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revision 908, Thu Sep 8 15:30:08 2005 UTC revision 1646, Sun Oct 22 22:42:40 2006 UTC
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1    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
4    
5    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/AllClass.R (corMatrix): add 'validity' check;
8                    comment out unused "LDL" class definition
9            * NAMESPACE: mention, but do not export "LDL" class
10            * R/corMatrix.R: new (simple), needed for R-devel with
11            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
12              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
13    
14    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
15    
16            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
17            use Rprintf and R's error handling.
18    
19    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
22            * tests/matprod.R: add tests for the bug fixed.
23    
24    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
25    
26            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
27            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
28    
29    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
30    
31            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
32    
33    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * DESCRIPTION (Version): 0.9975-3
36    
37            * R/diagMatrix.R (bdiag): new function constructing block diagonal
38            (sparse) matrices.
39            * man/bdiag.Rd: docu + examples
40    
41            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
42    
43            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
44            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
45    
46            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
47            that result is sparse or diagonal (and not dense).
48    
49            * man/Subassign-methods.Rd: fix examples
50    
51            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
52            should always return a sparse (and not sometimes a diagonal) matrix.
53    
54    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
57    
58    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * DESCRIPTION (Version): 0.9975-2
61    
62            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
63    
64    2006-10-02  Douglas Bates  <bates@R-project.org>
65    
66            * tests/dg_Matrix.R: Simplify test taking into account new code.
67    
68    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
71    
72            * R/lsTMatrix.R: new files w/ missing methods
73            * R/nsTMatrix.R:  "  'for completeness'
74    
75            * tests/Class+Meth.R: a bit less 'not.ok.classes'
76    
77            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
78    
79    
80    2006-09-28  Douglas Bates  <bates@R-project.org>
81    
82            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
83            included.
84    
85            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
86            Export C-callable functions used in Zt_create in lme4.
87    
88    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * DESCRIPTION (Version): 0.9975-1
91    
92            * tests/simple.R: less checks fail; using NA, found that our
93                    kronecker() is not base-compatible with NA's.
94    
95            * R/dMatrix.R: "Compare" method now implemented for all cases
96    
97            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
98    
99            * man/dtpMatrix-class.Rd: mention length of 'x' slot
100    
101            * src/dtpMatrix.c (dtpMatrix_validate): fix check
102            * src/dspMatrix.c (dspMatrix_validate): ditto
103    
104            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
105              including coercion to [nl]tTMatrix.
106    
107            * R/diagMatrix.R (show): print a header line as for other classes.
108    
109    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/Makefile.win (SUBDIRS): fix typo
112    
113    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
116    
117    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
120            symmetric and y missing in R code using %*% (cholmod_aat doesn't
121            accept a symmetric matrix).
122            * tests/group-methods.R: Uncomment test of crossprod applied to
123            lsCMatrix objects.
124    
125    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R (symmetricMatrix): add validity method (available
128            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
129    
130            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
131    
132            * tests/indexing.Rout.save:
133            * tests/indexing.R: additions, mainly for 'lsparse'
134    
135            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
136            case.
137    
138            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
139    
140    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
143                    as 'N' (1-letter - Ok?)
144    
145            * tests/group-methods.R: add test for logical + NAs
146    
147            * R/dMatrix.R ("Compare"): fix to work with NA's
148    
149            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
150    
151            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
152                    which is implemented.
153    
154    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/chm_common.c: coerce logical <-> double instead of
157            typecasting;  needed for "l" matrix handling in cholmod.
158    
159            * tests/other-pkgs.R (graph): small extension in "graph" checks.
160    
161            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
162            (Tsp2grNEL): other fixes needed
163    
164    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
167                    Matrices, since "lMatrix", also "lsparseM" can have NA
168            * R/ndenseMatrix.R, etc: new source files
169            * man/nsparseMatrix-classes.Rd, etc: new help files
170            * tests/: adaptions
171            * src/chm_common.c (chm_dense_to_SEXP): and others:
172                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
173            * src/Csparse.c, etc: ditto
174    
175    2006-09-11  Douglas Bates  <bates@R-project.org>
176    
177            * src/Mutils.[ch],init.c inst/include/*.h: Move the
178            alloc_d**Matrix functions to the lme4 package.
179    
180    2006-09-09  Douglas Bates  <bates@R-project.org>
181    
182            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
183            fixed
184    
185    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/lMatrix.R: new
188    
189            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
190    
191            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
192            * man/tcrossprod.Rd: ditto
193    
194    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
197            for exported functions
198            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
199            Remove partitioning algorithms for sparse matrix reordering.  The
200            copyright on the Metis code was problematic and the methods were
201            rarely used.
202            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
203            operations are now done entirely in CHOLMOD code.
204    
205    2006-09-06  Douglas Bates  <bates@R-project.org>
206    
207            * src/Mutils.h: Remove functions that are no longer used.
208    
209    2006-09-04  Douglas Bates  <bates@R-project.org>
210    
211            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
212            * src/DEPS.mkf: update
213    
214    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * created branches/Matrix-for-R-2.3.x;  on trunk: do
217            * DESCRIPTION (Version): 0.9975-0
218            (Depends): R (>= 2.4.0)
219    
220    2006-09-01  Douglas Bates  <bates@R-project.org>
221    
222            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
223    
224    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
227            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
228    
229            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
230    
231    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
234            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
235            * R/dsparseMatrix.R: ditto
236            * R/Csparse.R: ditto
237    
238    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/dMatrix.R (Compare): improve availability of "<", etc
241            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
242    
243    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
246            of a 0-index which was used as 1-index (..hmm)
247    
248            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
249    
250            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
251            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
252            (.is.diagonal): ditto
253    
254            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
255    
256            * R/Matrix.R (Matrix): also work for NA data
257    
258    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
261            in all cases.
262    
263    2006-08-27  Douglas Bates  <bates@R-project.org>
264    
265            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
266            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
267    
268    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
271            subclasses of "ddenseMatrix"
272            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
273            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
274            instead of half dozen specialized ones.
275    
276    2006-08-25  Douglas Bates  <bates@R-project.org>
277    
278            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
279            <tillard@cirad.fr> - ordering standard errors to match effects.
280    
281    2006-08-24  Douglas Bates  <bates@R-project.org>
282    
283            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
284            on R_ldl.
285            * R/lCholCMatrix.R,
286            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
287            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
288            * many files in ./R and ./src: Use more general version of
289            dup_mMatrix_as_dgeMatrix to simplify method definitions.
290            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
291            dtpMatrix, dspMatrix and dppMatrix conversions.
292    
293    
294    2006-08-23  Douglas Bates  <bates@R-project.org>
295    
296            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
297            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
298            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
299            dgeMatrix_crossprod (may need to do this in other places).
300            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
301            generic and method for dsCMatrix.  Use CHOLMOD for chol().
302    
303    2006-08-22  Douglas Bates  <bates@R-project.org>
304    
305            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
306            types of classed Matrices, matrices or numeric or logical vectors.
307            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
308            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
309            to Mutils.h (as an inline) and change name to Matrix_check_class;
310            fixes in as_cholmod_factor and chm_factor_to_SEXP.
311            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
312            dsCMatrix_matrix_solve.  Comment out vestigial functions.
313            * src/Csparse.c: use diag_P and uplo_P macros.
314    
315    2006-08-21  Douglas Bates  <bates@R-project.org>
316    
317            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
318            valgrind.
319            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
320            inverses.
321            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
322            -Wall warnings.
323            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
324            Use dup_mMatrix_as_dgeMatrix.
325    
326    2006-08-20  Douglas Bates  <bates@R-project.org>
327    
328            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
329            * tests/sparseQR.R: Added
330            * man/sparseQR-class.Rd: Document methods for qr.* generics
331            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
332    
333    2006-08-19  Douglas Bates  <bates@R-project.org>
334    
335            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
336            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
337            and qr.fitted.
338            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
339            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
340    
341    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
344            the base version has no "..." argument.
345    
346            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
347    
348            * R/Matrix.R: define and
349            * NAMESPACE: export as.numeric() and as.logical() methods.
350                    Let's hope these do not badly slow down something...
351            Finally export the zapsmall() method.
352    
353    2006-08-17  Douglas Bates  <bates@R-project.org>
354    
355            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
356            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
357            * src/dtCMatrix.c :Remove code that is no longer used
358            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
359    
360    2006-08-14  Douglas Bates  <bates@R-project.org>
361    
362            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
363            Csparse_to_logical and Csparse_symmetric_to_general.
364            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
365            coercion methods between CsparseMatrix and TsparseMatrix.
366    
367    2006-08-14  Douglas Bates  <bates@R-project.org>
368    
369            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
370            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
371            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
372            possible.
373    
374    2006-08-12  Douglas Bates  <bates@R-project.org>
375    
376            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
377              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
378              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
379              generalize conversions between TsparseMatrix, CsparseMatrix,
380              denseMatrix and matrix.  Preserve triangularity property and
381              propagate Dimnames in the easy cases.
382    
383    2006-08-10  Douglas Bates  <bates@R-project.org>
384    
385            * src/lmer.c: adjust checks in glmer_init for S4SXP
386            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
387            before S4SXP but for the wrong reasons.
388    
389    2006-08-08  Douglas Bates  <bates@R-project.org>
390    
391            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
392            Later modified to return the upper triangle only.
393            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
394    
395    2006-08-07  Douglas Bates  <bates@R-project.org>
396    
397            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
398            R-level conversion to a sparse symmetric class.
399            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
400            Remove conversion to sparse symmetric classes (now done in C code).
401    
402    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
405            * man/band.Rd:  adapt the \dontshow{} unit test.
406    
407    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * DESCRIPTION (Version): 0.995-14  for CRAN
410    
411            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
412    
413            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
414            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
415    
416            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
417            * R/Tsparse.R (tril, triu, band): methods
418            * R/dgRMatrix.R (tril, ...):    ditto
419            * man/band.Rd:                  ditto
420    
421    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/Matrix.R (head, tail): directly use utils:::head.matrix
424                    to be up-to-date automatically.
425    
426    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
429    
430            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
431            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
432            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
433            such that the S4 objects are always created by the current version
434            of R and 'Matrix' class definitions.
435    
436    2006-08-01  Douglas Bates  <bates@R-project.org>
437    
438            * R/lmer.R (LMEoptimize method), tests/lmer.R,
439            inst/external/test3comp.rda: Added warnings for convergence on
440            boundary and test cases.
441    
442            * src/lmer.c (mer_postVar): Modified to return the variances that
443            are marginal to the fixed effects, not conditional on them (which
444            is what the bVar slot contents represent).
445    
446    2006-07-31  Douglas Bates  <bates@R-project.org>
447    
448            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
449            function which calls the C function mer_hat_trace2.
450    
451            * man/ranef.Rd: Include description of "postVar" argument and
452            producing a caterpillar plot.
453    
454    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * NAMESPACE:    change  "correlation" to "corMatrix"
457            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
458            * R/dpoMatrix.R: ditto
459            * R/lmer.R:      ditto
460    
461    2006-07-28  Douglas Bates  <bates@R-project.org>
462    
463            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
464            RZXinv slot's contents into a separate internal function that can
465            be used in mer_hat_trace.
466    
467    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
470            via new smart
471            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
472            utility functions.
473    
474    
475    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Csparse.R (tril, triu, band): do return *triangular* classed
478            matrices when appropriate; band() even symmetric ones.
479            (replCmat): extend to potentially all "CsparseMatrix"
480            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
481            allow subassignment for special sparse matrices.
482    
483            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
484    
485            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
486            argument; in glmer_*(): print only if(verbose).
487    
488            speed-optimize a few places by moving REAL(.) out of loops.
489    
490            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
491    
492    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
495                    since that wrongly triggers also for M[ logi , ]
496    
497            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
498            a symmetric matrix that results in a non-symmetric one.
499            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
500    
501            * R/dMatrix.R: make round(M) work as round(M, 0)
502    
503            * R/dgTMatrix.R (image): coordinate system and axis now use
504            1-based indices, not 0-based ones.
505    
506            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
507            * tests/indexing.R: test it.
508    
509            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
510            * man/isSymmetric-methods.Rd: and document it.
511    
512            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
513            * man/SparseM-conv.Rd: docu them
514    
515            * tests/other-pkgs.R: renamed from tests/graph.R and add example
516                    for 'SparseM' conversions
517    
518    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
519    
520            * R/Matrix.R (head): added head() and tail() methods.
521    
522    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * DESCRIPTION (Version): 0.995-12 released to CRAN
525    
526    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * tests/simple.R: add check for correct dsT -> dgT coercion;
529                    add check for correct printing of symmetric sparse matrices.
530    
531            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
532            for sparse symmetric matrices.
533    
534            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
535            diagonal twice.
536    
537    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
538    
539            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
540            being applied to the x slot (detected by Brian Ripley).
541    
542    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
545    
546            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
547    
548    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * src/lgCMatrix.c (lgCMatrix_diag): new function
551            * R/lgCMatrix.R (diag): for new method
552    
553            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
554                 ==> construction of illegal "*gTMatrix" via new() should
555                 now be much less easy:
556            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
557    
558            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
559                    directly.
560            * man/Matrix.Rd: documents it.
561    
562    2006-07-06  Douglas Bates  <bates@R-project.org>
563    
564            * src/pedigree.c (pedigree_inbreeding): Correction in
565            initialization.  This function is not currently being used and is
566            not fully tested.
567    
568            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
569            Introduced the glmer class.  Added code for mcmcmsamp on glmer
570            objects.  Modified validity check on pedigree objects to account
571            for nonparallel patterns of missingness of parents.
572    
573            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
574            class.
575    
576    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/pMatrix.R: coercion pMatrix -> Tsparse
579    
580    2006-06-12  Douglas Bates  <bates@R-project.org>
581    
582            * DESCRIPTION (Version): 0.995-11 released to CRAN
583    
584            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
585            the output from mcmcsamp.
586    
587    2006-06-10  Douglas Bates  <bates@R-project.org>
588    
589            * R/lmer.R (simulestimate): added C code for calculating the trace
590            of the hat matrix.
591    
592    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
595            classes.
596            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
597    
598    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/dgTMatrix.R (colSums): etc. All four of
601            colSums(), rowSums(), colMeans(), rowMeans() now should work for
602            all "Matrices".
603    
604    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
605    
606            * R/lmer.R (panel.ci): Add a reference line at zero and a
607            background grid to the qqmath plot of ranef.lmer.
608    
609    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
610    
611            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
612            grouping factors to be specified in the formula as (1|foo/bar).
613    
614    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
615    
616            * R/lmer.R (findbars and others): Change check of is.numeric to
617            !is.language to resolve the bug reported by Jacob Wegelin.
618    
619            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
620            code to evaluate inbreeding coefficients without calculating T,
621            based on code in Sargolzaei and Iwaisaki's paper.
622    
623    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
624    
625            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
626            generic and mer methods for isNested and denomDF. This denomDF was
627            an attempt to emulate that in lme but I don't think that makes
628            sense.  Use the trace of the hat matrix instead.
629    
630    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
633            the C code depending on a slot structure that's no longer valid.
634            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
635    
636    
637    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
638    
639            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
640            of lowerTriMatrix generic and methods to tril (also upper to triu)
641            and added a general band extractor.
642    
643    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
644    
645            * R/pedigree.R (pedigree): Replace sire and dam values outside the
646            allowable range with NAs. Added a corresponding check in the
647            validity check for the pedigree class.
648    
649            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
650            crossprod methods now inherits from symmetricMatrix.
651    
652    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
653    
654            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
655            generics lowerTriMatrix and upperTriMatrix along with methods for
656            the Csparse virtual class.  Also added a C function Csparse_band
657            that implements these methods by calling cholmod_band.
658    
659    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
662            erased when it was NULL.  This led to invalid subselections!
663    
664    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
665    
666            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
667            in method for "t" so as not to lose the unit diagonal property.
668    
669    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
670    
671            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
672            and methods.  This is now an option to the ranef method for the
673            mer class.
674    
675            * src/cs_utils.c: Ensure that the nz component is -1 for a
676            compressed column-oriented matrix.  Minor formatting cleanup.
677    
678            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
679            objects.
680    
681    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
684            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
685    
686    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
687    
688            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
689            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
690    
691            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
692            for the dtCMatrix class.
693    
694    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
695    
696            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
697            and methods for it.
698    
699    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
702            arguments, such that M %*% 1:6 now works
703            * Tests/matprod.R: test the above
704    
705    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
706    
707            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
708            the ranef.lmer class.
709    
710            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
711            methods to extract the posterior variances from the bVar slot.
712    
713    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
716            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
717    
718            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
719            * tests/simple: (extended)
720    
721            * R/sparseMatrix.R (isTriangular): now using much improved
722            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
723    
724    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
725    
726            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
727            (problem report from Franklin Parlamis).  This should be done
728            generally.
729    
730    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
731    
732            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
733            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
734            update the plot methods.
735    
736    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
737    
738            * R/lmer.R (resid and ranef methods):  Added methods for the
739            "residuals" and "resid" generic but only for linear mixed model
740            fits.  Changed the ranef method to return a list of data frames so
741            that the plot methods now work.
742    
743    2006-03-16  Douglas Bates  <bates@bates2>
744    
745            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
746            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
747    
748            * DESCRIPTION (Date): New release
749    
750    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
753    
754            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
755            * man/KNex.Rd: and other help files
756            * tests/*.R: several ones needed adaption
757            * inst/doc/Comparisons.Rnw: ditto
758    
759    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
760    
761            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
762    
763            * tests/indexing.R: tests for new [<- methods for sparse matrices.
764    
765    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
768    
769            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
770    
771    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/dMatrix.R: enable things like  M [ M < 10 ]
774            * R/dgeMatrix.R: implement it
775    
776    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/AllClass.R: define "summary.mer" and "*.lmer"
779            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
780            * R/lmer.R (show): now works with summary()
781    
782    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
785            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
786                    support the above
787    
788    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
789    
790            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
791            Use glmFit$prior.weights for weights in a glmm.
792            Allow an option usePQL = FALSE to skip the PQL steps for the
793            Laplace method (and, in time, the AGQ method).
794    
795            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
796            into a separate function internal_mer_Xfactor to be able to call
797            it from internal_bhat.
798    
799    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * tests/Class+Meth.R (tstMatrixClass): function for much better
802            testing; now again of all actual classes.
803    
804            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
805                    use macros and define make_d_matrix_* and make_i_matrix_*
806                    where _i_ is for the ldense routines:
807    
808            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
809            * src/ldense.c (lsyMatrix_as_lgeMatrix):
810    
811            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
812    
813    
814    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
815    
816            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
817                    many different kinds of matrices.
818            * R/*.R: quite a few new methods were needed for R CMD check with
819                    new Matrix().  Very good for users playing around.
820    
821    
822    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * src/dgeMatrix.c (dMatrix_validate): new
825            * src/Mutils.c (dense_nonpacked_validate): new
826    
827            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
828    
829    
830    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
831    
832            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
833    
834    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
835    
836            * DESCRIPTION (Version): 0.99-6 released to CRAN
837    
838            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
839            segfault in cases with multiple non-nested grouping factors.
840    
841    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
842    
843            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
844                    (Depends): also on 'utils'
845    
846            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
847            * R/diagMatrix.R (Diagonal): constructor and methods for
848            diagonal matrices
849    
850            * R/ltTMatrix.R: new "minimal methods"
851    
852    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
855            all methods (and help files).
856    
857    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
860                    for case (dimn.  op  no_dimn.)
861    
862    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
863    
864            * DESCRIPTION (Version): 0.99-2  released to CRAN
865    
866    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
867    
868            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
869            by Julian Faraway.
870    
871    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * R/Auxiliaries.R (try_as): new utility
874            * R/sparseMatrix.R: use try_as() in coercion to original class
875    
876    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
879    
880    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * R/Auxiliaries.R (dimNamesCheck): added
883    
884            * R/Matrix.R (as.array), (as.vector): new
885    
886    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
889                    default.
890            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
891                    "pMatrix" now contains "sparseMatrix"
892    
893    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
894    
895            * tests/Class+Meth.R: new tests; t(t(m)) == m
896    
897            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
898    
899            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
900            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
901    
902            * R/dspMatrix.R: typo in "t" method
903    
904    2005-09-18  Douglas Bates  <bates@wisc.edu>
905    
906            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
907            * R/Tsparse.R: instead of R/gTMatrix.R
908            * R/Csparse.R: new
909            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
910            * src/Tsparse.c: new; many trivial methods calling cholmod_()
911            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
912                            via cholmod
913    
914    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * R/Auxiliaries.R (non0ind): new function using new C code
917            * src/dgCMatrix.c (compressed_non_0_ij): new utility
918    
919    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
920    
921            * src/chm_common.h: header file required by all C sources that
922            call CHOLMOD functions.  It defines a cholmod_common structure
923            called 'c' whose address is passed as the last argument to
924            (virtually) every CHOLMOD function.
925    
926            * src/Pattern.c: Simple example of the use of CHOLMOD.
927    
928            * src/init.c: initialize and finalize the cholmod_common structure.
929    
930            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
931            LDL and CCOLAMD from the U. of Florida sparse matrix library.
932    
933  2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
934    
935          * inst/test-tools.R: new file collecting the utility functions used          * inst/test-tools.R: new file collecting the utility functions used
# Line 26  Line 958 
958  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
961          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
962          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
963    
964  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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