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 726, Thu May 12 14:59:04 2005 UTC revision 1619, Fri Oct 6 21:29:15 2006 UTC
# Line 1  Line 1 
1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-3
4    
5            * R/diagMatrix.R (bdiag): new function constructing block diagonal
6            (sparse) matrices.
7            * man/bdiag.Rd: docu + examples
8    
9            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
10    
11            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
12            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
13    
14            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
15            that result is sparse or diagonal (and not dense).
16    
17            * man/Subassign-methods.Rd: fix examples
18    
19            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
20            should always return a sparse (and not sometimes a diagonal) matrix.
21    
22    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
25    
26    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * DESCRIPTION (Version): 0.9975-2
29    
30            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
31    
32    2006-10-02  Douglas Bates  <bates@R-project.org>
33    
34            * tests/dg_Matrix.R: Simplify test taking into account new code.
35    
36    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
39    
40            * R/lsTMatrix.R: new files w/ missing methods
41            * R/nsTMatrix.R:  "  'for completeness'
42    
43            * tests/Class+Meth.R: a bit less 'not.ok.classes'
44    
45            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
46    
47    
48    2006-09-28  Douglas Bates  <bates@R-project.org>
49    
50            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
51            included.
52    
53            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
54            Export C-callable functions used in Zt_create in lme4.
55    
56    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version): 0.9975-1
59    
60            * tests/simple.R: less checks fail; using NA, found that our
61                    kronecker() is not base-compatible with NA's.
62    
63            * R/dMatrix.R: "Compare" method now implemented for all cases
64    
65            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
66    
67            * man/dtpMatrix-class.Rd: mention length of 'x' slot
68    
69            * src/dtpMatrix.c (dtpMatrix_validate): fix check
70            * src/dspMatrix.c (dspMatrix_validate): ditto
71    
72            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
73              including coercion to [nl]tTMatrix.
74    
75            * R/diagMatrix.R (show): print a header line as for other classes.
76    
77    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/Makefile.win (SUBDIRS): fix typo
80    
81    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
84    
85    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
88            symmetric and y missing in R code using %*% (cholmod_aat doesn't
89            accept a symmetric matrix).
90            * tests/group-methods.R: Uncomment test of crossprod applied to
91            lsCMatrix objects.
92    
93    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/AllClass.R (symmetricMatrix): add validity method (available
96            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
97    
98            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
99    
100            * tests/indexing.Rout.save:
101            * tests/indexing.R: additions, mainly for 'lsparse'
102    
103            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
104            case.
105    
106            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
107    
108    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
111                    as 'N' (1-letter - Ok?)
112    
113            * tests/group-methods.R: add test for logical + NAs
114    
115            * R/dMatrix.R ("Compare"): fix to work with NA's
116    
117            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
118    
119            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
120                    which is implemented.
121    
122    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/chm_common.c: coerce logical <-> double instead of
125            typecasting;  needed for "l" matrix handling in cholmod.
126    
127            * tests/other-pkgs.R (graph): small extension in "graph" checks.
128    
129            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
130            (Tsp2grNEL): other fixes needed
131    
132    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
135                    Matrices, since "lMatrix", also "lsparseM" can have NA
136            * R/ndenseMatrix.R, etc: new source files
137            * man/nsparseMatrix-classes.Rd, etc: new help files
138            * tests/: adaptions
139            * src/chm_common.c (chm_dense_to_SEXP): and others:
140                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
141            * src/Csparse.c, etc: ditto
142    
143    2006-09-11  Douglas Bates  <bates@R-project.org>
144    
145            * src/Mutils.[ch],init.c inst/include/*.h: Move the
146            alloc_d**Matrix functions to the lme4 package.
147    
148    2006-09-09  Douglas Bates  <bates@R-project.org>
149    
150            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
151            fixed
152    
153    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/lMatrix.R: new
156    
157            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
158    
159            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
160            * man/tcrossprod.Rd: ditto
161    
162    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
165            for exported functions
166            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
167            Remove partitioning algorithms for sparse matrix reordering.  The
168            copyright on the Metis code was problematic and the methods were
169            rarely used.
170            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
171            operations are now done entirely in CHOLMOD code.
172    
173    2006-09-06  Douglas Bates  <bates@R-project.org>
174    
175            * src/Mutils.h: Remove functions that are no longer used.
176    
177    2006-09-04  Douglas Bates  <bates@R-project.org>
178    
179            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
180            * src/DEPS.mkf: update
181    
182    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * created branches/Matrix-for-R-2.3.x;  on trunk: do
185            * DESCRIPTION (Version): 0.9975-0
186            (Depends): R (>= 2.4.0)
187    
188    2006-09-01  Douglas Bates  <bates@R-project.org>
189    
190            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
191    
192    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
195            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
196    
197            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
198    
199    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
202            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
203            * R/dsparseMatrix.R: ditto
204            * R/Csparse.R: ditto
205    
206    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/dMatrix.R (Compare): improve availability of "<", etc
209            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
210    
211    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
214            of a 0-index which was used as 1-index (..hmm)
215    
216            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
217    
218            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
219            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
220            (.is.diagonal): ditto
221    
222            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
223    
224            * R/Matrix.R (Matrix): also work for NA data
225    
226    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
229            in all cases.
230    
231    2006-08-27  Douglas Bates  <bates@R-project.org>
232    
233            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
234            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
235    
236    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
239            subclasses of "ddenseMatrix"
240            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
241            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
242            instead of half dozen specialized ones.
243    
244    2006-08-25  Douglas Bates  <bates@R-project.org>
245    
246            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
247            <tillard@cirad.fr> - ordering standard errors to match effects.
248    
249    2006-08-24  Douglas Bates  <bates@R-project.org>
250    
251            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
252            on R_ldl.
253            * R/lCholCMatrix.R,
254            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
255            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
256            * many files in ./R and ./src: Use more general version of
257            dup_mMatrix_as_dgeMatrix to simplify method definitions.
258            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
259            dtpMatrix, dspMatrix and dppMatrix conversions.
260    
261    
262    2006-08-23  Douglas Bates  <bates@R-project.org>
263    
264            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
265            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
266            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
267            dgeMatrix_crossprod (may need to do this in other places).
268            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
269            generic and method for dsCMatrix.  Use CHOLMOD for chol().
270    
271    2006-08-22  Douglas Bates  <bates@R-project.org>
272    
273            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
274            types of classed Matrices, matrices or numeric or logical vectors.
275            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
276            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
277            to Mutils.h (as an inline) and change name to Matrix_check_class;
278            fixes in as_cholmod_factor and chm_factor_to_SEXP.
279            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
280            dsCMatrix_matrix_solve.  Comment out vestigial functions.
281            * src/Csparse.c: use diag_P and uplo_P macros.
282    
283    2006-08-21  Douglas Bates  <bates@R-project.org>
284    
285            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
286            valgrind.
287            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
288            inverses.
289            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
290            -Wall warnings.
291            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
292            Use dup_mMatrix_as_dgeMatrix.
293    
294    2006-08-20  Douglas Bates  <bates@R-project.org>
295    
296            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
297            * tests/sparseQR.R: Added
298            * man/sparseQR-class.Rd: Document methods for qr.* generics
299            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
300    
301    2006-08-19  Douglas Bates  <bates@R-project.org>
302    
303            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
304            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
305            and qr.fitted.
306            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
307            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
308    
309    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
312            the base version has no "..." argument.
313    
314            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
315    
316            * R/Matrix.R: define and
317            * NAMESPACE: export as.numeric() and as.logical() methods.
318                    Let's hope these do not badly slow down something...
319            Finally export the zapsmall() method.
320    
321    2006-08-17  Douglas Bates  <bates@R-project.org>
322    
323            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
324            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
325            * src/dtCMatrix.c :Remove code that is no longer used
326            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
327    
328    2006-08-14  Douglas Bates  <bates@R-project.org>
329    
330            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
331            Csparse_to_logical and Csparse_symmetric_to_general.
332            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
333            coercion methods between CsparseMatrix and TsparseMatrix.
334    
335    2006-08-14  Douglas Bates  <bates@R-project.org>
336    
337            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
338            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
339            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
340            possible.
341    
342    2006-08-12  Douglas Bates  <bates@R-project.org>
343    
344            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
345              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
346              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
347              generalize conversions between TsparseMatrix, CsparseMatrix,
348              denseMatrix and matrix.  Preserve triangularity property and
349              propagate Dimnames in the easy cases.
350    
351    2006-08-10  Douglas Bates  <bates@R-project.org>
352    
353            * src/lmer.c: adjust checks in glmer_init for S4SXP
354            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
355            before S4SXP but for the wrong reasons.
356    
357    2006-08-08  Douglas Bates  <bates@R-project.org>
358    
359            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
360            Later modified to return the upper triangle only.
361            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
362    
363    2006-08-07  Douglas Bates  <bates@R-project.org>
364    
365            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
366            R-level conversion to a sparse symmetric class.
367            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
368            Remove conversion to sparse symmetric classes (now done in C code).
369    
370    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
373            * man/band.Rd:  adapt the \dontshow{} unit test.
374    
375    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * DESCRIPTION (Version): 0.995-14  for CRAN
378    
379            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
380    
381            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
382            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
383    
384            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
385            * R/Tsparse.R (tril, triu, band): methods
386            * R/dgRMatrix.R (tril, ...):    ditto
387            * man/band.Rd:                  ditto
388    
389    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Matrix.R (head, tail): directly use utils:::head.matrix
392                    to be up-to-date automatically.
393    
394    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
397    
398            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
399            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
400            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
401            such that the S4 objects are always created by the current version
402            of R and 'Matrix' class definitions.
403    
404    2006-08-01  Douglas Bates  <bates@R-project.org>
405    
406            * R/lmer.R (LMEoptimize method), tests/lmer.R,
407            inst/external/test3comp.rda: Added warnings for convergence on
408            boundary and test cases.
409    
410            * src/lmer.c (mer_postVar): Modified to return the variances that
411            are marginal to the fixed effects, not conditional on them (which
412            is what the bVar slot contents represent).
413    
414    2006-07-31  Douglas Bates  <bates@R-project.org>
415    
416            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
417            function which calls the C function mer_hat_trace2.
418    
419            * man/ranef.Rd: Include description of "postVar" argument and
420            producing a caterpillar plot.
421    
422    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * NAMESPACE:    change  "correlation" to "corMatrix"
425            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
426            * R/dpoMatrix.R: ditto
427            * R/lmer.R:      ditto
428    
429    2006-07-28  Douglas Bates  <bates@R-project.org>
430    
431            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
432            RZXinv slot's contents into a separate internal function that can
433            be used in mer_hat_trace.
434    
435    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
438            via new smart
439            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
440            utility functions.
441    
442    
443    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/Csparse.R (tril, triu, band): do return *triangular* classed
446            matrices when appropriate; band() even symmetric ones.
447            (replCmat): extend to potentially all "CsparseMatrix"
448            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
449            allow subassignment for special sparse matrices.
450    
451            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
452    
453            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
454            argument; in glmer_*(): print only if(verbose).
455    
456            speed-optimize a few places by moving REAL(.) out of loops.
457    
458            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
459    
460    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
463                    since that wrongly triggers also for M[ logi , ]
464    
465            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
466            a symmetric matrix that results in a non-symmetric one.
467            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
468    
469            * R/dMatrix.R: make round(M) work as round(M, 0)
470    
471            * R/dgTMatrix.R (image): coordinate system and axis now use
472            1-based indices, not 0-based ones.
473    
474            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
475            * tests/indexing.R: test it.
476    
477            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
478            * man/isSymmetric-methods.Rd: and document it.
479    
480            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
481            * man/SparseM-conv.Rd: docu them
482    
483            * tests/other-pkgs.R: renamed from tests/graph.R and add example
484                    for 'SparseM' conversions
485    
486    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
487    
488            * R/Matrix.R (head): added head() and tail() methods.
489    
490    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * DESCRIPTION (Version): 0.995-12 released to CRAN
493    
494    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * tests/simple.R: add check for correct dsT -> dgT coercion;
497                    add check for correct printing of symmetric sparse matrices.
498    
499            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
500            for sparse symmetric matrices.
501    
502            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
503            diagonal twice.
504    
505    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
506    
507            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
508            being applied to the x slot (detected by Brian Ripley).
509    
510    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
513    
514            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
515    
516    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * src/lgCMatrix.c (lgCMatrix_diag): new function
519            * R/lgCMatrix.R (diag): for new method
520    
521            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
522                 ==> construction of illegal "*gTMatrix" via new() should
523                 now be much less easy:
524            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
525    
526            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
527                    directly.
528            * man/Matrix.Rd: documents it.
529    
530    2006-07-06  Douglas Bates  <bates@R-project.org>
531    
532            * src/pedigree.c (pedigree_inbreeding): Correction in
533            initialization.  This function is not currently being used and is
534            not fully tested.
535    
536            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
537            Introduced the glmer class.  Added code for mcmcmsamp on glmer
538            objects.  Modified validity check on pedigree objects to account
539            for nonparallel patterns of missingness of parents.
540    
541            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
542            class.
543    
544    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/pMatrix.R: coercion pMatrix -> Tsparse
547    
548    2006-06-12  Douglas Bates  <bates@R-project.org>
549    
550            * DESCRIPTION (Version): 0.995-11 released to CRAN
551    
552            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
553            the output from mcmcsamp.
554    
555    2006-06-10  Douglas Bates  <bates@R-project.org>
556    
557            * R/lmer.R (simulestimate): added C code for calculating the trace
558            of the hat matrix.
559    
560    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
563            classes.
564            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
565    
566    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/dgTMatrix.R (colSums): etc. All four of
569            colSums(), rowSums(), colMeans(), rowMeans() now should work for
570            all "Matrices".
571    
572    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
573    
574            * R/lmer.R (panel.ci): Add a reference line at zero and a
575            background grid to the qqmath plot of ranef.lmer.
576    
577    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
578    
579            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
580            grouping factors to be specified in the formula as (1|foo/bar).
581    
582    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
583    
584            * R/lmer.R (findbars and others): Change check of is.numeric to
585            !is.language to resolve the bug reported by Jacob Wegelin.
586    
587            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
588            code to evaluate inbreeding coefficients without calculating T,
589            based on code in Sargolzaei and Iwaisaki's paper.
590    
591    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
592    
593            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
594            generic and mer methods for isNested and denomDF. This denomDF was
595            an attempt to emulate that in lme but I don't think that makes
596            sense.  Use the trace of the hat matrix instead.
597    
598    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
601            the C code depending on a slot structure that's no longer valid.
602            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
603    
604    
605    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
606    
607            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
608            of lowerTriMatrix generic and methods to tril (also upper to triu)
609            and added a general band extractor.
610    
611    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
612    
613            * R/pedigree.R (pedigree): Replace sire and dam values outside the
614            allowable range with NAs. Added a corresponding check in the
615            validity check for the pedigree class.
616    
617            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
618            crossprod methods now inherits from symmetricMatrix.
619    
620    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
623            generics lowerTriMatrix and upperTriMatrix along with methods for
624            the Csparse virtual class.  Also added a C function Csparse_band
625            that implements these methods by calling cholmod_band.
626    
627    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
630            erased when it was NULL.  This led to invalid subselections!
631    
632    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
633    
634            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
635            in method for "t" so as not to lose the unit diagonal property.
636    
637    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
638    
639            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
640            and methods.  This is now an option to the ranef method for the
641            mer class.
642    
643            * src/cs_utils.c: Ensure that the nz component is -1 for a
644            compressed column-oriented matrix.  Minor formatting cleanup.
645    
646            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
647            objects.
648    
649    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
652            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
653    
654    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
655    
656            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
657            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
658    
659            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
660            for the dtCMatrix class.
661    
662    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
663    
664            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
665            and methods for it.
666    
667    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
670            arguments, such that M %*% 1:6 now works
671            * Tests/matprod.R: test the above
672    
673    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
674    
675            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
676            the ranef.lmer class.
677    
678            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
679            methods to extract the posterior variances from the bVar slot.
680    
681    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
684            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
685    
686            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
687            * tests/simple: (extended)
688    
689            * R/sparseMatrix.R (isTriangular): now using much improved
690            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
691    
692    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
693    
694            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
695            (problem report from Franklin Parlamis).  This should be done
696            generally.
697    
698    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
699    
700            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
701            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
702            update the plot methods.
703    
704    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
705    
706            * R/lmer.R (resid and ranef methods):  Added methods for the
707            "residuals" and "resid" generic but only for linear mixed model
708            fits.  Changed the ranef method to return a list of data frames so
709            that the plot methods now work.
710    
711    2006-03-16  Douglas Bates  <bates@bates2>
712    
713            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
714            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
715    
716            * DESCRIPTION (Date): New release
717    
718    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
721    
722            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
723            * man/KNex.Rd: and other help files
724            * tests/*.R: several ones needed adaption
725            * inst/doc/Comparisons.Rnw: ditto
726    
727    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
730    
731            * tests/indexing.R: tests for new [<- methods for sparse matrices.
732    
733    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
736    
737            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
738    
739    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * R/dMatrix.R: enable things like  M [ M < 10 ]
742            * R/dgeMatrix.R: implement it
743    
744    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/AllClass.R: define "summary.mer" and "*.lmer"
747            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
748            * R/lmer.R (show): now works with summary()
749    
750    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
753            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
754                    support the above
755    
756    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
757    
758            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
759            Use glmFit$prior.weights for weights in a glmm.
760            Allow an option usePQL = FALSE to skip the PQL steps for the
761            Laplace method (and, in time, the AGQ method).
762    
763            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
764            into a separate function internal_mer_Xfactor to be able to call
765            it from internal_bhat.
766    
767    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * tests/Class+Meth.R (tstMatrixClass): function for much better
770            testing; now again of all actual classes.
771    
772            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
773                    use macros and define make_d_matrix_* and make_i_matrix_*
774                    where _i_ is for the ldense routines:
775    
776            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
777            * src/ldense.c (lsyMatrix_as_lgeMatrix):
778    
779            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
780    
781    
782    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
785                    many different kinds of matrices.
786            * R/*.R: quite a few new methods were needed for R CMD check with
787                    new Matrix().  Very good for users playing around.
788    
789    
790    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * src/dgeMatrix.c (dMatrix_validate): new
793            * src/Mutils.c (dense_nonpacked_validate): new
794    
795            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
796    
797    
798    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
799    
800            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
801    
802    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
803    
804            * DESCRIPTION (Version): 0.99-6 released to CRAN
805    
806            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
807            segfault in cases with multiple non-nested grouping factors.
808    
809    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
812                    (Depends): also on 'utils'
813    
814            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
815            * R/diagMatrix.R (Diagonal): constructor and methods for
816            diagonal matrices
817    
818            * R/ltTMatrix.R: new "minimal methods"
819    
820    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
823            all methods (and help files).
824    
825    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
826    
827            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
828                    for case (dimn.  op  no_dimn.)
829    
830    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
831    
832            * DESCRIPTION (Version): 0.99-2  released to CRAN
833    
834    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
835    
836            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
837            by Julian Faraway.
838    
839    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * R/Auxiliaries.R (try_as): new utility
842            * R/sparseMatrix.R: use try_as() in coercion to original class
843    
844    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
847    
848    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/Auxiliaries.R (dimNamesCheck): added
851    
852            * R/Matrix.R (as.array), (as.vector): new
853    
854    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
857                    default.
858            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
859                    "pMatrix" now contains "sparseMatrix"
860    
861    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * tests/Class+Meth.R: new tests; t(t(m)) == m
864    
865            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
866    
867            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
868            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
869    
870            * R/dspMatrix.R: typo in "t" method
871    
872    2005-09-18  Douglas Bates  <bates@wisc.edu>
873    
874            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
875            * R/Tsparse.R: instead of R/gTMatrix.R
876            * R/Csparse.R: new
877            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
878            * src/Tsparse.c: new; many trivial methods calling cholmod_()
879            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
880                            via cholmod
881    
882    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * R/Auxiliaries.R (non0ind): new function using new C code
885            * src/dgCMatrix.c (compressed_non_0_ij): new utility
886    
887    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
888    
889            * src/chm_common.h: header file required by all C sources that
890            call CHOLMOD functions.  It defines a cholmod_common structure
891            called 'c' whose address is passed as the last argument to
892            (virtually) every CHOLMOD function.
893    
894            * src/Pattern.c: Simple example of the use of CHOLMOD.
895    
896            * src/init.c: initialize and finalize the cholmod_common structure.
897    
898            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
899            LDL and CCOLAMD from the U. of Florida sparse matrix library.
900    
901    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * inst/test-tools.R: new file collecting the utility functions used
904                    in ./tests/*.R
905    
906            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
907            * R/Matrix.R (cbind2): methods for NULL and missing
908    
909    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * R/AllClass.R: new "index" class for "[" and "[<-":
912                    First cut at "symmetricMatrix" and "triangularMatrix"
913            * R/gTMatrix.R (.ind.prep): new function;
914                    Logical and character indexing now work too.
915            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
916            * tests/indexing.R: new, including *.Rout.save
917            * tests/dgTMatrix.R: new
918    
919    2005-08-29  Douglas Bates  <bates@wisc.edu>
920    
921            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
922            indicator pos not being updated.  Also enforced upper triangular
923            for symmetric case.  Need to coerce edges component of elements of
924            edge list - grr! (Why don't they define their classes cleanly?)
925    
926    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
927    
928            * R/Matrix.R:  added first "[<-" methods; not yet functional
929            * R/denseMatrix.R: ditto
930            * man/Subassign-methods.Rd: new help file for these
931    
932    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * DESCRIPTION (Version): 0.98-6
935    
936            * R/denseMatrix.R: new file for "[" fallback methods for all dense
937            matrices.
938    
939    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
942                    as( <logical>, "matrix")
943    
944            * R/pMatrix.R: coercion to "lgTMatrix"
945    
946            * R/gTMatrix.R: new virtual class to define "[" methods for.
947            * man/gTMatrix-class.Rd:
948            * General slight re-organization of where "[" methods are defined.
949              more to come.
950    
951    2005-08-18  Douglas Bates  <bates@wisc.edu>
952    
953            * DESCRIPTION (Version): 0.98-5  released to CRAN
954    
955            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
956            * .....
957    
958    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
959    
960            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
961            or glmer objects.
962    
963    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
966    
967    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
968    
969            * R/HBMM.R: finish re-writing R-only code.
970    
971    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
972    
973            * man/externalFormats.Rd: move documentation for writeHB and
974            writeMM here.
975    
976            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
977            (suggested by Paul Roecker).
978    
979            * tests/validObj.R (assertError): Comment out test that is failing
980            after recent changes in r-devel.
981    
982    
983    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * R/AllClass.R: intermediate virtual class "denseMatrix"
986            * man/denseMatrix-class.Rd
987            * NAMESPACE: export it, and also export
988            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
989    
990    2005-08-10  Douglas Bates  <bates@wisc.edu>
991    
992            * DESCRIPTION (Version): 0.98-3 to CRAN
993    
994            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
995            matrix_solve code (which was really, really wrong).
996    
997    2005-08-07  Douglas Bates  <bates@wisc.edu>
998    
999            * DESCRIPTION (Version): 0.98-2
1000    
1001            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1002    
1003            * R/lmer.R (abbrvNms): new
1004            * R/lmer.R (mcmcsamp): allow transformed parameters
1005            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1006            for the Harwell-Boeing and the MatrixMarket formats.
1007    
1008    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1009    
1010            * man/dtrMatrix-class.Rd: add examples
1011            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1012    
1013            * TODO: note the dtpMatrix (docu) bug
1014    
1015            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1016            in order to ensure that new as.matrix() is used by old functions,
1017            e.g., svd(), qr(), eigen(), dist(),..;
1018                  apply(), also matplot() or pairs().
1019    
1020    
1021    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1024              add comments about 'control' / lmerControl() arguments
1025    
1026    2005-07-27  Douglas Bates  <bates@wisc.edu>
1027    
1028            * man/sleepstudy.Rd: Added the sleep data set.
1029            * DESCRIPTION (Version): 0.98-1  released to CRAN
1030    
1031    2005-07-12  Douglas Bates  <bates@wisc.edu>
1032            * man/sleepstudy.Rd: Added the sleep data set.
1033    
1034            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1035            .Call calls that were producing spurious output.
1036    
1037    2005-07-05  Douglas Bates  <bates@wisc.edu>
1038    
1039            * R/lmer.R (lmer): stored updated variance component estimates in
1040            mer object for the generalized model.  (Bug reported by Renaud
1041            Lancelot).
1042    
1043    2005-07-03  Douglas Bates  <bates@wisc.edu>
1044    
1045            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1046            unidimensional case.
1047    
1048    2005-06-08  Douglas Bates  <bates@wisc.edu>
1049    
1050            * DESCRIPTION (Version): 0.96-1
1051    
1052            * moved  lmer-class' R and C code moved from lme4 to here
1053    
1054    2005-06-04  Douglas Bates  <bates@wisc.edu>
1055    
1056            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1057            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1058    
1059    2005-06-02  Douglas Bates  <bates@wisc.edu>
1060    
1061            * src/Makefile.win: Forgot to update this when Makefile changed.
1062    
1063    2005-05-11  Douglas Bates  <bates@wisc.edu>
1064    
1065          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1066          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1067    
1068  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1069    
1070          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1071          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 1074 
1074          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1075          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
1076    
1077  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1078    
1079          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1080          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1081    
1082  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1083    
1084          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1085          multiplication operation.          multiplication operation.
# Line 30  Line 1092 
1092    
1093          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1094    
1095  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1096    
1097          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1098    
1099          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1100    
1101    
1102  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1103    
1104          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1105    
# Line 46  Line 1108 
1108          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1109          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1110    
1111  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1112    
1113          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1114    
# Line 72  Line 1134 
1134          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1135            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1136    
1137  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1138    
1139          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1140          * ....          * ....
1141    
1142  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1143    
1144          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1145    
# Line 92  Line 1154 
1154            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1155          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1156    
1157  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1158    
1159          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1160    
1161  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1162    
1163          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1164    
1165  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1166    
1167          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1168          the package.          the package.
# Line 148  Line 1210 
1210    
1211          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1212    
1213  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1214    
1215          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1216          for the geMatrix class.          for the geMatrix class.
1217    
1218  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1219    
1220          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1221    
1222          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1223    
1224  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1225    
1226          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1227          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1228    
1229  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1230    
1231          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1232    
1233  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1234    
1235          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1236          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1237    
1238  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1239    
1240          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1241    
1242          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1243          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1244    
1245  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1246    
1247          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1248          no longer used.          no longer used.
# Line 192  Line 1254 
1254          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1255          Fixes part but not all of #15.          Fixes part but not all of #15.
1256    
1257  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1258    
1259          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1260          scalar grouping factors corrected.          scalar grouping factors corrected.
1261    
1262  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1263    
1264          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1265    
1266  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1267    
1268          * 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
1269          .h file can be included.          .h file can be included.
1270    
1271  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1272    
1273          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1274          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1275    
1276          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1277    
1278  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1279    
1280          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1281    
1282  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1283    
1284          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1285    
1286  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1287    
1288          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1289    
1290  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1291    
1292          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1293    
1294  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1295    
1296          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1297          routines.          routines.
1298    
1299  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1300    
1301          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1302    
1303  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1304    
1305          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1306    

Legend:
Removed from v.726  
changed lines
  Added in v.1619

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