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revision 976, Fri Oct 7 20:18:29 2005 UTC revision 1654, Fri Oct 27 16:58:15 2006 UTC
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1    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R: solve(a, b="missing") based on
4            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
5            RHS = NULL.
6    
7            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
8            add more (needed) [t]crossprod() methods.
9    
10            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
11    
12            * R/Auxiliaries.R (as_CspClass): cleanup
13            (drop0): internal utility for "Csparse_drop(*, 0)"
14            (.bail.out.2): encourage active feedback
15    
16    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/dMatrix.R(Compare): new(), then slots [no validity check]
19    
20            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
21            non-valid or 'sorted' case).
22    
23            * R/dsparseMatrix.R: add "chol" method.
24            * R/ddenseMatrix.R: ditto
25    
26            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
27            * NAMESPACE (Ops)
28            * R/diagMatrix.R (diag2T): simple utility used "higher level"
29            coercion; deprecating direct lower level coercions.
30    
31            * R/*.R (seq): use seq_len() and seq_along() where possible.
32    
33    
34    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.9975-5 ready for release
37    
38    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
41    
42    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/AllClass.R (corMatrix): add 'validity' check;
45                    comment out unused "LDL" class definition
46            * NAMESPACE: mention, but do not export "LDL" class
47            * R/corMatrix.R: new (simple), needed for R-devel with
48            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
49              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
50    
51    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
54            use Rprintf and R's error handling.
55    
56    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
59            * tests/matprod.R: add tests for the bug fixed.
60    
61    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
64            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
65    
66    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
69    
70    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Version): 0.9975-3
73    
74            * R/diagMatrix.R (bdiag): new function constructing block diagonal
75            (sparse) matrices.
76            * man/bdiag.Rd: docu + examples
77    
78            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
79    
80            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
81            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
82    
83            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
84            that result is sparse or diagonal (and not dense).
85    
86            * man/Subassign-methods.Rd: fix examples
87    
88            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
89            should always return a sparse (and not sometimes a diagonal) matrix.
90    
91    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
94    
95    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
96    
97            * DESCRIPTION (Version): 0.9975-2
98    
99            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
100    
101    2006-10-02  Douglas Bates  <bates@R-project.org>
102    
103            * tests/dg_Matrix.R: Simplify test taking into account new code.
104    
105    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
108    
109            * R/lsTMatrix.R: new files w/ missing methods
110            * R/nsTMatrix.R:  "  'for completeness'
111    
112            * tests/Class+Meth.R: a bit less 'not.ok.classes'
113    
114            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
115    
116    
117    2006-09-28  Douglas Bates  <bates@R-project.org>
118    
119            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
120            included.
121    
122            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
123            Export C-callable functions used in Zt_create in lme4.
124    
125    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * DESCRIPTION (Version): 0.9975-1
128    
129            * tests/simple.R: less checks fail; using NA, found that our
130                    kronecker() is not base-compatible with NA's.
131    
132            * R/dMatrix.R: "Compare" method now implemented for all cases
133    
134            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
135    
136            * man/dtpMatrix-class.Rd: mention length of 'x' slot
137    
138            * src/dtpMatrix.c (dtpMatrix_validate): fix check
139            * src/dspMatrix.c (dspMatrix_validate): ditto
140    
141            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
142              including coercion to [nl]tTMatrix.
143    
144            * R/diagMatrix.R (show): print a header line as for other classes.
145    
146    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * src/Makefile.win (SUBDIRS): fix typo
149    
150    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
153    
154    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
155    
156            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
157            symmetric and y missing in R code using %*% (cholmod_aat doesn't
158            accept a symmetric matrix).
159            * tests/group-methods.R: Uncomment test of crossprod applied to
160            lsCMatrix objects.
161    
162    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/AllClass.R (symmetricMatrix): add validity method (available
165            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
166    
167            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
168    
169            * tests/indexing.Rout.save:
170            * tests/indexing.R: additions, mainly for 'lsparse'
171    
172            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
173            case.
174    
175            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
176    
177    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
180                    as 'N' (1-letter - Ok?)
181    
182            * tests/group-methods.R: add test for logical + NAs
183    
184            * R/dMatrix.R ("Compare"): fix to work with NA's
185    
186            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
187    
188            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
189                    which is implemented.
190    
191    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * src/chm_common.c: coerce logical <-> double instead of
194            typecasting;  needed for "l" matrix handling in cholmod.
195    
196            * tests/other-pkgs.R (graph): small extension in "graph" checks.
197    
198            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
199            (Tsp2grNEL): other fixes needed
200    
201    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
204                    Matrices, since "lMatrix", also "lsparseM" can have NA
205            * R/ndenseMatrix.R, etc: new source files
206            * man/nsparseMatrix-classes.Rd, etc: new help files
207            * tests/: adaptions
208            * src/chm_common.c (chm_dense_to_SEXP): and others:
209                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
210            * src/Csparse.c, etc: ditto
211    
212    2006-09-11  Douglas Bates  <bates@R-project.org>
213    
214            * src/Mutils.[ch],init.c inst/include/*.h: Move the
215            alloc_d**Matrix functions to the lme4 package.
216    
217    2006-09-09  Douglas Bates  <bates@R-project.org>
218    
219            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
220            fixed
221    
222    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/lMatrix.R: new
225    
226            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
227    
228            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
229            * man/tcrossprod.Rd: ditto
230    
231    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
232    
233            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
234            for exported functions
235            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
236            Remove partitioning algorithms for sparse matrix reordering.  The
237            copyright on the Metis code was problematic and the methods were
238            rarely used.
239            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
240            operations are now done entirely in CHOLMOD code.
241    
242    2006-09-06  Douglas Bates  <bates@R-project.org>
243    
244            * src/Mutils.h: Remove functions that are no longer used.
245    
246    2006-09-04  Douglas Bates  <bates@R-project.org>
247    
248            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
249            * src/DEPS.mkf: update
250    
251    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * created branches/Matrix-for-R-2.3.x;  on trunk: do
254            * DESCRIPTION (Version): 0.9975-0
255            (Depends): R (>= 2.4.0)
256    
257    2006-09-01  Douglas Bates  <bates@R-project.org>
258    
259            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
260    
261    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
264            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
265    
266            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
267    
268    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
271            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
272            * R/dsparseMatrix.R: ditto
273            * R/Csparse.R: ditto
274    
275    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/dMatrix.R (Compare): improve availability of "<", etc
278            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
279    
280    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
283            of a 0-index which was used as 1-index (..hmm)
284    
285            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
286    
287            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
288            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
289            (.is.diagonal): ditto
290    
291            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
292    
293            * R/Matrix.R (Matrix): also work for NA data
294    
295    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
298            in all cases.
299    
300    2006-08-27  Douglas Bates  <bates@R-project.org>
301    
302            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
303            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
304    
305    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
308            subclasses of "ddenseMatrix"
309            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
310            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
311            instead of half dozen specialized ones.
312    
313    2006-08-25  Douglas Bates  <bates@R-project.org>
314    
315            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
316            <tillard@cirad.fr> - ordering standard errors to match effects.
317    
318    2006-08-24  Douglas Bates  <bates@R-project.org>
319    
320            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
321            on R_ldl.
322            * R/lCholCMatrix.R,
323            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
324            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
325            * many files in ./R and ./src: Use more general version of
326            dup_mMatrix_as_dgeMatrix to simplify method definitions.
327            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
328            dtpMatrix, dspMatrix and dppMatrix conversions.
329    
330    
331    2006-08-23  Douglas Bates  <bates@R-project.org>
332    
333            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
334            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
335            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
336            dgeMatrix_crossprod (may need to do this in other places).
337            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
338            generic and method for dsCMatrix.  Use CHOLMOD for chol().
339    
340    2006-08-22  Douglas Bates  <bates@R-project.org>
341    
342            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
343            types of classed Matrices, matrices or numeric or logical vectors.
344            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
345            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
346            to Mutils.h (as an inline) and change name to Matrix_check_class;
347            fixes in as_cholmod_factor and chm_factor_to_SEXP.
348            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
349            dsCMatrix_matrix_solve.  Comment out vestigial functions.
350            * src/Csparse.c: use diag_P and uplo_P macros.
351    
352    2006-08-21  Douglas Bates  <bates@R-project.org>
353    
354            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
355            valgrind.
356            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
357            inverses.
358            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
359            -Wall warnings.
360            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
361            Use dup_mMatrix_as_dgeMatrix.
362    
363    2006-08-20  Douglas Bates  <bates@R-project.org>
364    
365            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
366            * tests/sparseQR.R: Added
367            * man/sparseQR-class.Rd: Document methods for qr.* generics
368            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
369    
370    2006-08-19  Douglas Bates  <bates@R-project.org>
371    
372            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
373            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
374            and qr.fitted.
375            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
376            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
377    
378    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
381            the base version has no "..." argument.
382    
383            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
384    
385            * R/Matrix.R: define and
386            * NAMESPACE: export as.numeric() and as.logical() methods.
387                    Let's hope these do not badly slow down something...
388            Finally export the zapsmall() method.
389    
390    2006-08-17  Douglas Bates  <bates@R-project.org>
391    
392            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
393            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
394            * src/dtCMatrix.c :Remove code that is no longer used
395            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
396    
397    2006-08-14  Douglas Bates  <bates@R-project.org>
398    
399            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
400            Csparse_to_logical and Csparse_symmetric_to_general.
401            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
402            coercion methods between CsparseMatrix and TsparseMatrix.
403    
404    2006-08-14  Douglas Bates  <bates@R-project.org>
405    
406            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
407            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
408            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
409            possible.
410    
411    2006-08-12  Douglas Bates  <bates@R-project.org>
412    
413            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
414              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
415              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
416              generalize conversions between TsparseMatrix, CsparseMatrix,
417              denseMatrix and matrix.  Preserve triangularity property and
418              propagate Dimnames in the easy cases.
419    
420    2006-08-10  Douglas Bates  <bates@R-project.org>
421    
422            * src/lmer.c: adjust checks in glmer_init for S4SXP
423            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
424            before S4SXP but for the wrong reasons.
425    
426    2006-08-08  Douglas Bates  <bates@R-project.org>
427    
428            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
429            Later modified to return the upper triangle only.
430            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
431    
432    2006-08-07  Douglas Bates  <bates@R-project.org>
433    
434            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
435            R-level conversion to a sparse symmetric class.
436            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
437            Remove conversion to sparse symmetric classes (now done in C code).
438    
439    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
442            * man/band.Rd:  adapt the \dontshow{} unit test.
443    
444    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * DESCRIPTION (Version): 0.995-14  for CRAN
447    
448            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
449    
450            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
451            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
452    
453            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
454            * R/Tsparse.R (tril, triu, band): methods
455            * R/dgRMatrix.R (tril, ...):    ditto
456            * man/band.Rd:                  ditto
457    
458    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/Matrix.R (head, tail): directly use utils:::head.matrix
461                    to be up-to-date automatically.
462    
463    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
466    
467            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
468            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
469            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
470            such that the S4 objects are always created by the current version
471            of R and 'Matrix' class definitions.
472    
473    2006-08-01  Douglas Bates  <bates@R-project.org>
474    
475            * R/lmer.R (LMEoptimize method), tests/lmer.R,
476            inst/external/test3comp.rda: Added warnings for convergence on
477            boundary and test cases.
478    
479            * src/lmer.c (mer_postVar): Modified to return the variances that
480            are marginal to the fixed effects, not conditional on them (which
481            is what the bVar slot contents represent).
482    
483    2006-07-31  Douglas Bates  <bates@R-project.org>
484    
485            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
486            function which calls the C function mer_hat_trace2.
487    
488            * man/ranef.Rd: Include description of "postVar" argument and
489            producing a caterpillar plot.
490    
491    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * NAMESPACE:    change  "correlation" to "corMatrix"
494            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
495            * R/dpoMatrix.R: ditto
496            * R/lmer.R:      ditto
497    
498    2006-07-28  Douglas Bates  <bates@R-project.org>
499    
500            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
501            RZXinv slot's contents into a separate internal function that can
502            be used in mer_hat_trace.
503    
504    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
507            via new smart
508            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
509            utility functions.
510    
511    
512    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Csparse.R (tril, triu, band): do return *triangular* classed
515            matrices when appropriate; band() even symmetric ones.
516            (replCmat): extend to potentially all "CsparseMatrix"
517            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
518            allow subassignment for special sparse matrices.
519    
520            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
521    
522            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
523            argument; in glmer_*(): print only if(verbose).
524    
525            speed-optimize a few places by moving REAL(.) out of loops.
526    
527            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
528    
529    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
532                    since that wrongly triggers also for M[ logi , ]
533    
534            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
535            a symmetric matrix that results in a non-symmetric one.
536            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
537    
538            * R/dMatrix.R: make round(M) work as round(M, 0)
539    
540            * R/dgTMatrix.R (image): coordinate system and axis now use
541            1-based indices, not 0-based ones.
542    
543            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
544            * tests/indexing.R: test it.
545    
546            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
547            * man/isSymmetric-methods.Rd: and document it.
548    
549            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
550            * man/SparseM-conv.Rd: docu them
551    
552            * tests/other-pkgs.R: renamed from tests/graph.R and add example
553                    for 'SparseM' conversions
554    
555    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
556    
557            * R/Matrix.R (head): added head() and tail() methods.
558    
559    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * DESCRIPTION (Version): 0.995-12 released to CRAN
562    
563    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * tests/simple.R: add check for correct dsT -> dgT coercion;
566                    add check for correct printing of symmetric sparse matrices.
567    
568            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
569            for sparse symmetric matrices.
570    
571            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
572            diagonal twice.
573    
574    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
575    
576            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
577            being applied to the x slot (detected by Brian Ripley).
578    
579    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
582    
583            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
584    
585    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * src/lgCMatrix.c (lgCMatrix_diag): new function
588            * R/lgCMatrix.R (diag): for new method
589    
590            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
591                 ==> construction of illegal "*gTMatrix" via new() should
592                 now be much less easy:
593            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
594    
595            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
596                    directly.
597            * man/Matrix.Rd: documents it.
598    
599    2006-07-06  Douglas Bates  <bates@R-project.org>
600    
601            * src/pedigree.c (pedigree_inbreeding): Correction in
602            initialization.  This function is not currently being used and is
603            not fully tested.
604    
605            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
606            Introduced the glmer class.  Added code for mcmcmsamp on glmer
607            objects.  Modified validity check on pedigree objects to account
608            for nonparallel patterns of missingness of parents.
609    
610            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
611            class.
612    
613    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/pMatrix.R: coercion pMatrix -> Tsparse
616    
617    2006-06-12  Douglas Bates  <bates@R-project.org>
618    
619            * DESCRIPTION (Version): 0.995-11 released to CRAN
620    
621            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
622            the output from mcmcsamp.
623    
624    2006-06-10  Douglas Bates  <bates@R-project.org>
625    
626            * R/lmer.R (simulestimate): added C code for calculating the trace
627            of the hat matrix.
628    
629    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
632            classes.
633            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
634    
635    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/dgTMatrix.R (colSums): etc. All four of
638            colSums(), rowSums(), colMeans(), rowMeans() now should work for
639            all "Matrices".
640    
641    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
642    
643            * R/lmer.R (panel.ci): Add a reference line at zero and a
644            background grid to the qqmath plot of ranef.lmer.
645    
646    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
649            grouping factors to be specified in the formula as (1|foo/bar).
650    
651    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
652    
653            * R/lmer.R (findbars and others): Change check of is.numeric to
654            !is.language to resolve the bug reported by Jacob Wegelin.
655    
656            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
657            code to evaluate inbreeding coefficients without calculating T,
658            based on code in Sargolzaei and Iwaisaki's paper.
659    
660    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
661    
662            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
663            generic and mer methods for isNested and denomDF. This denomDF was
664            an attempt to emulate that in lme but I don't think that makes
665            sense.  Use the trace of the hat matrix instead.
666    
667    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
670            the C code depending on a slot structure that's no longer valid.
671            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
672    
673    
674    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
675    
676            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
677            of lowerTriMatrix generic and methods to tril (also upper to triu)
678            and added a general band extractor.
679    
680    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
681    
682            * R/pedigree.R (pedigree): Replace sire and dam values outside the
683            allowable range with NAs. Added a corresponding check in the
684            validity check for the pedigree class.
685    
686            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
687            crossprod methods now inherits from symmetricMatrix.
688    
689    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
690    
691            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
692            generics lowerTriMatrix and upperTriMatrix along with methods for
693            the Csparse virtual class.  Also added a C function Csparse_band
694            that implements these methods by calling cholmod_band.
695    
696    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
699            erased when it was NULL.  This led to invalid subselections!
700    
701    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
702    
703            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
704            in method for "t" so as not to lose the unit diagonal property.
705    
706    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
709            and methods.  This is now an option to the ranef method for the
710            mer class.
711    
712            * src/cs_utils.c: Ensure that the nz component is -1 for a
713            compressed column-oriented matrix.  Minor formatting cleanup.
714    
715            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
716            objects.
717    
718    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
721            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
722    
723    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
724    
725            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
726            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
727    
728            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
729            for the dtCMatrix class.
730    
731    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
732    
733            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
734            and methods for it.
735    
736    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
739            arguments, such that M %*% 1:6 now works
740            * Tests/matprod.R: test the above
741    
742    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
743    
744            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
745            the ranef.lmer class.
746    
747            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
748            methods to extract the posterior variances from the bVar slot.
749    
750    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
753            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
754    
755            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
756            * tests/simple: (extended)
757    
758            * R/sparseMatrix.R (isTriangular): now using much improved
759            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
760    
761    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
762    
763            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
764            (problem report from Franklin Parlamis).  This should be done
765            generally.
766    
767    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
768    
769            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
770            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
771            update the plot methods.
772    
773    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
774    
775            * R/lmer.R (resid and ranef methods):  Added methods for the
776            "residuals" and "resid" generic but only for linear mixed model
777            fits.  Changed the ranef method to return a list of data frames so
778            that the plot methods now work.
779    
780    2006-03-16  Douglas Bates  <bates@bates2>
781    
782            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
783            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
784    
785            * DESCRIPTION (Date): New release
786    
787    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
790    
791            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
792            * man/KNex.Rd: and other help files
793            * tests/*.R: several ones needed adaption
794            * inst/doc/Comparisons.Rnw: ditto
795    
796    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
799    
800            * tests/indexing.R: tests for new [<- methods for sparse matrices.
801    
802    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
805    
806            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
807    
808    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * R/dMatrix.R: enable things like  M [ M < 10 ]
811            * R/dgeMatrix.R: implement it
812    
813    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * R/AllClass.R: define "summary.mer" and "*.lmer"
816            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
817            * R/lmer.R (show): now works with summary()
818    
819    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
822            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
823                    support the above
824    
825    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
826    
827            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
828            Use glmFit$prior.weights for weights in a glmm.
829            Allow an option usePQL = FALSE to skip the PQL steps for the
830            Laplace method (and, in time, the AGQ method).
831    
832            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
833            into a separate function internal_mer_Xfactor to be able to call
834            it from internal_bhat.
835    
836    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * tests/Class+Meth.R (tstMatrixClass): function for much better
839            testing; now again of all actual classes.
840    
841            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
842                    use macros and define make_d_matrix_* and make_i_matrix_*
843                    where _i_ is for the ldense routines:
844    
845            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
846            * src/ldense.c (lsyMatrix_as_lgeMatrix):
847    
848            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
849    
850    
851    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
854                    many different kinds of matrices.
855            * R/*.R: quite a few new methods were needed for R CMD check with
856                    new Matrix().  Very good for users playing around.
857    
858    
859    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * src/dgeMatrix.c (dMatrix_validate): new
862            * src/Mutils.c (dense_nonpacked_validate): new
863    
864            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
865    
866    
867    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
868    
869            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
870    
871    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
872    
873            * DESCRIPTION (Version): 0.99-6 released to CRAN
874    
875            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
876            segfault in cases with multiple non-nested grouping factors.
877    
878    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
881                    (Depends): also on 'utils'
882    
883            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
884            * R/diagMatrix.R (Diagonal): constructor and methods for
885            diagonal matrices
886    
887            * R/ltTMatrix.R: new "minimal methods"
888    
889    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
892            all methods (and help files).
893    
894    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
897                    for case (dimn.  op  no_dimn.)
898    
899    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
900    
901            * DESCRIPTION (Version): 0.99-2  released to CRAN
902    
903    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
904    
905            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
906            by Julian Faraway.
907    
908  2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910          * R/Auxiliaries.R (try_as): new utility          * R/Auxiliaries.R (try_as): new utility
# Line 88  Line 995 
995  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
998          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
999          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1000    
1001  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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