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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1575, Mon Sep 18 14:47:40 2006 UTC
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1    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (symmetricMatrix): add validity method (available
4            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
5    
6            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
7    
8            * tests/indexing.Rout.save:
9            * tests/indexing.R: additions, mainly for 'lsparse'
10    
11            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
12            case.
13    
14            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
15    
16    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
19                    as 'N' (1-letter - Ok?)
20    
21            * tests/group-methods.R: add test for logical + NAs
22    
23            * R/dMatrix.R ("Compare"): fix to work with NA's
24    
25            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
26    
27            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
28                    which is implemented.
29    
30    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * src/chm_common.c: coerce logical <-> double instead of
33            typecasting;  needed for "l" matrix handling in cholmod.
34    
35            * tests/other-pkgs.R (graph): small extension in "graph" checks.
36    
37            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
38            (Tsp2grNEL): other fixes needed
39    
40    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
43                    Matrices, since "lMatrix", also "lsparseM" can have NA
44            * R/ndenseMatrix.R, etc: new source files
45            * man/nsparseMatrix-classes.Rd, etc: new help files
46            * tests/: adaptions
47            * src/chm_common.c (chm_dense_to_SEXP): and others:
48                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
49            * src/Csparse.c, etc: dito
50    
51    2006-09-11  Douglas Bates  <bates@R-project.org>
52    
53            * src/Mutils.[ch],init.c inst/include/*.h: Move the
54            alloc_d**Matrix functions to the lme4 package.
55    
56    2006-09-09  Douglas Bates  <bates@R-project.org>
57    
58            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
59            fixed
60    
61    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/lMatrix.R: new
64    
65            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
66    
67            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
68            * man/tcrossprod.Rd: dito
69    
70    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
71    
72            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
73            for exported functions
74            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
75            Remove partitioning algorithms for sparse matrix reordering.  The
76            copyright on the Metis code was problematic and the methods were
77            rarely used.
78            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
79            operations are now done entirely in CHOLMOD code.
80    
81    2006-09-06  Douglas Bates  <bates@R-project.org>
82    
83            * src/Mutils.h: Remove functions that are no longer used.
84    
85    2006-09-04  Douglas Bates  <bates@R-project.org>
86    
87            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
88            * src/DEPS.mkf: update
89    
90    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * created branches/Matrix-for-R-2.3.x;  on trunk: do
93            * DESCRIPTION (Version): 0.9975-0
94            (Depends): R (>= 2.4.0)
95    
96    2006-09-01  Douglas Bates  <bates@R-project.org>
97    
98            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
99    
100    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
103            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
104    
105            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
106    
107    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
110            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
111            * R/dsparseMatrix.R: dito
112            * R/Csparse.R: dito
113    
114    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dMatrix.R (Compare): improve availability of "<", etc
117            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
118    
119    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
122            of a 0-index which was used as 1-index (..hmm)
123    
124            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
125    
126            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
127            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
128            (.is.diagonal): dito
129    
130            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
131    
132            * R/Matrix.R (Matrix): also work for NA data
133    
134    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
137            in all cases.
138    
139    2006-08-27  Douglas Bates  <bates@R-project.org>
140    
141            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
142            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
143    
144    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
147            subclasses of "ddenseMatrix"
148            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
149            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
150            instead of half dozen specialized ones.
151    
152    2006-08-25  Douglas Bates  <bates@R-project.org>
153    
154            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
155            <tillard@cirad.fr> - ordering standard errors to match effects.
156    
157    2006-08-24  Douglas Bates  <bates@R-project.org>
158    
159            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
160            on R_ldl.
161            * R/lCholCMatrix.R,
162            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
163            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
164            * many files in ./R and ./src: Use more general version of
165            dup_mMatrix_as_dgeMatrix to simplify method definitions.
166            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
167            dtpMatrix, dspMatrix and dppMatrix conversions.
168    
169    
170    2006-08-23  Douglas Bates  <bates@R-project.org>
171    
172            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
173            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
174            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
175            dgeMatrix_crossprod (may need to do this in other places).
176            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
177            generic and method for dsCMatrix.  Use CHOLMOD for chol().
178    
179    2006-08-22  Douglas Bates  <bates@R-project.org>
180    
181            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
182            types of classed Matrices, matrices or numeric or logical vectors.
183            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
184            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
185            to Mutils.h (as an inline) and change name to Matrix_check_class;
186            fixes in as_cholmod_factor and chm_factor_to_SEXP.
187            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
188            dsCMatrix_matrix_solve.  Comment out vestigial functions.
189            * src/Csparse.c: use diag_P and uplo_P macros.
190    
191    2006-08-21  Douglas Bates  <bates@R-project.org>
192    
193            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
194            valgrind.
195            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
196            inverses.
197            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
198            -Wall warnings.
199            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
200            Use dup_mMatrix_as_dgeMatrix.
201    
202    2006-08-20  Douglas Bates  <bates@R-project.org>
203    
204            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
205            * tests/sparseQR.R: Added
206            * man/sparseQR-class.Rd: Document methods for qr.* generics
207            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
208    
209    2006-08-19  Douglas Bates  <bates@R-project.org>
210    
211            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
212            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
213            and qr.fitted.
214            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
215            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
216    
217    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
220            the base version has no "..." argument.
221    
222            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
223    
224            * R/Matrix.R: define and
225            * NAMESPACE: export as.numeric() and as.logical() methods.
226                    Let's hope these do not badly slow down something...
227            Finally export the zapsmall() method.
228    
229    2006-08-17  Douglas Bates  <bates@R-project.org>
230    
231            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
232            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
233            * src/dtCMatrix.c :Remove code that is no longer used
234            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
235    
236    2006-08-14  Douglas Bates  <bates@R-project.org>
237    
238            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
239            Csparse_to_logical and Csparse_symmetric_to_general.
240            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
241            coercion methods between CsparseMatrix and TsparseMatrix.
242    
243    2006-08-14  Douglas Bates  <bates@R-project.org>
244    
245            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
246            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
247            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
248            possible.
249    
250    2006-08-12  Douglas Bates  <bates@R-project.org>
251    
252            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
253              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
254              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
255              generalize conversions between TsparseMatrix, CsparseMatrix,
256              denseMatrix and matrix.  Preserve triangularity property and
257              propagate Dimnames in the easy cases.
258    
259    2006-08-10  Douglas Bates  <bates@R-project.org>
260    
261            * src/lmer.c: adjust checks in glmer_init for S4SXP
262            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
263            before S4SXP but for the wrong reasons.
264    
265    2006-08-08  Douglas Bates  <bates@R-project.org>
266    
267            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
268            Later modified to return the upper triangle only.
269            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
270    
271    2006-08-07  Douglas Bates  <bates@R-project.org>
272    
273            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
274            R-level conversion to a sparse symmetric class.
275            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
276            Remove conversion to sparse symmetric classes (now done in C code).
277    
278    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
281            * man/band.Rd:  adapt the \dontshow{} unit test.
282    
283    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * DESCRIPTION (Version): 0.995-14  for CRAN
286    
287            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
288    
289            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
290            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
291    
292            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
293            * R/Tsparse.R (tril, triu, band): methods
294            * R/dgRMatrix.R (tril, ...):    ditto
295            * man/band.Rd:                  ditto
296    
297    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Matrix.R (head, tail): directly use utils:::head.matrix
300                    to be up-to-date automatically.
301    
302    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
305    
306            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
307            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
308            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
309            such that the S4 objects are always created by the current version
310            of R and 'Matrix' class definitions.
311    
312    2006-08-01  Douglas Bates  <bates@R-project.org>
313    
314            * R/lmer.R (LMEoptimize method), tests/lmer.R,
315            inst/external/test3comp.rda: Added warnings for convergence on
316            boundary and test cases.
317    
318            * src/lmer.c (mer_postVar): Modified to return the variances that
319            are marginal to the fixed effects, not conditional on them (which
320            is what the bVar slot contents represent).
321    
322    2006-07-31  Douglas Bates  <bates@R-project.org>
323    
324            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
325            function which calls the C function mer_hat_trace2.
326    
327            * man/ranef.Rd: Include description of "postVar" argument and
328            producing a caterpillar plot.
329    
330    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * NAMESPACE:    change  "correlation" to "corMatrix"
333            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
334            * R/dpoMatrix.R: ditto
335            * R/lmer.R:      ditto
336    
337    2006-07-28  Douglas Bates  <bates@R-project.org>
338    
339            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
340            RZXinv slot's contents into a separate internal function that can
341            be used in mer_hat_trace.
342    
343    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
346            via new smart
347            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
348            utility functions.
349    
350    
351    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Csparse.R (tril, triu, band): do return *triangular* classed
354            matrices when appropriate; band() even symmetric ones.
355            (replCmat): extend to potentially all "CsparseMatrix"
356            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
357            allow subassignment for special sparse matrices.
358    
359            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
360    
361            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
362            argument; in glmer_*(): print only if(verbose).
363    
364            speed-optimize a few places by moving REAL(.) out of loops.
365    
366            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
367    
368    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
371                    since that wrongly triggers also for M[ logi , ]
372    
373            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
374            a symmetric matrix that results in a non-symmetric one.
375            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
376    
377            * R/dMatrix.R: make round(M) work as round(M, 0)
378    
379            * R/dgTMatrix.R (image): coordinate system and axis now use
380            1-based indices, not 0-based ones.
381    
382            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
383            * tests/indexing.R: test it.
384    
385            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
386            * man/isSymmetric-methods.Rd: and document it.
387    
388            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
389            * man/SparseM-conv.Rd: docu them
390    
391            * tests/other-pkgs.R: renamed from tests/graph.R and add example
392                    for 'SparseM' conversions
393    
394    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
395    
396            * R/Matrix.R (head): added head() and tail() methods.
397    
398    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * DESCRIPTION (Version): 0.995-12 released to CRAN
401    
402    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * tests/simple.R: add check for correct dsT -> dgT coercion;
405                    add check for correct printing of symmetric sparse matrices.
406    
407            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
408            for sparse symmetric matrices.
409    
410            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
411            diagonal twice.
412    
413    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
414    
415            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
416            being applied to the x slot (detected by Brian Ripley).
417    
418    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
421    
422            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
423    
424    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * src/lgCMatrix.c (lgCMatrix_diag): new function
427            * R/lgCMatrix.R (diag): for new method
428    
429            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
430                 ==> construction of illegal "*gTMatrix" via new() should
431                 now be much less easy:
432            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
433    
434            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
435                    directly.
436            * man/Matrix.Rd: documents it.
437    
438    2006-07-06  Douglas Bates  <bates@R-project.org>
439    
440            * src/pedigree.c (pedigree_inbreeding): Correction in
441            initialization.  This function is not currently being used and is
442            not fully tested.
443    
444            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
445            Introduced the glmer class.  Added code for mcmcmsamp on glmer
446            objects.  Modified validity check on pedigree objects to account
447            for nonparallel patterns of missingness of parents.
448    
449            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
450            class.
451    
452    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/pMatrix.R: coercion pMatrix -> Tsparse
455    
456    2006-06-12  Douglas Bates  <bates@R-project.org>
457    
458            * DESCRIPTION (Version): 0.995-11 released to CRAN
459    
460            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
461            the output from mcmcsamp.
462    
463    2006-06-10  Douglas Bates  <bates@R-project.org>
464    
465            * R/lmer.R (simulestimate): added C code for calculating the trace
466            of the hat matrix.
467    
468    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
471            classes.
472            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
473    
474    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/dgTMatrix.R (colSums): etc. All four of
477            colSums(), rowSums(), colMeans(), rowMeans() now should work for
478            all "Matrices".
479    
480    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
481    
482            * R/lmer.R (panel.ci): Add a reference line at zero and a
483            background grid to the qqmath plot of ranef.lmer.
484    
485    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
486    
487            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
488            grouping factors to be specified in the formula as (1|foo/bar).
489    
490    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
491    
492            * R/lmer.R (findbars and others): Change check of is.numeric to
493            !is.language to resolve the bug reported by Jacob Wegelin.
494    
495            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
496            code to evaluate inbreeding coefficients without calculating T,
497            based on code in Sargolzaei and Iwaisaki's paper.
498    
499    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
500    
501            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
502            generic and mer methods for isNested and denomDF. This denomDF was
503            an attempt to emulate that in lme but I don't think that makes
504            sense.  Use the trace of the hat matrix instead.
505    
506    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
509            the C code depending on a slot structure that's no longer valid.
510            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
511    
512    
513    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
514    
515            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
516            of lowerTriMatrix generic and methods to tril (also upper to triu)
517            and added a general band extractor.
518    
519    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
520    
521            * R/pedigree.R (pedigree): Replace sire and dam values outside the
522            allowable range with NAs. Added a corresponding check in the
523            validity check for the pedigree class.
524    
525            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
526            crossprod methods now inherits from symmetricMatrix.
527    
528    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
531            generics lowerTriMatrix and upperTriMatrix along with methods for
532            the Csparse virtual class.  Also added a C function Csparse_band
533            that implements these methods by calling cholmod_band.
534    
535    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
538            erased when it was NULL.  This led to invalid subselections!
539    
540    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
541    
542            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
543            in method for "t" so as not to lose the unit diagonal property.
544    
545    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
546    
547            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
548            and methods.  This is now an option to the ranef method for the
549            mer class.
550    
551            * src/cs_utils.c: Ensure that the nz component is -1 for a
552            compressed column-oriented matrix.  Minor formatting cleanup.
553    
554            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
555            objects.
556    
557    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
560            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
561    
562    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
563    
564            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
565            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
566    
567            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
568            for the dtCMatrix class.
569    
570    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
571    
572            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
573            and methods for it.
574    
575    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
578            arguments, such that M %*% 1:6 now works
579            * Tests/matprod.R: test the above
580    
581    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
582    
583            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
584            the ranef.lmer class.
585    
586            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
587            methods to extract the posterior variances from the bVar slot.
588    
589    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
592            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
593    
594            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
595            * tests/simple: (extended)
596    
597            * R/sparseMatrix.R (isTriangular): now using much improved
598            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
599    
600    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
603            (problem report from Franklin Parlamis).  This should be done
604            generally.
605    
606    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
607    
608            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
609            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
610            update the plot methods.
611    
612    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
613    
614            * R/lmer.R (resid and ranef methods):  Added methods for the
615            "residuals" and "resid" generic but only for linear mixed model
616            fits.  Changed the ranef method to return a list of data frames so
617            that the plot methods now work.
618    
619    2006-03-16  Douglas Bates  <bates@bates2>
620    
621            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
622            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
623    
624            * DESCRIPTION (Date): New release
625    
626    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
629    
630            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
631            * man/KNex.Rd: and other help files
632            * tests/*.R: several ones needed adaption
633            * inst/doc/Comparisons.Rnw: ditto
634    
635    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
638    
639            * tests/indexing.R: tests for new [<- methods for sparse matrices.
640    
641    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
644    
645            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
646    
647    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/dMatrix.R: enable things like  M [ M < 10 ]
650            * R/dgeMatrix.R: implement it
651    
652    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/AllClass.R: define "summary.mer" and "*.lmer"
655            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
656            * R/lmer.R (show): now works with summary()
657    
658    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
661            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
662                    support the above
663    
664    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
665    
666            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
667            Use glmFit$prior.weights for weights in a glmm.
668            Allow an option usePQL = FALSE to skip the PQL steps for the
669            Laplace method (and, in time, the AGQ method).
670    
671            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
672            into a separate function internal_mer_Xfactor to be able to call
673            it from internal_bhat.
674    
675    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * tests/Class+Meth.R (tstMatrixClass): function for much better
678            testing; now again of all actual classes.
679    
680            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
681                    use macros and define make_d_matrix_* and make_i_matrix_*
682                    where _i_ is for the ldense routines:
683    
684            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
685            * src/ldense.c (lsyMatrix_as_lgeMatrix):
686    
687            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
688    
689    
690    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
693                    many different kinds of matrices.
694            * R/*.R: quite a few new methods were needed for R CMD check with
695                    new Matrix().  Very good for users playing around.
696    
697    
698    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * src/dgeMatrix.c (dMatrix_validate): new
701            * src/Mutils.c (dense_nonpacked_validate): new
702    
703            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
704    
705    
706    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
709    
710    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
711    
712            * DESCRIPTION (Version): 0.99-6 released to CRAN
713    
714            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
715            segfault in cases with multiple non-nested grouping factors.
716    
717    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
720                    (Depends): also on 'utils'
721    
722            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
723            * R/diagMatrix.R (Diagonal): constructor and methods for
724            diagonal matrices
725    
726            * R/ltTMatrix.R: new "minimal methods"
727    
728    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
731            all methods (and help files).
732    
733    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
736                    for case (dimn.  op  no_dimn.)
737    
738    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
739    
740            * DESCRIPTION (Version): 0.99-2  released to CRAN
741    
742    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
743    
744            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
745            by Julian Faraway.
746    
747    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/Auxiliaries.R (try_as): new utility
750            * R/sparseMatrix.R: use try_as() in coercion to original class
751    
752    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
755    
756    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/Auxiliaries.R (dimNamesCheck): added
759    
760            * R/Matrix.R (as.array), (as.vector): new
761    
762    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
765                    default.
766            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
767                    "pMatrix" now contains "sparseMatrix"
768    
769    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * tests/Class+Meth.R: new tests; t(t(m)) == m
772    
773            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
774    
775            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
776            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
777    
778            * R/dspMatrix.R: typo in "t" method
779    
780    2005-09-18  Douglas Bates  <bates@wisc.edu>
781    
782            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
783            * R/Tsparse.R: instead of R/gTMatrix.R
784            * R/Csparse.R: new
785            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
786            * src/Tsparse.c: new; many trivial methods calling cholmod_()
787            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
788                            via cholmod
789    
790    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/Auxiliaries.R (non0ind): new function using new C code
793            * src/dgCMatrix.c (compressed_non_0_ij): new utility
794    
795    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
796    
797            * src/chm_common.h: header file required by all C sources that
798            call CHOLMOD functions.  It defines a cholmod_common structure
799            called 'c' whose address is passed as the last argument to
800            (virtually) every CHOLMOD function.
801    
802            * src/Pattern.c: Simple example of the use of CHOLMOD.
803    
804            * src/init.c: initialize and finalize the cholmod_common structure.
805    
806            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
807            LDL and CCOLAMD from the U. of Florida sparse matrix library.
808    
809    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * inst/test-tools.R: new file collecting the utility functions used
812                    in ./tests/*.R
813    
814            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
815            * R/Matrix.R (cbind2): methods for NULL and missing
816    
817    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/AllClass.R: new "index" class for "[" and "[<-":
820                    First cut at "symmetricMatrix" and "triangularMatrix"
821            * R/gTMatrix.R (.ind.prep): new function;
822                    Logical and character indexing now work too.
823            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
824            * tests/indexing.R: new, including *.Rout.save
825            * tests/dgTMatrix.R: new
826    
827  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
828    
829          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 834 
834  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
837          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
838          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
839    
840  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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