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revision 726, Thu May 12 14:59:04 2005 UTC revision 1661, Thu Nov 2 13:10:50 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  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>
721    
722            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
723            the C code depending on a slot structure that's no longer valid.
724            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
725    
726    
727    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
728    
729            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
730            of lowerTriMatrix generic and methods to tril (also upper to triu)
731            and added a general band extractor.
732    
733    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
734    
735            * R/pedigree.R (pedigree): Replace sire and dam values outside the
736            allowable range with NAs. Added a corresponding check in the
737            validity check for the pedigree class.
738    
739            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
740            crossprod methods now inherits from symmetricMatrix.
741    
742    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
743    
744            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
745            generics lowerTriMatrix and upperTriMatrix along with methods for
746            the Csparse virtual class.  Also added a C function Csparse_band
747            that implements these methods by calling cholmod_band.
748    
749    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
752            erased when it was NULL.  This led to invalid subselections!
753    
754    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
757            in method for "t" so as not to lose the unit diagonal property.
758    
759    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
760    
761            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
762            and methods.  This is now an option to the ranef method for the
763            mer class.
764    
765            * src/cs_utils.c: Ensure that the nz component is -1 for a
766            compressed column-oriented matrix.  Minor formatting cleanup.
767    
768            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
769            objects.
770    
771    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
774            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
775    
776    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
777    
778            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
779            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
780    
781            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
782            for the dtCMatrix class.
783    
784    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
785    
786            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
787            and methods for it.
788    
789    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
792            arguments, such that M %*% 1:6 now works
793            * Tests/matprod.R: test the above
794    
795    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
796    
797            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
798            the ranef.lmer class.
799    
800            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
801            methods to extract the posterior variances from the bVar slot.
802    
803    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
806            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
807    
808            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
809            * tests/simple: (extended)
810    
811            * R/sparseMatrix.R (isTriangular): now using much improved
812            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
813    
814    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
815    
816            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
817            (problem report from Franklin Parlamis).  This should be done
818            generally.
819    
820    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
821    
822            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
823            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
824            update the plot methods.
825    
826    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
827    
828            * R/lmer.R (resid and ranef methods):  Added methods for the
829            "residuals" and "resid" generic but only for linear mixed model
830            fits.  Changed the ranef method to return a list of data frames so
831            that the plot methods now work.
832    
833    2006-03-16  Douglas Bates  <bates@bates2>
834    
835            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
836            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
837    
838            * DESCRIPTION (Date): New release
839    
840    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
843    
844            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
845            * man/KNex.Rd: and other help files
846            * tests/*.R: several ones needed adaption
847            * inst/doc/Comparisons.Rnw: ditto
848    
849    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
852    
853            * tests/indexing.R: tests for new [<- methods for sparse matrices.
854    
855    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
858    
859            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
860    
861    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/dMatrix.R: enable things like  M [ M < 10 ]
864            * R/dgeMatrix.R: implement it
865    
866    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/AllClass.R: define "summary.mer" and "*.lmer"
869            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
870            * R/lmer.R (show): now works with summary()
871    
872    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
875            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
876                    support the above
877    
878    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
879    
880            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
881            Use glmFit$prior.weights for weights in a glmm.
882            Allow an option usePQL = FALSE to skip the PQL steps for the
883            Laplace method (and, in time, the AGQ method).
884    
885            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
886            into a separate function internal_mer_Xfactor to be able to call
887            it from internal_bhat.
888    
889    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * tests/Class+Meth.R (tstMatrixClass): function for much better
892            testing; now again of all actual classes.
893    
894            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
895                    use macros and define make_d_matrix_* and make_i_matrix_*
896                    where _i_ is for the ldense routines:
897    
898            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
899            * src/ldense.c (lsyMatrix_as_lgeMatrix):
900    
901            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
902    
903    
904    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
907                    many different kinds of matrices.
908            * R/*.R: quite a few new methods were needed for R CMD check with
909                    new Matrix().  Very good for users playing around.
910    
911    
912    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
913    
914            * src/dgeMatrix.c (dMatrix_validate): new
915            * src/Mutils.c (dense_nonpacked_validate): new
916    
917            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
918    
919    
920    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
921    
922            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
923    
924    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
925    
926            * DESCRIPTION (Version): 0.99-6 released to CRAN
927    
928            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
929            segfault in cases with multiple non-nested grouping factors.
930    
931    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
934                    (Depends): also on 'utils'
935    
936            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
937            * R/diagMatrix.R (Diagonal): constructor and methods for
938            diagonal matrices
939    
940            * R/ltTMatrix.R: new "minimal methods"
941    
942    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
945            all methods (and help files).
946    
947    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
948    
949            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
950                    for case (dimn.  op  no_dimn.)
951    
952    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
953    
954            * DESCRIPTION (Version): 0.99-2  released to CRAN
955    
956    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
957    
958            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
959            by Julian Faraway.
960    
961    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * R/Auxiliaries.R (try_as): new utility
964            * R/sparseMatrix.R: use try_as() in coercion to original class
965    
966    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
969    
970    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
971    
972            * R/Auxiliaries.R (dimNamesCheck): added
973    
974            * R/Matrix.R (as.array), (as.vector): new
975    
976    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
979                    default.
980            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
981                    "pMatrix" now contains "sparseMatrix"
982    
983    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * tests/Class+Meth.R: new tests; t(t(m)) == m
986    
987            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
988    
989            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
990            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
991    
992            * R/dspMatrix.R: typo in "t" method
993    
994    2005-09-18  Douglas Bates  <bates@wisc.edu>
995    
996            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
997            * R/Tsparse.R: instead of R/gTMatrix.R
998            * R/Csparse.R: new
999            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1000            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1001            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1002                            via cholmod
1003    
1004    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/Auxiliaries.R (non0ind): new function using new C code
1007            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1008    
1009    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1010    
1011            * src/chm_common.h: header file required by all C sources that
1012            call CHOLMOD functions.  It defines a cholmod_common structure
1013            called 'c' whose address is passed as the last argument to
1014            (virtually) every CHOLMOD function.
1015    
1016            * src/Pattern.c: Simple example of the use of CHOLMOD.
1017    
1018            * src/init.c: initialize and finalize the cholmod_common structure.
1019    
1020            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1021            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1022    
1023    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * inst/test-tools.R: new file collecting the utility functions used
1026                    in ./tests/*.R
1027    
1028            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1029            * R/Matrix.R (cbind2): methods for NULL and missing
1030    
1031    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/AllClass.R: new "index" class for "[" and "[<-":
1034                    First cut at "symmetricMatrix" and "triangularMatrix"
1035            * R/gTMatrix.R (.ind.prep): new function;
1036                    Logical and character indexing now work too.
1037            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1038            * tests/indexing.R: new, including *.Rout.save
1039            * tests/dgTMatrix.R: new
1040    
1041    2005-08-29  Douglas Bates  <bates@wisc.edu>
1042    
1043            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1044            indicator pos not being updated.  Also enforced upper triangular
1045            for symmetric case.  Need to coerce edges component of elements of
1046            edge list - grr! (Why don't they define their classes cleanly?)
1047    
1048    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1049    
1050            * R/Matrix.R:  added first "[<-" methods; not yet functional
1051            * R/denseMatrix.R: ditto
1052            * man/Subassign-methods.Rd: new help file for these
1053    
1054    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1055    
1056            * DESCRIPTION (Version): 0.98-6
1057    
1058            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1059            matrices.
1060    
1061    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1062    
1063            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1064                    as( <logical>, "matrix")
1065    
1066            * R/pMatrix.R: coercion to "lgTMatrix"
1067    
1068            * R/gTMatrix.R: new virtual class to define "[" methods for.
1069            * man/gTMatrix-class.Rd:
1070            * General slight re-organization of where "[" methods are defined.
1071              more to come.
1072    
1073    2005-08-18  Douglas Bates  <bates@wisc.edu>
1074    
1075            * DESCRIPTION (Version): 0.98-5  released to CRAN
1076    
1077            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1078            * .....
1079    
1080    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1081    
1082            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1083            or glmer objects.
1084    
1085    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1088    
1089    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1090    
1091            * R/HBMM.R: finish re-writing R-only code.
1092    
1093    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1094    
1095            * man/externalFormats.Rd: move documentation for writeHB and
1096            writeMM here.
1097    
1098            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1099            (suggested by Paul Roecker).
1100    
1101            * tests/validObj.R (assertError): Comment out test that is failing
1102            after recent changes in r-devel.
1103    
1104    
1105    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1106    
1107            * R/AllClass.R: intermediate virtual class "denseMatrix"
1108            * man/denseMatrix-class.Rd
1109            * NAMESPACE: export it, and also export
1110            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1111    
1112    2005-08-10  Douglas Bates  <bates@wisc.edu>
1113    
1114            * DESCRIPTION (Version): 0.98-3 to CRAN
1115    
1116            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1117            matrix_solve code (which was really, really wrong).
1118    
1119    2005-08-07  Douglas Bates  <bates@wisc.edu>
1120    
1121            * DESCRIPTION (Version): 0.98-2
1122    
1123            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1124    
1125            * R/lmer.R (abbrvNms): new
1126            * R/lmer.R (mcmcsamp): allow transformed parameters
1127            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1128            for the Harwell-Boeing and the MatrixMarket formats.
1129    
1130    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1131    
1132            * man/dtrMatrix-class.Rd: add examples
1133            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1134    
1135            * TODO: note the dtpMatrix (docu) bug
1136    
1137            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1138            in order to ensure that new as.matrix() is used by old functions,
1139            e.g., svd(), qr(), eigen(), dist(),..;
1140                  apply(), also matplot() or pairs().
1141    
1142    
1143    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1144    
1145            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1146              add comments about 'control' / lmerControl() arguments
1147    
1148    2005-07-27  Douglas Bates  <bates@wisc.edu>
1149    
1150            * man/sleepstudy.Rd: Added the sleep data set.
1151            * DESCRIPTION (Version): 0.98-1  released to CRAN
1152    
1153    2005-07-12  Douglas Bates  <bates@wisc.edu>
1154            * man/sleepstudy.Rd: Added the sleep data set.
1155    
1156            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1157            .Call calls that were producing spurious output.
1158    
1159    2005-07-05  Douglas Bates  <bates@wisc.edu>
1160    
1161            * R/lmer.R (lmer): stored updated variance component estimates in
1162            mer object for the generalized model.  (Bug reported by Renaud
1163            Lancelot).
1164    
1165    2005-07-03  Douglas Bates  <bates@wisc.edu>
1166    
1167            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1168            unidimensional case.
1169    
1170    2005-06-08  Douglas Bates  <bates@wisc.edu>
1171    
1172            * DESCRIPTION (Version): 0.96-1
1173    
1174            * moved  lmer-class' R and C code moved from lme4 to here
1175    
1176    2005-06-04  Douglas Bates  <bates@wisc.edu>
1177    
1178            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1179            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1180    
1181    2005-06-02  Douglas Bates  <bates@wisc.edu>
1182    
1183            * src/Makefile.win: Forgot to update this when Makefile changed.
1184    
1185    2005-05-11  Douglas Bates  <bates@wisc.edu>
1186    
1187          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1188          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1189    
1190  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1191    
1192          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1193          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 1196 
1196          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1197          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1198    
1199  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1200    
1201          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1202          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1203    
1204  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1205    
1206          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1207          multiplication operation.          multiplication operation.
# Line 30  Line 1214 
1214    
1215          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1216    
1217  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1218    
1219          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1220    
1221          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1222    
1223    
1224  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1225    
1226          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1227    
# Line 46  Line 1230 
1230          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1231          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1232    
1233  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1234    
1235          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1236    
# Line 72  Line 1256 
1256          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1257            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1258    
1259  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1260    
1261          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1262          * ....          * ....
1263    
1264  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1265    
1266          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1267    
# Line 92  Line 1276 
1276            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1277          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1278    
1279  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1280    
1281          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1282    
1283  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1284    
1285          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1286    
1287  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1288    
1289          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1290          the package.          the package.
# Line 148  Line 1332 
1332    
1333          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1334    
1335  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1336    
1337          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1338          for the geMatrix class.          for the geMatrix class.
1339    
1340  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1341    
1342          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1343    
1344          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1345    
1346  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1347    
1348          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1349          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1350    
1351  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1352    
1353          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1354    
1355  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1356    
1357          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1358          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1359    
1360  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1361    
1362          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1363    
1364          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1365          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1366    
1367  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1368    
1369          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1370          no longer used.          no longer used.
# Line 192  Line 1376 
1376          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1377          Fixes part but not all of #15.          Fixes part but not all of #15.
1378    
1379  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1380    
1381          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1382          scalar grouping factors corrected.          scalar grouping factors corrected.
1383    
1384  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1385    
1386          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1387    
1388  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1389    
1390          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1391          .h file can be included.          .h file can be included.
1392    
1393  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1394    
1395          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1396          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1397    
1398          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1399    
1400  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1401    
1402          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1403    
1404  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1405    
1406          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1407    
1408  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1409    
1410          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1411    
1412  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1413    
1414          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1415    
1416  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1417    
1418          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1419          routines.          routines.
1420    
1421  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1422    
1423          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1424    
1425  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1426    
1427          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1428    

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