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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1655, Mon Oct 30 17:16:27 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/matprod.R: add a variation of Harri's example
4    
5            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
6            recursive infinitely.
7    
8            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
9    
10            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
11    
12    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
15            matrix if possible; test m+m == 2*m; now test dgRMatrix.
16            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
17            satisfy the above test.
18    
19    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
22    
23            * R/dgCMatrix.R: solve(a, b="missing") based on
24            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
25            RHS = NULL.
26    
27            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
28            add more (needed) [t]crossprod() methods.
29    
30            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
31    
32            * R/Auxiliaries.R (as_CspClass): cleanup
33            (drop0): internal utility for "Csparse_drop(*, 0)"
34            (.bail.out.2): encourage active feedback
35    
36    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dMatrix.R(Compare): new(), then slots [no validity check]
39    
40            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
41            non-valid or 'sorted' case).
42    
43            * R/dsparseMatrix.R: add "chol" method.
44            * R/ddenseMatrix.R: ditto
45    
46            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
47            * NAMESPACE (Ops)
48            * R/diagMatrix.R (diag2T): simple utility used "higher level"
49            coercion; deprecating direct lower level coercions.
50    
51            * R/*.R (seq): use seq_len() and seq_along() where possible.
52    
53    
54    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Version): 0.9975-5 ready for release
57    
58    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
61    
62    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (corMatrix): add 'validity' check;
65                    comment out unused "LDL" class definition
66            * NAMESPACE: mention, but do not export "LDL" class
67            * R/corMatrix.R: new (simple), needed for R-devel with
68            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
69              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
70    
71    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
72    
73            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
74            use Rprintf and R's error handling.
75    
76    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
79            * tests/matprod.R: add tests for the bug fixed.
80    
81    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
84            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
85    
86    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
89    
90    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Version): 0.9975-3
93    
94            * R/diagMatrix.R (bdiag): new function constructing block diagonal
95            (sparse) matrices.
96            * man/bdiag.Rd: docu + examples
97    
98            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
99    
100            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
101            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
102    
103            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
104            that result is sparse or diagonal (and not dense).
105    
106            * man/Subassign-methods.Rd: fix examples
107    
108            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
109            should always return a sparse (and not sometimes a diagonal) matrix.
110    
111    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
114    
115    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * DESCRIPTION (Version): 0.9975-2
118    
119            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
120    
121    2006-10-02  Douglas Bates  <bates@R-project.org>
122    
123            * tests/dg_Matrix.R: Simplify test taking into account new code.
124    
125    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
128    
129            * R/lsTMatrix.R: new files w/ missing methods
130            * R/nsTMatrix.R:  "  'for completeness'
131    
132            * tests/Class+Meth.R: a bit less 'not.ok.classes'
133    
134            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
135    
136    
137    2006-09-28  Douglas Bates  <bates@R-project.org>
138    
139            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
140            included.
141    
142            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
143            Export C-callable functions used in Zt_create in lme4.
144    
145    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.9975-1
148    
149            * tests/simple.R: less checks fail; using NA, found that our
150                    kronecker() is not base-compatible with NA's.
151    
152            * R/dMatrix.R: "Compare" method now implemented for all cases
153    
154            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
155    
156            * man/dtpMatrix-class.Rd: mention length of 'x' slot
157    
158            * src/dtpMatrix.c (dtpMatrix_validate): fix check
159            * src/dspMatrix.c (dspMatrix_validate): ditto
160    
161            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
162              including coercion to [nl]tTMatrix.
163    
164            * R/diagMatrix.R (show): print a header line as for other classes.
165    
166    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/Makefile.win (SUBDIRS): fix typo
169    
170    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
173    
174    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
175    
176            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
177            symmetric and y missing in R code using %*% (cholmod_aat doesn't
178            accept a symmetric matrix).
179            * tests/group-methods.R: Uncomment test of crossprod applied to
180            lsCMatrix objects.
181    
182    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/AllClass.R (symmetricMatrix): add validity method (available
185            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
186    
187            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
188    
189            * tests/indexing.Rout.save:
190            * tests/indexing.R: additions, mainly for 'lsparse'
191    
192            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
193            case.
194    
195            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
196    
197    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
200                    as 'N' (1-letter - Ok?)
201    
202            * tests/group-methods.R: add test for logical + NAs
203    
204            * R/dMatrix.R ("Compare"): fix to work with NA's
205    
206            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
207    
208            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
209                    which is implemented.
210    
211    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/chm_common.c: coerce logical <-> double instead of
214            typecasting;  needed for "l" matrix handling in cholmod.
215    
216            * tests/other-pkgs.R (graph): small extension in "graph" checks.
217    
218            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
219            (Tsp2grNEL): other fixes needed
220    
221    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
224                    Matrices, since "lMatrix", also "lsparseM" can have NA
225            * R/ndenseMatrix.R, etc: new source files
226            * man/nsparseMatrix-classes.Rd, etc: new help files
227            * tests/: adaptions
228            * src/chm_common.c (chm_dense_to_SEXP): and others:
229                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
230            * src/Csparse.c, etc: ditto
231    
232    2006-09-11  Douglas Bates  <bates@R-project.org>
233    
234            * src/Mutils.[ch],init.c inst/include/*.h: Move the
235            alloc_d**Matrix functions to the lme4 package.
236    
237    2006-09-09  Douglas Bates  <bates@R-project.org>
238    
239            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
240            fixed
241    
242    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/lMatrix.R: new
245    
246            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
247    
248            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
249            * man/tcrossprod.Rd: ditto
250    
251    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
254            for exported functions
255            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
256            Remove partitioning algorithms for sparse matrix reordering.  The
257            copyright on the Metis code was problematic and the methods were
258            rarely used.
259            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
260            operations are now done entirely in CHOLMOD code.
261    
262    2006-09-06  Douglas Bates  <bates@R-project.org>
263    
264            * src/Mutils.h: Remove functions that are no longer used.
265    
266    2006-09-04  Douglas Bates  <bates@R-project.org>
267    
268            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
269            * src/DEPS.mkf: update
270    
271    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * created branches/Matrix-for-R-2.3.x;  on trunk: do
274            * DESCRIPTION (Version): 0.9975-0
275            (Depends): R (>= 2.4.0)
276    
277    2006-09-01  Douglas Bates  <bates@R-project.org>
278    
279            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
280    
281    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
284            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
285    
286            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
287    
288    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
291            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
292            * R/dsparseMatrix.R: ditto
293            * R/Csparse.R: ditto
294    
295    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/dMatrix.R (Compare): improve availability of "<", etc
298            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
299    
300    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
303            of a 0-index which was used as 1-index (..hmm)
304    
305            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
306    
307            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
308            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
309            (.is.diagonal): ditto
310    
311            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
312    
313            * R/Matrix.R (Matrix): also work for NA data
314    
315    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
318            in all cases.
319    
320    2006-08-27  Douglas Bates  <bates@R-project.org>
321    
322            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
323            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
324    
325    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
328            subclasses of "ddenseMatrix"
329            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
330            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
331            instead of half dozen specialized ones.
332    
333    2006-08-25  Douglas Bates  <bates@R-project.org>
334    
335            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
336            <tillard@cirad.fr> - ordering standard errors to match effects.
337    
338    2006-08-24  Douglas Bates  <bates@R-project.org>
339    
340            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
341            on R_ldl.
342            * R/lCholCMatrix.R,
343            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
344            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
345            * many files in ./R and ./src: Use more general version of
346            dup_mMatrix_as_dgeMatrix to simplify method definitions.
347            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
348            dtpMatrix, dspMatrix and dppMatrix conversions.
349    
350    
351    2006-08-23  Douglas Bates  <bates@R-project.org>
352    
353            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
354            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
355            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
356            dgeMatrix_crossprod (may need to do this in other places).
357            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
358            generic and method for dsCMatrix.  Use CHOLMOD for chol().
359    
360    2006-08-22  Douglas Bates  <bates@R-project.org>
361    
362            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
363            types of classed Matrices, matrices or numeric or logical vectors.
364            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
365            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
366            to Mutils.h (as an inline) and change name to Matrix_check_class;
367            fixes in as_cholmod_factor and chm_factor_to_SEXP.
368            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
369            dsCMatrix_matrix_solve.  Comment out vestigial functions.
370            * src/Csparse.c: use diag_P and uplo_P macros.
371    
372    2006-08-21  Douglas Bates  <bates@R-project.org>
373    
374            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
375            valgrind.
376            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
377            inverses.
378            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
379            -Wall warnings.
380            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
381            Use dup_mMatrix_as_dgeMatrix.
382    
383    2006-08-20  Douglas Bates  <bates@R-project.org>
384    
385            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
386            * tests/sparseQR.R: Added
387            * man/sparseQR-class.Rd: Document methods for qr.* generics
388            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
389    
390    2006-08-19  Douglas Bates  <bates@R-project.org>
391    
392            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
393            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
394            and qr.fitted.
395            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
396            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
397    
398    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
401            the base version has no "..." argument.
402    
403            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
404    
405            * R/Matrix.R: define and
406            * NAMESPACE: export as.numeric() and as.logical() methods.
407                    Let's hope these do not badly slow down something...
408            Finally export the zapsmall() method.
409    
410    2006-08-17  Douglas Bates  <bates@R-project.org>
411    
412            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
413            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
414            * src/dtCMatrix.c :Remove code that is no longer used
415            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
416    
417    2006-08-14  Douglas Bates  <bates@R-project.org>
418    
419            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
420            Csparse_to_logical and Csparse_symmetric_to_general.
421            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
422            coercion methods between CsparseMatrix and TsparseMatrix.
423    
424    2006-08-14  Douglas Bates  <bates@R-project.org>
425    
426            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
427            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
428            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
429            possible.
430    
431    2006-08-12  Douglas Bates  <bates@R-project.org>
432    
433            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
434              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
435              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
436              generalize conversions between TsparseMatrix, CsparseMatrix,
437              denseMatrix and matrix.  Preserve triangularity property and
438              propagate Dimnames in the easy cases.
439    
440    2006-08-10  Douglas Bates  <bates@R-project.org>
441    
442            * src/lmer.c: adjust checks in glmer_init for S4SXP
443            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
444            before S4SXP but for the wrong reasons.
445    
446    2006-08-08  Douglas Bates  <bates@R-project.org>
447    
448            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
449            Later modified to return the upper triangle only.
450            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
451    
452    2006-08-07  Douglas Bates  <bates@R-project.org>
453    
454            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
455            R-level conversion to a sparse symmetric class.
456            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
457            Remove conversion to sparse symmetric classes (now done in C code).
458    
459    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
462            * man/band.Rd:  adapt the \dontshow{} unit test.
463    
464    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * DESCRIPTION (Version): 0.995-14  for CRAN
467    
468            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
469    
470            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
471            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
472    
473            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
474            * R/Tsparse.R (tril, triu, band): methods
475            * R/dgRMatrix.R (tril, ...):    ditto
476            * man/band.Rd:                  ditto
477    
478    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/Matrix.R (head, tail): directly use utils:::head.matrix
481                    to be up-to-date automatically.
482    
483    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
486    
487            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
488            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
489            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
490            such that the S4 objects are always created by the current version
491            of R and 'Matrix' class definitions.
492    
493    2006-08-01  Douglas Bates  <bates@R-project.org>
494    
495            * R/lmer.R (LMEoptimize method), tests/lmer.R,
496            inst/external/test3comp.rda: Added warnings for convergence on
497            boundary and test cases.
498    
499            * src/lmer.c (mer_postVar): Modified to return the variances that
500            are marginal to the fixed effects, not conditional on them (which
501            is what the bVar slot contents represent).
502    
503    2006-07-31  Douglas Bates  <bates@R-project.org>
504    
505            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
506            function which calls the C function mer_hat_trace2.
507    
508            * man/ranef.Rd: Include description of "postVar" argument and
509            producing a caterpillar plot.
510    
511    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * NAMESPACE:    change  "correlation" to "corMatrix"
514            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
515            * R/dpoMatrix.R: ditto
516            * R/lmer.R:      ditto
517    
518    2006-07-28  Douglas Bates  <bates@R-project.org>
519    
520            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
521            RZXinv slot's contents into a separate internal function that can
522            be used in mer_hat_trace.
523    
524    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
527            via new smart
528            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
529            utility functions.
530    
531    
532    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/Csparse.R (tril, triu, band): do return *triangular* classed
535            matrices when appropriate; band() even symmetric ones.
536            (replCmat): extend to potentially all "CsparseMatrix"
537            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
538            allow subassignment for special sparse matrices.
539    
540            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
541    
542            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
543            argument; in glmer_*(): print only if(verbose).
544    
545            speed-optimize a few places by moving REAL(.) out of loops.
546    
547            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
548    
549    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
552                    since that wrongly triggers also for M[ logi , ]
553    
554            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
555            a symmetric matrix that results in a non-symmetric one.
556            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
557    
558            * R/dMatrix.R: make round(M) work as round(M, 0)
559    
560            * R/dgTMatrix.R (image): coordinate system and axis now use
561            1-based indices, not 0-based ones.
562    
563            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
564            * tests/indexing.R: test it.
565    
566            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
567            * man/isSymmetric-methods.Rd: and document it.
568    
569            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
570            * man/SparseM-conv.Rd: docu them
571    
572            * tests/other-pkgs.R: renamed from tests/graph.R and add example
573                    for 'SparseM' conversions
574    
575    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
576    
577            * R/Matrix.R (head): added head() and tail() methods.
578    
579    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * DESCRIPTION (Version): 0.995-12 released to CRAN
582    
583    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * tests/simple.R: add check for correct dsT -> dgT coercion;
586                    add check for correct printing of symmetric sparse matrices.
587    
588            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
589            for sparse symmetric matrices.
590    
591            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
592            diagonal twice.
593    
594    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
595    
596            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
597            being applied to the x slot (detected by Brian Ripley).
598    
599    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
602    
603            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
604    
605    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * src/lgCMatrix.c (lgCMatrix_diag): new function
608            * R/lgCMatrix.R (diag): for new method
609    
610            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
611                 ==> construction of illegal "*gTMatrix" via new() should
612                 now be much less easy:
613            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
614    
615            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
616                    directly.
617            * man/Matrix.Rd: documents it.
618    
619    2006-07-06  Douglas Bates  <bates@R-project.org>
620    
621            * src/pedigree.c (pedigree_inbreeding): Correction in
622            initialization.  This function is not currently being used and is
623            not fully tested.
624    
625            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
626            Introduced the glmer class.  Added code for mcmcmsamp on glmer
627            objects.  Modified validity check on pedigree objects to account
628            for nonparallel patterns of missingness of parents.
629    
630            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
631            class.
632    
633    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/pMatrix.R: coercion pMatrix -> Tsparse
636    
637    2006-06-12  Douglas Bates  <bates@R-project.org>
638    
639            * DESCRIPTION (Version): 0.995-11 released to CRAN
640    
641            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
642            the output from mcmcsamp.
643    
644    2006-06-10  Douglas Bates  <bates@R-project.org>
645    
646            * R/lmer.R (simulestimate): added C code for calculating the trace
647            of the hat matrix.
648    
649    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
652            classes.
653            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
654    
655    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/dgTMatrix.R (colSums): etc. All four of
658            colSums(), rowSums(), colMeans(), rowMeans() now should work for
659            all "Matrices".
660    
661    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
662    
663            * R/lmer.R (panel.ci): Add a reference line at zero and a
664            background grid to the qqmath plot of ranef.lmer.
665    
666    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
667    
668            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
669            grouping factors to be specified in the formula as (1|foo/bar).
670    
671    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * R/lmer.R (findbars and others): Change check of is.numeric to
674            !is.language to resolve the bug reported by Jacob Wegelin.
675    
676            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
677            code to evaluate inbreeding coefficients without calculating T,
678            based on code in Sargolzaei and Iwaisaki's paper.
679    
680    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
681    
682            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
683            generic and mer methods for isNested and denomDF. This denomDF was
684            an attempt to emulate that in lme but I don't think that makes
685            sense.  Use the trace of the hat matrix instead.
686    
687    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
690            the C code depending on a slot structure that's no longer valid.
691            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
692    
693    
694    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
695    
696            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
697            of lowerTriMatrix generic and methods to tril (also upper to triu)
698            and added a general band extractor.
699    
700    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
701    
702            * R/pedigree.R (pedigree): Replace sire and dam values outside the
703            allowable range with NAs. Added a corresponding check in the
704            validity check for the pedigree class.
705    
706            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
707            crossprod methods now inherits from symmetricMatrix.
708    
709    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
710    
711            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
712            generics lowerTriMatrix and upperTriMatrix along with methods for
713            the Csparse virtual class.  Also added a C function Csparse_band
714            that implements these methods by calling cholmod_band.
715    
716    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
719            erased when it was NULL.  This led to invalid subselections!
720    
721    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
722    
723            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
724            in method for "t" so as not to lose the unit diagonal property.
725    
726    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
727    
728            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
729            and methods.  This is now an option to the ranef method for the
730            mer class.
731    
732            * src/cs_utils.c: Ensure that the nz component is -1 for a
733            compressed column-oriented matrix.  Minor formatting cleanup.
734    
735            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
736            objects.
737    
738    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
741            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
742    
743    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
744    
745            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
746            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
747    
748            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
749            for the dtCMatrix class.
750    
751    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
752    
753            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
754            and methods for it.
755    
756    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
759            arguments, such that M %*% 1:6 now works
760            * Tests/matprod.R: test the above
761    
762    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
763    
764            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
765            the ranef.lmer class.
766    
767            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
768            methods to extract the posterior variances from the bVar slot.
769    
770    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
773            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
774    
775            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
776            * tests/simple: (extended)
777    
778            * R/sparseMatrix.R (isTriangular): now using much improved
779            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
780    
781    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
782    
783            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
784            (problem report from Franklin Parlamis).  This should be done
785            generally.
786    
787    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
788    
789            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
790            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
791            update the plot methods.
792    
793    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
794    
795            * R/lmer.R (resid and ranef methods):  Added methods for the
796            "residuals" and "resid" generic but only for linear mixed model
797            fits.  Changed the ranef method to return a list of data frames so
798            that the plot methods now work.
799    
800    2006-03-16  Douglas Bates  <bates@bates2>
801    
802            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
803            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
804    
805            * DESCRIPTION (Date): New release
806    
807    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
810    
811            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
812            * man/KNex.Rd: and other help files
813            * tests/*.R: several ones needed adaption
814            * inst/doc/Comparisons.Rnw: ditto
815    
816    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
819    
820            * tests/indexing.R: tests for new [<- methods for sparse matrices.
821    
822    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
825    
826            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
827    
828    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/dMatrix.R: enable things like  M [ M < 10 ]
831            * R/dgeMatrix.R: implement it
832    
833    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/AllClass.R: define "summary.mer" and "*.lmer"
836            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
837            * R/lmer.R (show): now works with summary()
838    
839    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
842            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
843                    support the above
844    
845    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
846    
847            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
848            Use glmFit$prior.weights for weights in a glmm.
849            Allow an option usePQL = FALSE to skip the PQL steps for the
850            Laplace method (and, in time, the AGQ method).
851    
852            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
853            into a separate function internal_mer_Xfactor to be able to call
854            it from internal_bhat.
855    
856    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * tests/Class+Meth.R (tstMatrixClass): function for much better
859            testing; now again of all actual classes.
860    
861            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
862                    use macros and define make_d_matrix_* and make_i_matrix_*
863                    where _i_ is for the ldense routines:
864    
865            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
866            * src/ldense.c (lsyMatrix_as_lgeMatrix):
867    
868            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
869    
870    
871    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
874                    many different kinds of matrices.
875            * R/*.R: quite a few new methods were needed for R CMD check with
876                    new Matrix().  Very good for users playing around.
877    
878    
879    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * src/dgeMatrix.c (dMatrix_validate): new
882            * src/Mutils.c (dense_nonpacked_validate): new
883    
884            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
885    
886    
887    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
888    
889            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
890    
891    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
892    
893            * DESCRIPTION (Version): 0.99-6 released to CRAN
894    
895            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
896            segfault in cases with multiple non-nested grouping factors.
897    
898    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
900            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
901                    (Depends): also on 'utils'
902    
903            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
904            * R/diagMatrix.R (Diagonal): constructor and methods for
905            diagonal matrices
906    
907            * R/ltTMatrix.R: new "minimal methods"
908    
909    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
912            all methods (and help files).
913    
914    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
917                    for case (dimn.  op  no_dimn.)
918    
919    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
920    
921            * DESCRIPTION (Version): 0.99-2  released to CRAN
922    
923    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
924    
925            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
926            by Julian Faraway.
927    
928    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/Auxiliaries.R (try_as): new utility
931            * R/sparseMatrix.R: use try_as() in coercion to original class
932    
933    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
934    
935            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
936    
937    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/Auxiliaries.R (dimNamesCheck): added
940    
941            * R/Matrix.R (as.array), (as.vector): new
942    
943    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
946                    default.
947            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
948                    "pMatrix" now contains "sparseMatrix"
949    
950    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * tests/Class+Meth.R: new tests; t(t(m)) == m
953    
954            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
955    
956            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
957            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
958    
959            * R/dspMatrix.R: typo in "t" method
960    
961    2005-09-18  Douglas Bates  <bates@wisc.edu>
962    
963            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
964            * R/Tsparse.R: instead of R/gTMatrix.R
965            * R/Csparse.R: new
966            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
967            * src/Tsparse.c: new; many trivial methods calling cholmod_()
968            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
969                            via cholmod
970    
971    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * R/Auxiliaries.R (non0ind): new function using new C code
974            * src/dgCMatrix.c (compressed_non_0_ij): new utility
975    
976    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
977    
978            * src/chm_common.h: header file required by all C sources that
979            call CHOLMOD functions.  It defines a cholmod_common structure
980            called 'c' whose address is passed as the last argument to
981            (virtually) every CHOLMOD function.
982    
983            * src/Pattern.c: Simple example of the use of CHOLMOD.
984    
985            * src/init.c: initialize and finalize the cholmod_common structure.
986    
987            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
988            LDL and CCOLAMD from the U. of Florida sparse matrix library.
989    
990    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * inst/test-tools.R: new file collecting the utility functions used
993                    in ./tests/*.R
994    
995            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
996            * R/Matrix.R (cbind2): methods for NULL and missing
997    
998    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/AllClass.R: new "index" class for "[" and "[<-":
1001                    First cut at "symmetricMatrix" and "triangularMatrix"
1002            * R/gTMatrix.R (.ind.prep): new function;
1003                    Logical and character indexing now work too.
1004            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1005            * tests/indexing.R: new, including *.Rout.save
1006            * tests/dgTMatrix.R: new
1007    
1008    2005-08-29  Douglas Bates  <bates@wisc.edu>
1009    
1010            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1011            indicator pos not being updated.  Also enforced upper triangular
1012            for symmetric case.  Need to coerce edges component of elements of
1013            edge list - grr! (Why don't they define their classes cleanly?)
1014    
1015    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * R/Matrix.R:  added first "[<-" methods; not yet functional
1018            * R/denseMatrix.R: ditto
1019            * man/Subassign-methods.Rd: new help file for these
1020    
1021    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * DESCRIPTION (Version): 0.98-6
1024    
1025            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1026            matrices.
1027    
1028    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1031                    as( <logical>, "matrix")
1032    
1033            * R/pMatrix.R: coercion to "lgTMatrix"
1034    
1035            * R/gTMatrix.R: new virtual class to define "[" methods for.
1036            * man/gTMatrix-class.Rd:
1037            * General slight re-organization of where "[" methods are defined.
1038              more to come.
1039    
1040    2005-08-18  Douglas Bates  <bates@wisc.edu>
1041    
1042            * DESCRIPTION (Version): 0.98-5  released to CRAN
1043    
1044            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1045            * .....
1046    
1047    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1048    
1049            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1050            or glmer objects.
1051    
1052    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1053    
1054            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1055    
1056    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1057    
1058            * R/HBMM.R: finish re-writing R-only code.
1059    
1060    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1061    
1062            * man/externalFormats.Rd: move documentation for writeHB and
1063            writeMM here.
1064    
1065            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1066            (suggested by Paul Roecker).
1067    
1068            * tests/validObj.R (assertError): Comment out test that is failing
1069            after recent changes in r-devel.
1070    
1071    
1072    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * R/AllClass.R: intermediate virtual class "denseMatrix"
1075            * man/denseMatrix-class.Rd
1076            * NAMESPACE: export it, and also export
1077            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1078    
1079    2005-08-10  Douglas Bates  <bates@wisc.edu>
1080    
1081            * DESCRIPTION (Version): 0.98-3 to CRAN
1082    
1083            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1084            matrix_solve code (which was really, really wrong).
1085    
1086    2005-08-07  Douglas Bates  <bates@wisc.edu>
1087    
1088            * DESCRIPTION (Version): 0.98-2
1089    
1090            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1091    
1092            * R/lmer.R (abbrvNms): new
1093            * R/lmer.R (mcmcsamp): allow transformed parameters
1094            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1095            for the Harwell-Boeing and the MatrixMarket formats.
1096    
1097    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * man/dtrMatrix-class.Rd: add examples
1100            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1101    
1102            * TODO: note the dtpMatrix (docu) bug
1103    
1104            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1105            in order to ensure that new as.matrix() is used by old functions,
1106            e.g., svd(), qr(), eigen(), dist(),..;
1107                  apply(), also matplot() or pairs().
1108    
1109    
1110    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1111    
1112            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1113              add comments about 'control' / lmerControl() arguments
1114    
1115    2005-07-27  Douglas Bates  <bates@wisc.edu>
1116    
1117            * man/sleepstudy.Rd: Added the sleep data set.
1118            * DESCRIPTION (Version): 0.98-1  released to CRAN
1119    
1120    2005-07-12  Douglas Bates  <bates@wisc.edu>
1121            * man/sleepstudy.Rd: Added the sleep data set.
1122    
1123            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1124            .Call calls that were producing spurious output.
1125    
1126    2005-07-05  Douglas Bates  <bates@wisc.edu>
1127    
1128            * R/lmer.R (lmer): stored updated variance component estimates in
1129            mer object for the generalized model.  (Bug reported by Renaud
1130            Lancelot).
1131    
1132    2005-07-03  Douglas Bates  <bates@wisc.edu>
1133    
1134            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1135            unidimensional case.
1136    
1137    2005-06-08  Douglas Bates  <bates@wisc.edu>
1138    
1139            * DESCRIPTION (Version): 0.96-1
1140    
1141            * moved  lmer-class' R and C code moved from lme4 to here
1142    
1143    2005-06-04  Douglas Bates  <bates@wisc.edu>
1144    
1145            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1146            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1147    
1148    2005-06-02  Douglas Bates  <bates@wisc.edu>
1149    
1150            * src/Makefile.win: Forgot to update this when Makefile changed.
1151    
1152    2005-05-11  Douglas Bates  <bates@wisc.edu>
1153    
1154            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1155            bug reported by Kurt Hornik and Michael Hahsler.
1156    
1157    2005-05-10  Douglas Bates  <bates@wisc.edu>
1158    
1159            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1160            logical sparse matrices.  These will also be used in the symbolic
1161            analysis for lmer objects.
1162    
1163            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1164            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1165    
1166    2005-05-06  Douglas Bates  <bates@wisc.edu>
1167    
1168            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1169            colMeans, colSums, rowMeans and rowSums.
1170    
1171    2005-04-18  Douglas Bates  <bates@wisc.edu>
1172    
1173            * src/lgCMatrix.[ch]: code for _validate method and stub for
1174            multiplication operation.
1175    
1176            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1177            to dgetrs.
1178    
1179            * src/init.c: Fix cut-and-paste error in definition of
1180            dgeMatrix_matrix_solve
1181    
1182            * src/{many files}: Tighten code by using ALLOC_SLOT.
1183    
1184    2005-04-15  Douglas Bates  <bates@wisc.edu>
1185    
1186            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1187    
1188            * DESCRIPTION: Eliminate import of stats.
1189    
1190    
1191    2005-04-06  Douglas Bates  <bates@wisc.edu>
1192    
1193            * R/AllClass.R : add logical sparse matrix classes
1194    
1195    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * R/dgTMatrix.R: add "[" method for triplet matrices
1198            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1199    
1200    2005-03-31  Douglas Bates  <bates@wisc.edu>
1201    
1202            * DESCRIPTION (Version): release 0.95-5 to CRAN
1203    
1204            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1205            * R/sparseMatrix.R: %*%, crossprod()
1206            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1207            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1208            * src/lmer.c (lmer_fitted): fix thinko
1209    
1210    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1211    
1212            * R/AllClass.R: add two virtual sparse classes ``on top''
1213    
1214    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1215    
1216            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1217                    correspondingly fix examples and tests/ since new()
1218                    doesn't work for virtual classes.
1219    
1220    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1221    
1222            * R/Matrix.R (as.matrix): method and one for unname()
1223            * tests/dpoMatrix.R: tests should now be less platform dependent;
1224              also run for R 2.1.0; using as.matrix()
1225    
1226    2005-03-15  Douglas Bates  <bates@wisc.edu>
1227    
1228            * R/pMatrix.R: "pMatrix" class added
1229            * ....
1230    
1231    2005-03-14  Douglas Bates  <bates@wisc.edu>
1232    
1233            * R/dtpMatrix.R: Add unpack method and an example.
1234    
1235            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1236            of general symmetric matrices and associated S4 methods.
1237    
1238    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1239            +
1240    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1241    
1242            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1243              crossprod() and "%*%" methods added; tests, too.
1244            * tests/matprod.R: new, for testing these
1245    
1246    2005-03-03  Douglas Bates  <bates@wisc.edu>
1247    
1248            * src/lmer.c (lmer_fitted): Added.
1249    
1250    2005-03-02  Douglas Bates  <bates@wisc.edu>
1251    
1252            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1253    
1254    2005-02-28  Douglas Bates  <bates@wisc.edu>
1255    
1256            * src/*.c,po/,inst/po: Internationalization and localization of
1257            the package.
1258    
1259            * src/ldl.[ch]: Removed these as their contents are referenced in the
1260            R_ldl.c file.
1261    
1262            * src/flame.[ch]: Removed these source files.
1263    
1264            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1265    
1266            * src/LU.[ch],src/init.c: absorb in factorizations
1267    
1268            * src/Mutils.h: prepare for internationalization
1269    
1270            * src/cblas.h: move the enum definitions to Mutils.h and remove
1271            this file
1272    
1273    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1274    
1275            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1276    
1277            * R/dtrMatrix.R: fix t() method
1278    
1279            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1280            * NAMESPACE: export them (and import generics from "methods")
1281            * tests/group-methods.R : and test them.
1282    
1283            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1284            border case
1285    
1286    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1287    
1288            * DESCRIPTION (Version): 0.95-2  released to CRAN
1289    
1290            * src/dgBCMatrix.c:
1291            * src/lmer.c: many changes
1292            * ...
1293    
1294    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/Matrix.R: add more sophisticated show() method.
1297    
1298    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1299    
1300            * */* : almost complete reorganization of classes.
1301    
1302    2005-01-26  Douglas Bates  <bates@wisc.edu>
1303    
1304            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1305            for the geMatrix class.
1306    
1307    2005-01-24  Douglas Bates  <bates@wisc.edu>
1308    
1309            * src/Makefile (clean): Remove *.a and *.so
1310    
1311            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1312    
1313    2005-01-23  Douglas Bates  <bates@wisc.edu>
1314    
1315            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1316            had an effect in cases with more than 2 grouping factors.
1317    
1318    2005-01-03  Douglas Bates  <bates@wisc.edu>
1319    
1320            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1321    
1322    2004-12-23  Douglas Bates  <bates@wisc.edu>
1323    
1324            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1325            and R_useDynamicSymbols (suggested by B.D.Ripley).
1326    
1327    2004-12-14  Douglas Bates  <bates@wisc.edu>
1328    
1329            * R/sscMatrix.R: Add determinant methods
1330    
1331            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1332            for tripletMatrix to matrix.
1333    
1334    2004-12-13  Douglas Bates  <bates@wisc.edu>
1335    
1336            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1337            no longer used.
1338    
1339          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1340          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1343 
1343          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1344          Fixes part but not all of #15.          Fixes part but not all of #15.
1345    
1346  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1347    
1348          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1349          scalar grouping factors corrected.          scalar grouping factors corrected.
1350    
1351  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1352    
1353          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1354    
1355  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1356    
1357          * 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
1358          .h file can be included.          .h file can be included.
1359    
1360  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1361    
1362          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1363          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1364    
1365          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1366    
1367  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1368    
1369          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1370    
1371  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1372    
1373          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1374    
1375  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1376    
1377          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1378    
1379  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1380    
1381          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1382    
1383  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1384    
1385          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1386          routines.          routines.
1387    
1388  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1389    
1390          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1391    
1392  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1393    
1394          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1395    

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