (as.array), (as.vector): new
818    
819    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
822                    default.
823            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
824                    "pMatrix" now contains "sparseMatrix"
825    
826    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * tests/Class+Meth.R: new tests; t(t(m)) == m
829    
830            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
831    
832            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
833            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
834    
835            * R/dspMatrix.R: typo in "t" method
836    
837    2005-09-18  Douglas Bates  <bates@wisc.edu>
838    
839            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
840            * R/Tsparse.R: instead of R/gTMatrix.R
841            * R/Csparse.R: new
842            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
843            * src/Tsparse.c: new; many trivial methods calling cholmod_()
844            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
845                            via cholmod
846    
847    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/Auxiliaries.R (non0ind): new function using new C code
850            * src/dgCMatrix.c (compressed_non_0_ij): new utility
851    
852    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
853    
854            * src/chm_common.h: header file required by all C sources that
855            call CHOLMOD functions.  It defines a cholmod_common structure
856            called 'c' whose address is passed as the last argument to
857            (virtually) every CHOLMOD function.
858    
859            * src/Pattern.c: Simple example of the use of CHOLMOD.
860    
861            * src/init.c: initialize and finalize the cholmod_common structure.
862    
863            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
864            LDL and CCOLAMD from the U. of Florida sparse matrix library.
865    
866    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * inst/test-tools.R: new file collecting the utility functions used
869                    in ./tests/*.R
870    
871            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
872            * R/Matrix.R (cbind2): methods for NULL and missing
873    
874    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/AllClass.R: new "index" class for "[" and "[<-":
877                    First cut at "symmetricMatrix" and "triangularMatrix"
878            * R/gTMatrix.R (.ind.prep): new function;
879                    Logical and character indexing now work too.
880            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
881            * tests/indexing.R: new, including *.Rout.save
882            * tests/dgTMatrix.R: new
883    
884    2005-08-29  Douglas Bates  <bates@wisc.edu>
885    
886            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
887            indicator pos not being updated.  Also enforced upper triangular
888            for symmetric case.  Need to coerce edges component of elements of
889            edge list - grr! (Why don't they define their classes cleanly?)
890    
891    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/Matrix.R:  added first "[<-" methods; not yet functional
894            * R/denseMatrix.R: ditto
895            * man/Subassign-methods.Rd: new help file for these
896    
897    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * DESCRIPTION (Version): 0.98-6
900    
901            * R/denseMatrix.R: new file for "[" fallback methods for all dense
902            matrices.
903    
904    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
907                    as( <logical>, "matrix")
908    
909            * R/pMatrix.R: coercion to "lgTMatrix"
910    
911            * R/gTMatrix.R: new virtual class to define "[" methods for.
912            * man/gTMatrix-class.Rd:
913            * General slight re-organization of where "[" methods are defined.
914              more to come.
915    
916    2005-08-18  Douglas Bates  <bates@wisc.edu>
917    
918            * DESCRIPTION (Version): 0.98-5  released to CRAN
919    
920            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
921            * .....
922    
923    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
924    
925            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
926            or glmer objects.
927    
928    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
931    
932    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
933    
934            * R/HBMM.R: finish re-writing R-only code.
935    
936    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
937    
938            * man/externalFormats.Rd: move documentation for writeHB and
939            writeMM here.
940    
941            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
942            (suggested by Paul Roecker).
943    
944            * tests/validObj.R (assertError): Comment out test that is failing
945            after recent changes in r-devel.
946    
947    
948    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * R/AllClass.R: intermediate virtual class "denseMatrix"
951            * man/denseMatrix-class.Rd
952            * NAMESPACE: export it, and also export
953            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
954    
955    2005-08-10  Douglas Bates  <bates@wisc.edu>
956    
957            * DESCRIPTION (Version): 0.98-3 to CRAN
958    
959            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
960            matrix_solve code (which was really, really wrong).
961    
962    2005-08-07  Douglas Bates  <bates@wisc.edu>
963    
964            * DESCRIPTION (Version): 0.98-2
965    
966            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
967    
968            * R/lmer.R (abbrvNms): new
969            * R/lmer.R (mcmcsamp): allow transformed parameters
970            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
971            for the Harwell-Boeing and the MatrixMarket formats.
972    
973    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * man/dtrMatrix-class.Rd: add examples
976            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
977    
978            * TODO: note the dtpMatrix (docu) bug
979    
980            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
981            in order to ensure that new as.matrix() is used by old functions,
982            e.g., svd(), qr(), eigen(), dist(),..;
983                  apply(), also matplot() or pairs().
984    
985    
986    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
989              add comments about 'control' / lmerControl() arguments
990    
991    2005-07-27  Douglas Bates  <bates@wisc.edu>
992    
993            * man/sleepstudy.Rd: Added the sleep data set.
994            * DESCRIPTION (Version): 0.98-1  released to CRAN
995    
996    2005-07-12  Douglas Bates  <bates@wisc.edu>
997            * man/sleepstudy.Rd: Added the sleep data set.
998    
999            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1000            .Call calls that were producing spurious output.
1001    
1002    2005-07-05  Douglas Bates  <bates@wisc.edu>
1003    
1004            * R/lmer.R (lmer): stored updated variance component estimates in
1005            mer object for the generalized model.  (Bug reported by Renaud
1006            Lancelot).
1007    
1008    2005-07-03  Douglas Bates  <bates@wisc.edu>
1009    
1010            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1011            unidimensional case.
1012    
1013    2005-06-08  Douglas Bates  <bates@wisc.edu>
1014    
1015            * DESCRIPTION (Version): 0.96-1
1016    
1017            * moved  lmer-class' R and C code moved from lme4 to here
1018    
1019    2005-06-04  Douglas Bates  <bates@wisc.edu>
1020    
1021            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1022            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1023    
1024    2005-06-02  Douglas Bates  <bates@wisc.edu>
1025    
1026            * src/Makefile.win: Forgot to update this when Makefile changed.
1027    
1028    2005-05-11  Douglas Bates  <bates@wisc.edu>
1029    
1030            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1031            bug reported by Kurt Hornik and Michael Hahsler.
1032    
1033    2005-05-10  Douglas Bates  <bates@wisc.edu>
1034    
1035            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1036            logical sparse matrices.  These will also be used in the symbolic
1037            analysis for lmer objects.
1038    
1039            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1040            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1041    
1042    2005-05-06  Douglas Bates  <bates@wisc.edu>
1043    
1044            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1045            colMeans, colSums, rowMeans and rowSums.
1046    
1047    2005-04-18  Douglas Bates  <bates@wisc.edu>
1048    
1049            * src/lgCMatrix.[ch]: code for _validate method and stub for
1050            multiplication operation.
1051    
1052            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1053            to dgetrs.
1054    
1055            * src/init.c: Fix cut-and-paste error in definition of
1056            dgeMatrix_matrix_solve
1057    
1058            * src/{many files}: Tighten code by using ALLOC_SLOT.
1059    
1060    2005-04-15  Douglas Bates  <bates@wisc.edu>
1061    
1062            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1063    
1064            * DESCRIPTION: Eliminate import of stats.
1065    
1066    
1067    2005-04-06  Douglas Bates  <bates@wisc.edu>
1068    
1069            * R/AllClass.R : add logical sparse matrix classes
1070    
1071    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1072    
1073            * R/dgTMatrix.R: add "[" method for triplet matrices
1074            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1075    
1076    2005-03-31  Douglas Bates  <bates@wisc.edu>
1077    
1078            * DESCRIPTION (Version): release 0.95-5 to CRAN
1079    
1080            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1081            * R/sparseMatrix.R: %*%, crossprod()
1082            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1083            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1084            * src/lmer.c (lmer_fitted): fix thinko
1085    
1086    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1087    
1088            * R/AllClass.R: add two virtual sparse classes ``on top''
1089    
1090    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1091    
1092            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1093                    correspondingly fix examples and tests/ since new()
1094                    doesn't work for virtual classes.
1095    
1096    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1097    
1098            * R/Matrix.R (as.matrix): method and one for unname()
1099            * tests/dpoMatrix.R: tests should now be less platform dependent;
1100              also run for R 2.1.0; using as.matrix()
1101    
1102    2005-03-15  Douglas Bates  <bates@wisc.edu>
1103    
1104            * R/pMatrix.R: "pMatrix" class added
1105            * ....
1106    
1107    2005-03-14  Douglas Bates  <bates@wisc.edu>
1108    
1109            * R/dtpMatrix.R: Add unpack method and an example.
1110    
1111            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1112            of general symmetric matrices and associated S4 methods.
1113    
1114    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1115            +
1116    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1119              crossprod() and "%*%" methods added; tests, too.
1120            * tests/matprod.R: new, for testing these
1121    
1122    2005-03-03  Douglas Bates  <bates@wisc.edu>
1123    
1124            * src/lmer.c (lmer_fitted): Added.
1125    
1126    2005-03-02  Douglas Bates  <bates@wisc.edu>
1127    
1128            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1129    
1130    2005-02-28  Douglas Bates  <bates@wisc.edu>
1131    
1132            * src/*.c,po/,inst/po: Internationalization and localization of
1133            the package.
1134    
1135            * src/ldl.[ch]: Removed these as their contents are referenced in the
1136            R_ldl.c file.
1137    
1138            * src/flame.[ch]: Removed these source files.
1139    
1140            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1141    
1142            * src/LU.[ch],src/init.c: absorb in factorizations
1143    
1144            * src/Mutils.h: prepare for internationalization
1145    
1146            * src/cblas.h: move the enum definitions to Mutils.h and remove
1147            this file
1148    
1149    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1152    
1153            * R/dtrMatrix.R: fix t() method
1154    
1155            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1156            * NAMESPACE: export them (and import generics from "methods")
1157            * tests/group-methods.R : and test them.
1158    
1159            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1160            border case
1161    
1162    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1163    
1164            * DESCRIPTION (Version): 0.95-2  released to CRAN
1165    
1166            * src/dgBCMatrix.c:
1167            * src/lmer.c: many changes
1168            * ...
1169    
1170    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/Matrix.R: add more sophisticated show() method.
1173    
1174    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1175    
1176            * */* : almost complete reorganization of classes.
1177    
1178    2005-01-26  Douglas Bates  <bates@wisc.edu>
1179    
1180            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1181            for the geMatrix class.
1182    
1183    2005-01-24  Douglas Bates  <bates@wisc.edu>
1184    
1185            * src/Makefile (clean): Remove *.a and *.so
1186    
1187            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1188    
1189    2005-01-23  Douglas Bates  <bates@wisc.edu>
1190    
1191            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1192            had an effect in cases with more than 2 grouping factors.
1193    
1194    2005-01-03  Douglas Bates  <bates@wisc.edu>
1195    
1196            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1197    
1198    2004-12-23  Douglas Bates  <bates@wisc.edu>
1199    
1200            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1201            and R_useDynamicSymbols (suggested by B.D.Ripley).
1202    
1203    2004-12-14  Douglas Bates  <bates@wisc.edu>
1204    
1205            * R/sscMatrix.R: Add determinant methods
1206    
1207            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1208            for tripletMatrix to matrix.
1209    
1210    2004-12-13  Douglas Bates  <bates@wisc.edu>
1211    
1212            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1213            no longer used.
1214    
1215            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1216            with dynamic allocation of scratch arrays.
1217    
1218            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1219            for multivariate random effects with multiple grouping factors.
1220            Fixes part but not all of #15.
1221    
1222    2004-12-03  Douglas Bates  <bates@wisc.edu>
1223    
1224            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1225            scalar grouping factors corrected.
1226    
1227    2004-11-29  Douglas Bates  <bates@wisc.edu>
1228    
1229            * src/bCrosstab.c: remove diag_update which is no longer used
1230    
1231    2004-11-16  Douglas Bates  <bates@wisc.edu>
1232    
1233          * 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
1234          .h file can be included.          .h file can be included.
1235    
1236  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1237    
1238          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1239          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1240    
1241          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1242    
1243  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1244    
1245          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1246    
1247  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1248    
1249          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1250    
1251  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1252    
1253          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1254    
1255  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1256    
1257          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1258    
1259  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1260    
1261          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1262          routines.          routines.
1263    
1264  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1265    
1266          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1267    
1268  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1269    
1270          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1271    

Legend:
Removed from v.350  
changed lines
  Added in v.1600

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge