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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1655, Mon Oct 30 17:16:27 2006 UTC
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1    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/matprod.R: add a variation of Harri's example
4    
5            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
6            recursive infinitely.
7    
8            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
9    
10            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
11    
12    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
15            matrix if possible; test m+m == 2*m; now test dgRMatrix.
16            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
17            satisfy the above test.
18    
19    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
22    
23            * R/dgCMatrix.R: solve(a, b="missing") based on
24            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
25            RHS = NULL.
26    
27            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
28            add more (needed) [t]crossprod() methods.
29    
30            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
31    
32            * R/Auxiliaries.R (as_CspClass): cleanup
33            (drop0): internal utility for "Csparse_drop(*, 0)"
34            (.bail.out.2): encourage active feedback
35    
36    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dMatrix.R(Compare): new(), then slots [no validity check]
39    
40            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
41            non-valid or 'sorted' case).
42    
43            * R/dsparseMatrix.R: add "chol" method.
44            * R/ddenseMatrix.R: ditto
45    
46            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
47            * NAMESPACE (Ops)
48            * R/diagMatrix.R (diag2T): simple utility used "higher level"
49            coercion; deprecating direct lower level coercions.
50    
51            * R/*.R (seq): use seq_len() and seq_along() where possible.
52    
53    
54    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Version): 0.9975-5 ready for release
57    
58    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
61    
62    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (corMatrix): add 'validity' check;
65                    comment out unused "LDL" class definition
66            * NAMESPACE: mention, but do not export "LDL" class
67            * R/corMatrix.R: new (simple), needed for R-devel with
68            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
69              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
70    
71    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
72    
73            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
74            use Rprintf and R's error handling.
75    
76    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
79            * tests/matprod.R: add tests for the bug fixed.
80    
81    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
84            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
85    
86    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
89    
90    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Version): 0.9975-3
93    
94            * R/diagMatrix.R (bdiag): new function constructing block diagonal
95            (sparse) matrices.
96            * man/bdiag.Rd: docu + examples
97    
98            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
99    
100            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
101            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
102    
103            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
104            that result is sparse or diagonal (and not dense).
105    
106            * man/Subassign-methods.Rd: fix examples
107    
108            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
109            should always return a sparse (and not sometimes a diagonal) matrix.
110    
111    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
114    
115    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * DESCRIPTION (Version): 0.9975-2
118    
119            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
120    
121    2006-10-02  Douglas Bates  <bates@R-project.org>
122    
123            * tests/dg_Matrix.R: Simplify test taking into account new code.
124    
125    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
128    
129            * R/lsTMatrix.R: new files w/ missing methods
130            * R/nsTMatrix.R:  "  'for completeness'
131    
132            * tests/Class+Meth.R: a bit less 'not.ok.classes'
133    
134            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
135    
136    
137    2006-09-28  Douglas Bates  <bates@R-project.org>
138    
139            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
140            included.
141    
142            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
143            Export C-callable functions used in Zt_create in lme4.
144    
145    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.9975-1
148    
149            * tests/simple.R: less checks fail; using NA, found that our
150                    kronecker() is not base-compatible with NA's.
151    
152            * R/dMatrix.R: "Compare" method now implemented for all cases
153    
154            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
155    
156            * man/dtpMatrix-class.Rd: mention length of 'x' slot
157    
158            * src/dtpMatrix.c (dtpMatrix_validate): fix check
159            * src/dspMatrix.c (dspMatrix_validate): ditto
160    
161            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
162              including coercion to [nl]tTMatrix.
163    
164            * R/diagMatrix.R (show): print a header line as for other classes.
165    
166    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/Makefile.win (SUBDIRS): fix typo
169    
170    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
173    
174    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
175    
176            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
177            symmetric and y missing in R code using %*% (cholmod_aat doesn't
178            accept a symmetric matrix).
179            * tests/group-methods.R: Uncomment test of crossprod applied to
180            lsCMatrix objects.
181    
182    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/AllClass.R (symmetricMatrix): add validity method (available
185            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
186    
187            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
188    
189            * tests/indexing.Rout.save:
190            * tests/indexing.R: additions, mainly for 'lsparse'
191    
192            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
193            case.
194    
195            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
196    
197    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
200                    as 'N' (1-letter - Ok?)
201    
202            * tests/group-methods.R: add test for logical + NAs
203    
204            * R/dMatrix.R ("Compare"): fix to work with NA's
205    
206            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
207    
208            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
209                    which is implemented.
210    
211    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/chm_common.c: coerce logical <-> double instead of
214            typecasting;  needed for "l" matrix handling in cholmod.
215    
216            * tests/other-pkgs.R (graph): small extension in "graph" checks.
217    
218            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
219            (Tsp2grNEL): other fixes needed
220    
221    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
224                    Matrices, since "lMatrix", also "lsparseM" can have NA
225            * R/ndenseMatrix.R, etc: new source files
226            * man/nsparseMatrix-classes.Rd, etc: new help files
227            * tests/: adaptions
228            * src/chm_common.c (chm_dense_to_SEXP): and others:
229                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
230            * src/Csparse.c, etc: ditto
231    
232    2006-09-11  Douglas Bates  <bates@R-project.org>
233    
234            * src/Mutils.[ch],init.c inst/include/*.h: Move the
235            alloc_d**Matrix functions to the lme4 package.
236    
237    2006-09-09  Douglas Bates  <bates@R-project.org>
238    
239            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
240            fixed
241    
242    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/lMatrix.R: new
245    
246            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
247    
248            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
249            * man/tcrossprod.Rd: ditto
250    
251    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
254            for exported functions
255            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
256            Remove partitioning algorithms for sparse matrix reordering.  The
257            copyright on the Metis code was problematic and the methods were
258            rarely used.
259            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
260            operations are now done entirely in CHOLMOD code.
261    
262    2006-09-06  Douglas Bates  <bates@R-project.org>
263    
264            * src/Mutils.h: Remove functions that are no longer used.
265    
266    2006-09-04  Douglas Bates  <bates@R-project.org>
267    
268            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
269            * src/DEPS.mkf: update
270    
271    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * created branches/Matrix-for-R-2.3.x;  on trunk: do
274            * DESCRIPTION (Version): 0.9975-0
275            (Depends): R (>= 2.4.0)
276    
277    2006-09-01  Douglas Bates  <bates@R-project.org>
278    
279            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
280    
281    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
284            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
285    
286            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
287    
288    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
291            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
292            * R/dsparseMatrix.R: ditto
293            * R/Csparse.R: ditto
294    
295    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/dMatrix.R (Compare): improve availability of "<", etc
298            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
299    
300    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
303            of a 0-index which was used as 1-index (..hmm)
304    
305            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
306    
307            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
308            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
309            (.is.diagonal): ditto
310    
311            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
312    
313            * R/Matrix.R (Matrix): also work for NA data
314    
315    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
318            in all cases.
319    
320    2006-08-27  Douglas Bates  <bates@R-project.org>
321    
322            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
323            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
324    
325    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
328            subclasses of "ddenseMatrix"
329            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
330            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
331            instead of half dozen specialized ones.
332    
333    2006-08-25  Douglas Bates  <bates@R-project.org>
334    
335            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
336            <tillard@cirad.fr> - ordering standard errors to match effects.
337    
338    2006-08-24  Douglas Bates  <bates@R-project.org>
339    
340            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
341            on R_ldl.
342            * R/lCholCMatrix.R,
343            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
344            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
345            * many files in ./R and ./src: Use more general version of
346            dup_mMatrix_as_dgeMatrix to simplify method definitions.
347            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
348            dtpMatrix, dspMatrix and dppMatrix conversions.
349    
350    
351    2006-08-23  Douglas Bates  <bates@R-project.org>
352    
353            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
354            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
355            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
356            dgeMatrix_crossprod (may need to do this in other places).
357            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
358            generic and method for dsCMatrix.  Use CHOLMOD for chol().
359    
360    2006-08-22  Douglas Bates  <bates@R-project.org>
361    
362            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
363            types of classed Matrices, matrices or numeric or logical vectors.
364            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
365            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
366            to Mutils.h (as an inline) and change name to Matrix_check_class;
367            fixes in as_cholmod_factor and chm_factor_to_SEXP.
368            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
369            dsCMatrix_matrix_solve.  Comment out vestigial functions.
370            * src/Csparse.c: use diag_P and uplo_P macros.
371    
372    2006-08-21  Douglas Bates  <bates@R-project.org>
373    
374            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
375            valgrind.
376            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
377            inverses.
378            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
379            -Wall warnings.
380            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
381            Use dup_mMatrix_as_dgeMatrix.
382    
383    2006-08-20  Douglas Bates  <bates@R-project.org>
384    
385            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
386            * tests/sparseQR.R: Added
387            * man/sparseQR-class.Rd: Document methods for qr.* generics
388            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
389    
390    2006-08-19  Douglas Bates  <bates@R-project.org>
391    
392            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
393            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
394            and qr.fitted.
395            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
396            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
397    
398    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
401            the base version has no "..." argument.
402    
403            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
404    
405            * R/Matrix.R: define and
406            * NAMESPACE: export as.numeric() and as.logical() methods.
407                    Let's hope these do not badly slow down something...
408            Finally export the zapsmall() method.
409    
410    2006-08-17  Douglas Bates  <bates@R-project.org>
411    
412            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
413            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
414            * src/dtCMatrix.c :Remove code that is no longer used
415            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
416    
417    2006-08-14  Douglas Bates  <bates@R-project.org>
418    
419            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
420            Csparse_to_logical and Csparse_symmetric_to_general.
421            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
422            coercion methods between CsparseMatrix and TsparseMatrix.
423    
424    2006-08-14  Douglas Bates  <bates@R-project.org>
425    
426            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
427            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
428            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
429            possible.
430    
431    2006-08-12  Douglas Bates  <bates@R-project.org>
432    
433            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
434              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
435              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
436              generalize conversions between TsparseMatrix, CsparseMatrix,
437              denseMatrix and matrix.  Preserve triangularity property and
438              propagate Dimnames in the easy cases.
439    
440    2006-08-10  Douglas Bates  <bates@R-project.org>
441    
442            * src/lmer.c: adjust checks in glmer_init for S4SXP
443            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
444            before S4SXP but for the wrong reasons.
445    
446    2006-08-08  Douglas Bates  <bates@R-project.org>
447    
448            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
449            Later modified to return the upper triangle only.
450            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
451    
452    2006-08-07  Douglas Bates  <bates@R-project.org>
453    
454            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
455            R-level conversion to a sparse symmetric class.
456            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
457            Remove conversion to sparse symmetric classes (now done in C code).
458    
459    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
462            * man/band.Rd:  adapt the \dontshow{} unit test.
463    
464    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * DESCRIPTION (Version): 0.995-14  for CRAN
467    
468            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
469    
470            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
471            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
472    
473            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
474            * R/Tsparse.R (tril, triu, band): methods
475            * R/dgRMatrix.R (tril, ...):    ditto
476            * man/band.Rd:                  ditto
477    
478    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/Matrix.R (head, tail): directly use utils:::head.matrix
481                    to be up-to-date automatically.
482    
483    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
486    
487            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
488            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
489            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
490            such that the S4 objects are always created by the current version
491            of R and 'Matrix' class definitions.
492    
493    2006-08-01  Douglas Bates  <bates@R-project.org>
494    
495            * R/lmer.R (LMEoptimize method), tests/lmer.R,
496            inst/external/test3comp.rda: Added warnings for convergence on
497            boundary and test cases.
498    
499            * src/lmer.c (mer_postVar): Modified to return the variances that
500            are marginal to the fixed effects, not conditional on them (which
501            is what the bVar slot contents represent).
502    
503    2006-07-31  Douglas Bates  <bates@R-project.org>
504    
505            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
506            function which calls the C function mer_hat_trace2.
507    
508            * man/ranef.Rd: Include description of "postVar" argument and
509            producing a caterpillar plot.
510    
511    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * NAMESPACE:    change  "correlation" to "corMatrix"
514            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
515            * R/dpoMatrix.R: ditto
516            * R/lmer.R:      ditto
517    
518    2006-07-28  Douglas Bates  <bates@R-project.org>
519    
520            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
521            RZXinv slot's contents into a separate internal function that can
522            be used in mer_hat_trace.
523    
524    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
527            via new smart
528            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
529            utility functions.
530    
531    
532    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/Csparse.R (tril, triu, band): do return *triangular* classed
535            matrices when appropriate; band() even symmetric ones.
536            (replCmat): extend to potentially all "CsparseMatrix"
537            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
538            allow subassignment for special sparse matrices.
539    
540            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
541    
542            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
543            argument; in glmer_*(): print only if(verbose).
544    
545            speed-optimize a few places by moving REAL(.) out of loops.
546    
547            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
548    
549    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
552                    since that wrongly triggers also for M[ logi , ]
553    
554            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
555            a symmetric matrix that results in a non-symmetric one.
556            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
557    
558            * R/dMatrix.R: make round(M) work as round(M, 0)
559    
560            * R/dgTMatrix.R (image): coordinate system and axis now use
561            1-based indices, not 0-based ones.
562    
563            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
564            * tests/indexing.R: test it.
565    
566            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
567            * man/isSymmetric-methods.Rd: and document it.
568    
569            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
570            * man/SparseM-conv.Rd: docu them
571    
572            * tests/other-pkgs.R: renamed from tests/graph.R and add example
573                    for 'SparseM' conversions
574    
575    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
576    
577            * R/Matrix.R (head): added head() and tail() methods.
578    
579    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * DESCRIPTION (Version): 0.995-12 released to CRAN
582    
583    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * tests/simple.R: add check for correct dsT -> dgT coercion;
586                    add check for correct printing of symmetric sparse matrices.
587    
588            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
589            for sparse symmetric matrices.
590    
591            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
592            diagonal twice.
593    
594    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
595    
596            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
597            being applied to the x slot (detected by Brian Ripley).
598    
599    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
602    
603            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
604    
605    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * src/lgCMatrix.c (lgCMatrix_diag): new function
608            * R/lgCMatrix.R (diag): for new method
609    
610            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
611                 ==> construction of illegal "*gTMatrix" via new() should
612                 now be much less easy:
613            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
614    
615            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
616                    directly.
617            * man/Matrix.Rd: documents it.
618    
619    2006-07-06  Douglas Bates  <bates@R-project.org>
620    
621            * src/pedigree.c (pedigree_inbreeding): Correction in
622            initialization.  This function is not currently being used and is
623            not fully tested.
624    
625            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
626            Introduced the glmer class.  Added code for mcmcmsamp on glmer
627            objects.  Modified validity check on pedigree objects to account
628            for nonparallel patterns of missingness of parents.
629    
630            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
631            class.
632    
633    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/pMatrix.R: coercion pMatrix -> Tsparse
636    
637    2006-06-12  Douglas Bates  <bates@R-project.org>
638    
639            * DESCRIPTION (Version): 0.995-11 released to CRAN
640    
641            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
642            the output from mcmcsamp.
643    
644    2006-06-10  Douglas Bates  <bates@R-project.org>
645    
646            * R/lmer.R (simulestimate): added C code for calculating the trace
647            of the hat matrix.
648    
649    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
652            classes.
653            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
654    
655    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/dgTMatrix.R (colSums): etc. All four of
658            colSums(), rowSums(), colMeans(), rowMeans() now should work for
659            all "Matrices".
660    
661    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
662    
663            * R/lmer.R (panel.ci): Add a reference line at zero and a
664            background grid to the qqmath plot of ranef.lmer.
665    
666    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
667    
668            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
669            grouping factors to be specified in the formula as (1|foo/bar).
670    
671    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * R/lmer.R (findbars and others): Change check of is.numeric to
674            !is.language to resolve the bug reported by Jacob Wegelin.
675    
676            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
677            code to evaluate inbreeding coefficients without calculating T,
678            based on code in Sargolzaei and Iwaisaki's paper.
679    
680    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
681    
682            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
683            generic and mer methods for isNested and denomDF. This denomDF was
684            an attempt to emulate that in lme but I don't think that makes
685            sense.  Use the trace of the hat matrix instead.
686    
687  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
690          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
691          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
692    
693    
694  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 811 
811          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
812          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
813          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
814          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
815    
816  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
# Line 329  Line 1015 
1015  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1018          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1019          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1020    
1021  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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