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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1661, Thu Nov 2 13:10:50 2006 UTC
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1    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/Tsparse.c: use xTsparse_validate() , and hence remove
4    
5            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
6    
7    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
10    
11            * tests/simple.R: validObject() checking the above.
12    
13            * src/dgCMatrix.c (gCMatrix_validate): new, small and simple,
14            replacing both dgCMatrix_validate and lgCM*.
15    
16            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
17            fix dimnames setting in other places.
18            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
19    
20    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
23    
24            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
25            symmetry test, via
26            * R/Auxiliaries.R (.as.dgC.0.factors):
27    
28    2006-11-01  Douglas Bates  <bates@r-project.org>
29    
30            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
31            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
32            <CsparseMatrix>) added
33    
34    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * tests/matprod.R: add a variation of Harri's example
37    
38            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
39            recursive infinitely.
40    
41            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
42    
43            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
44    
45    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
48            matrix if possible; test m+m == 2*m; now test dgRMatrix.
49            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
50            satisfy the above test.
51    
52    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
55    
56            * R/dgCMatrix.R: solve(a, b="missing") based on
57            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
58            RHS = NULL.
59    
60            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
61            add more (needed) [t]crossprod() methods.
62    
63            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
64    
65            * R/Auxiliaries.R (as_CspClass): cleanup
66            (drop0): internal utility for "Csparse_drop(*, 0)"
67            (.bail.out.2): encourage active feedback
68    
69    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/dMatrix.R(Compare): new(), then slots [no validity check]
72    
73            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
74            non-valid or 'sorted' case).
75    
76            * R/dsparseMatrix.R: add "chol" method.
77            * R/ddenseMatrix.R: ditto
78    
79            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
80            * NAMESPACE (Ops)
81            * R/diagMatrix.R (diag2T): simple utility used "higher level"
82            coercion; deprecating direct lower level coercions.
83    
84            * R/*.R (seq): use seq_len() and seq_along() where possible.
85    
86    
87    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.9975-5 ready for release
90    
91    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
94    
95    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/AllClass.R (corMatrix): add 'validity' check;
98                    comment out unused "LDL" class definition
99            * NAMESPACE: mention, but do not export "LDL" class
100            * R/corMatrix.R: new (simple), needed for R-devel with
101            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
102              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
103    
104    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
105    
106            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
107            use Rprintf and R's error handling.
108    
109    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
112            * tests/matprod.R: add tests for the bug fixed.
113    
114    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
115    
116            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
117            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
118    
119    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
122    
123    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * DESCRIPTION (Version): 0.9975-3
126    
127            * R/diagMatrix.R (bdiag): new function constructing block diagonal
128            (sparse) matrices.
129            * man/bdiag.Rd: docu + examples
130    
131            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
132    
133            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
134            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
135    
136            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
137            that result is sparse or diagonal (and not dense).
138    
139            * man/Subassign-methods.Rd: fix examples
140    
141            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
142            should always return a sparse (and not sometimes a diagonal) matrix.
143    
144    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
147    
148    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * DESCRIPTION (Version): 0.9975-2
151    
152            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
153    
154    2006-10-02  Douglas Bates  <bates@R-project.org>
155    
156            * tests/dg_Matrix.R: Simplify test taking into account new code.
157    
158    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
161    
162            * R/lsTMatrix.R: new files w/ missing methods
163            * R/nsTMatrix.R:  "  'for completeness'
164    
165            * tests/Class+Meth.R: a bit less 'not.ok.classes'
166    
167            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
168    
169    
170    2006-09-28  Douglas Bates  <bates@R-project.org>
171    
172            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
173            included.
174    
175            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
176            Export C-callable functions used in Zt_create in lme4.
177    
178    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Version): 0.9975-1
181    
182            * tests/simple.R: less checks fail; using NA, found that our
183                    kronecker() is not base-compatible with NA's.
184    
185            * R/dMatrix.R: "Compare" method now implemented for all cases
186    
187            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
188    
189            * man/dtpMatrix-class.Rd: mention length of 'x' slot
190    
191            * src/dtpMatrix.c (dtpMatrix_validate): fix check
192            * src/dspMatrix.c (dspMatrix_validate): ditto
193    
194            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
195              including coercion to [nl]tTMatrix.
196    
197            * R/diagMatrix.R (show): print a header line as for other classes.
198    
199    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * src/Makefile.win (SUBDIRS): fix typo
202    
203    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
206    
207    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
210            symmetric and y missing in R code using %*% (cholmod_aat doesn't
211            accept a symmetric matrix).
212            * tests/group-methods.R: Uncomment test of crossprod applied to
213            lsCMatrix objects.
214    
215    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/AllClass.R (symmetricMatrix): add validity method (available
218            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
219    
220            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
221    
222            * tests/indexing.Rout.save:
223            * tests/indexing.R: additions, mainly for 'lsparse'
224    
225            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
226            case.
227    
228            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
229    
230    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
233                    as 'N' (1-letter - Ok?)
234    
235            * tests/group-methods.R: add test for logical + NAs
236    
237            * R/dMatrix.R ("Compare"): fix to work with NA's
238    
239            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
240    
241            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
242                    which is implemented.
243    
244    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/chm_common.c: coerce logical <-> double instead of
247            typecasting;  needed for "l" matrix handling in cholmod.
248    
249            * tests/other-pkgs.R (graph): small extension in "graph" checks.
250    
251            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
252            (Tsp2grNEL): other fixes needed
253    
254    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
257                    Matrices, since "lMatrix", also "lsparseM" can have NA
258            * R/ndenseMatrix.R, etc: new source files
259            * man/nsparseMatrix-classes.Rd, etc: new help files
260            * tests/: adaptions
261            * src/chm_common.c (chm_dense_to_SEXP): and others:
262                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
263            * src/Csparse.c, etc: ditto
264    
265    2006-09-11  Douglas Bates  <bates@R-project.org>
266    
267            * src/Mutils.[ch],init.c inst/include/*.h: Move the
268            alloc_d**Matrix functions to the lme4 package.
269    
270    2006-09-09  Douglas Bates  <bates@R-project.org>
271    
272            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
273            fixed
274    
275    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/lMatrix.R: new
278    
279            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
280    
281            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
282            * man/tcrossprod.Rd: ditto
283    
284    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
287            for exported functions
288            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
289            Remove partitioning algorithms for sparse matrix reordering.  The
290            copyright on the Metis code was problematic and the methods were
291            rarely used.
292            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
293            operations are now done entirely in CHOLMOD code.
294    
295    2006-09-06  Douglas Bates  <bates@R-project.org>
296    
297            * src/Mutils.h: Remove functions that are no longer used.
298    
299    2006-09-04  Douglas Bates  <bates@R-project.org>
300    
301            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
302            * src/DEPS.mkf: update
303    
304    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * created branches/Matrix-for-R-2.3.x;  on trunk: do
307            * DESCRIPTION (Version): 0.9975-0
308            (Depends): R (>= 2.4.0)
309    
310    2006-09-01  Douglas Bates  <bates@R-project.org>
311    
312            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
313    
314    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
317            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
318    
319            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
320    
321    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
324            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
325            * R/dsparseMatrix.R: ditto
326            * R/Csparse.R: ditto
327    
328    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/dMatrix.R (Compare): improve availability of "<", etc
331            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
332    
333    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
336            of a 0-index which was used as 1-index (..hmm)
337    
338            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
339    
340            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
341            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
342            (.is.diagonal): ditto
343    
344            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
345    
346            * R/Matrix.R (Matrix): also work for NA data
347    
348    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
351            in all cases.
352    
353    2006-08-27  Douglas Bates  <bates@R-project.org>
354    
355            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
356            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
357    
358    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
361            subclasses of "ddenseMatrix"
362            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
363            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
364            instead of half dozen specialized ones.
365    
366    2006-08-25  Douglas Bates  <bates@R-project.org>
367    
368            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
369            <tillard@cirad.fr> - ordering standard errors to match effects.
370    
371    2006-08-24  Douglas Bates  <bates@R-project.org>
372    
373            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
374            on R_ldl.
375            * R/lCholCMatrix.R,
376            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
377            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
378            * many files in ./R and ./src: Use more general version of
379            dup_mMatrix_as_dgeMatrix to simplify method definitions.
380            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
381            dtpMatrix, dspMatrix and dppMatrix conversions.
382    
383    
384    2006-08-23  Douglas Bates  <bates@R-project.org>
385    
386            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
387            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
388            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
389            dgeMatrix_crossprod (may need to do this in other places).
390            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
391            generic and method for dsCMatrix.  Use CHOLMOD for chol().
392    
393    2006-08-22  Douglas Bates  <bates@R-project.org>
394    
395            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
396            types of classed Matrices, matrices or numeric or logical vectors.
397            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
398            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
399            to Mutils.h (as an inline) and change name to Matrix_check_class;
400            fixes in as_cholmod_factor and chm_factor_to_SEXP.
401            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
402            dsCMatrix_matrix_solve.  Comment out vestigial functions.
403            * src/Csparse.c: use diag_P and uplo_P macros.
404    
405    2006-08-21  Douglas Bates  <bates@R-project.org>
406    
407            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
408            valgrind.
409            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
410            inverses.
411            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
412            -Wall warnings.
413            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
414            Use dup_mMatrix_as_dgeMatrix.
415    
416    2006-08-20  Douglas Bates  <bates@R-project.org>
417    
418            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
419            * tests/sparseQR.R: Added
420            * man/sparseQR-class.Rd: Document methods for qr.* generics
421            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
422    
423    2006-08-19  Douglas Bates  <bates@R-project.org>
424    
425            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
426            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
427            and qr.fitted.
428            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
429            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
430    
431    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
434            the base version has no "..." argument.
435    
436            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
437    
438            * R/Matrix.R: define and
439            * NAMESPACE: export as.numeric() and as.logical() methods.
440                    Let's hope these do not badly slow down something...
441            Finally export the zapsmall() method.
442    
443    2006-08-17  Douglas Bates  <bates@R-project.org>
444    
445            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
446            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
447            * src/dtCMatrix.c :Remove code that is no longer used
448            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
449    
450    2006-08-14  Douglas Bates  <bates@R-project.org>
451    
452            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
453            Csparse_to_logical and Csparse_symmetric_to_general.
454            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
455            coercion methods between CsparseMatrix and TsparseMatrix.
456    
457    2006-08-14  Douglas Bates  <bates@R-project.org>
458    
459            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
460            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
461            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
462            possible.
463    
464    2006-08-12  Douglas Bates  <bates@R-project.org>
465    
466            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
467              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
468              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
469              generalize conversions between TsparseMatrix, CsparseMatrix,
470              denseMatrix and matrix.  Preserve triangularity property and
471              propagate Dimnames in the easy cases.
472    
473    2006-08-10  Douglas Bates  <bates@R-project.org>
474    
475            * src/lmer.c: adjust checks in glmer_init for S4SXP
476            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
477            before S4SXP but for the wrong reasons.
478    
479    2006-08-08  Douglas Bates  <bates@R-project.org>
480    
481            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
482            Later modified to return the upper triangle only.
483            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
484    
485    2006-08-07  Douglas Bates  <bates@R-project.org>
486    
487            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
488            R-level conversion to a sparse symmetric class.
489            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
490            Remove conversion to sparse symmetric classes (now done in C code).
491    
492    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
495            * man/band.Rd:  adapt the \dontshow{} unit test.
496    
497    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * DESCRIPTION (Version): 0.995-14  for CRAN
500    
501            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
502    
503            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
504            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
505    
506            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
507            * R/Tsparse.R (tril, triu, band): methods
508            * R/dgRMatrix.R (tril, ...):    ditto
509            * man/band.Rd:                  ditto
510    
511    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/Matrix.R (head, tail): directly use utils:::head.matrix
514                    to be up-to-date automatically.
515    
516    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
519    
520            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
521            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
522            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
523            such that the S4 objects are always created by the current version
524            of R and 'Matrix' class definitions.
525    
526    2006-08-01  Douglas Bates  <bates@R-project.org>
527    
528            * R/lmer.R (LMEoptimize method), tests/lmer.R,
529            inst/external/test3comp.rda: Added warnings for convergence on
530            boundary and test cases.
531    
532            * src/lmer.c (mer_postVar): Modified to return the variances that
533            are marginal to the fixed effects, not conditional on them (which
534            is what the bVar slot contents represent).
535    
536    2006-07-31  Douglas Bates  <bates@R-project.org>
537    
538            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
539            function which calls the C function mer_hat_trace2.
540    
541            * man/ranef.Rd: Include description of "postVar" argument and
542            producing a caterpillar plot.
543    
544    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * NAMESPACE:    change  "correlation" to "corMatrix"
547            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
548            * R/dpoMatrix.R: ditto
549            * R/lmer.R:      ditto
550    
551    2006-07-28  Douglas Bates  <bates@R-project.org>
552    
553            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
554            RZXinv slot's contents into a separate internal function that can
555            be used in mer_hat_trace.
556    
557    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
560            via new smart
561            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
562            utility functions.
563    
564    
565    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/Csparse.R (tril, triu, band): do return *triangular* classed
568            matrices when appropriate; band() even symmetric ones.
569            (replCmat): extend to potentially all "CsparseMatrix"
570            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
571            allow subassignment for special sparse matrices.
572    
573            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
574    
575            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
576            argument; in glmer_*(): print only if(verbose).
577    
578            speed-optimize a few places by moving REAL(.) out of loops.
579    
580            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
581    
582    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
585                    since that wrongly triggers also for M[ logi , ]
586    
587            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
588            a symmetric matrix that results in a non-symmetric one.
589            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
590    
591            * R/dMatrix.R: make round(M) work as round(M, 0)
592    
593            * R/dgTMatrix.R (image): coordinate system and axis now use
594            1-based indices, not 0-based ones.
595    
596            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
597            * tests/indexing.R: test it.
598    
599            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
600            * man/isSymmetric-methods.Rd: and document it.
601    
602            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
603            * man/SparseM-conv.Rd: docu them
604    
605            * tests/other-pkgs.R: renamed from tests/graph.R and add example
606                    for 'SparseM' conversions
607    
608    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
609    
610            * R/Matrix.R (head): added head() and tail() methods.
611    
612    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * DESCRIPTION (Version): 0.995-12 released to CRAN
615    
616    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * tests/simple.R: add check for correct dsT -> dgT coercion;
619                    add check for correct printing of symmetric sparse matrices.
620    
621            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
622            for sparse symmetric matrices.
623    
624            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
625            diagonal twice.
626    
627    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
628    
629            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
630            being applied to the x slot (detected by Brian Ripley).
631    
632    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
635    
636            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
637    
638    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * src/lgCMatrix.c (lgCMatrix_diag): new function
641            * R/lgCMatrix.R (diag): for new method
642    
643            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
644                 ==> construction of illegal "*gTMatrix" via new() should
645                 now be much less easy:
646            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
647    
648            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
649                    directly.
650            * man/Matrix.Rd: documents it.
651    
652    2006-07-06  Douglas Bates  <bates@R-project.org>
653    
654            * src/pedigree.c (pedigree_inbreeding): Correction in
655            initialization.  This function is not currently being used and is
656            not fully tested.
657    
658            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
659            Introduced the glmer class.  Added code for mcmcmsamp on glmer
660            objects.  Modified validity check on pedigree objects to account
661            for nonparallel patterns of missingness of parents.
662    
663            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
664            class.
665    
666    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/pMatrix.R: coercion pMatrix -> Tsparse
669    
670    2006-06-12  Douglas Bates  <bates@R-project.org>
671    
672            * DESCRIPTION (Version): 0.995-11 released to CRAN
673    
674            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
675            the output from mcmcsamp.
676    
677    2006-06-10  Douglas Bates  <bates@R-project.org>
678    
679            * R/lmer.R (simulestimate): added C code for calculating the trace
680            of the hat matrix.
681    
682    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
685            classes.
686            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
687    
688    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * R/dgTMatrix.R (colSums): etc. All four of
691            colSums(), rowSums(), colMeans(), rowMeans() now should work for
692            all "Matrices".
693    
694    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
695    
696            * R/lmer.R (panel.ci): Add a reference line at zero and a
697            background grid to the qqmath plot of ranef.lmer.
698    
699    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
700    
701            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
702            grouping factors to be specified in the formula as (1|foo/bar).
703    
704    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
705    
706            * R/lmer.R (findbars and others): Change check of is.numeric to
707            !is.language to resolve the bug reported by Jacob Wegelin.
708    
709            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
710            code to evaluate inbreeding coefficients without calculating T,
711            based on code in Sargolzaei and Iwaisaki's paper.
712    
713    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
714    
715            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
716            generic and mer methods for isNested and denomDF. This denomDF was
717            an attempt to emulate that in lme but I don't think that makes
718            sense.  Use the trace of the hat matrix instead.
719    
720  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
723          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.
724          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
725    
726    
727  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 844 
844          * 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)
845          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
846          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
847          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
848    
849  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
# Line 329  Line 1048 
1048  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1049    
1050          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1051          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1052          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1053    
1054  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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